++ sed 's/,/\t/g;s/"//g'
++ echo USER_NAME=thomasgrnbk,TYPE=sRNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/,FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA,RUNname=2025-11-25-sRNAseq_HsBam_fullov_exclrepA,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/,LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/,SINGULARITYdir=/home/thomasgrnbk/AP_singu/,downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/,DEBUG=N,VERSION=r6.63,asmHUBpath=,ASMdir=,ASMname=,BAM=N,fwADAPTOR=,rvADAPTOR=,N_TRIMM=,rawPAIRED=N,onlyPAIRED=N,FASTQout=N,FASTQoutRAW=N,SUBSAMPLE=,MIN_LENGTH=18,MAX_LENGTH=1000,RAW=,TRIMM=,FIRST=1,LAST=1000,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=0,FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA,WIG=,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/,BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/,UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/,RELEASE=,VERSION=r6.63,UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/,nFILES=16,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/files.txt,FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA,GENOME_VERSION=dm6,subCOLOR=0~0~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=N,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/,newCOLLECTION=N,prepANNOTATIONgff=,prepGENOMEfasta=,prepTRANSCRIPTOMEfasta=,prepCDSfasta=,prepNCRNAfasta=
+ VARI='USER_NAME=thomasgrnbk	TYPE=sRNAseq	SLAM=N	BASE_FOLDER=/faststorage/project/PAN_illumina/results/	FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/	FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA	RUNname=2025-11-25-sRNAseq_HsBam_fullov_exclrepA	TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/	LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/	SINGULARITYdir=/home/thomasgrnbk/AP_singu/	downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/	DEBUG=N	VERSION=r6.63	asmHUBpath=	ASMdir=	ASMname=	BAM=N	fwADAPTOR=	rvADAPTOR=	N_TRIMM=	rawPAIRED=N	onlyPAIRED=N	FASTQout=N	FASTQoutRAW=N	SUBSAMPLE=	MIN_LENGTH=18	MAX_LENGTH=1000	RAW=	TRIMM=	FIRST=1	LAST=1000	INVERT=N	Ychrom=N	RANDOMmulti=N	MM=0	FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA	WIG=	WIG_FASTA=	spikeINnorm=N	noNORM=	EXTEND=0	COMPUTING=C	GRIDsystem=SLURM	keepTMP=N	SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/	BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/	UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/	RELEASE=	VERSION=r6.63	UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/	nFILES=16	FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/files.txt	FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA	GENOME_VERSION=dm6	subCOLOR=0~0~0	FORCE=	SYSTEM=EXTERN	LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/LOGs/	prepareREF=no	nSPLITS=1000000	SE=N	SE2nd=	maxCOUNT=1000000	demuxFASTA=N	autoViewLimits=	only5end=	PingPong=	DGE=N	GEO=	noSTRANDED=	FORCEimport=	exportBAM=N	exportBAMuncollapsed=N	RATIOtracks=N	GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/	newCOLLECTION=N	prepANNOTATIONgff=	prepGENOMEfasta=	prepTRANSCRIPTOMEfasta=	prepCDSfasta=	prepNCRNAfasta='
+ eval 'USER_NAME=thomasgrnbk	TYPE=sRNAseq	SLAM=N	BASE_FOLDER=/faststorage/project/PAN_illumina/results/	FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/	FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA	RUNname=2025-11-25-sRNAseq_HsBam_fullov_exclrepA	TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/	LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/	SINGULARITYdir=/home/thomasgrnbk/AP_singu/	downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/	DEBUG=N	VERSION=r6.63	asmHUBpath=	ASMdir=	ASMname=	BAM=N	fwADAPTOR=	rvADAPTOR=	N_TRIMM=	rawPAIRED=N	onlyPAIRED=N	FASTQout=N	FASTQoutRAW=N	SUBSAMPLE=	MIN_LENGTH=18	MAX_LENGTH=1000	RAW=	TRIMM=	FIRST=1	LAST=1000	INVERT=N	Ychrom=N	RANDOMmulti=N	MM=0	FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA	WIG=	WIG_FASTA=	spikeINnorm=N	noNORM=	EXTEND=0	COMPUTING=C	GRIDsystem=SLURM	keepTMP=N	SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/	BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/	UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/	RELEASE=	VERSION=r6.63	UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/	nFILES=16	FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/files.txt	FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA	GENOME_VERSION=dm6	subCOLOR=0~0~0	FORCE=	SYSTEM=EXTERN	LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/LOGs/	prepareREF=no	nSPLITS=1000000	SE=N	SE2nd=	maxCOUNT=1000000	demuxFASTA=N	autoViewLimits=	only5end=	PingPong=	DGE=N	GEO=	noSTRANDED=	FORCEimport=	exportBAM=N	exportBAMuncollapsed=N	RATIOtracks=N	GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/	newCOLLECTION=N	prepANNOTATIONgff=	prepGENOMEfasta=	prepTRANSCRIPTOMEfasta=	prepCDSfasta=	prepNCRNAfasta='
++ USER_NAME=thomasgrnbk
++ TYPE=sRNAseq
++ SLAM=N
++ BASE_FOLDER=/faststorage/project/PAN_illumina/results/
++ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/
++ FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA
++ RUNname=2025-11-25-sRNAseq_HsBam_fullov_exclrepA
++ TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/
++ LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/
++ SINGULARITYdir=/home/thomasgrnbk/AP_singu/
++ downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/
++ DEBUG=N
++ VERSION=r6.63
++ asmHUBpath=
++ ASMdir=
++ ASMname=
++ BAM=N
++ fwADAPTOR=
++ rvADAPTOR=
++ N_TRIMM=
++ rawPAIRED=N
++ onlyPAIRED=N
++ FASTQout=N
++ FASTQoutRAW=N
++ SUBSAMPLE=
++ MIN_LENGTH=18
++ MAX_LENGTH=1000
++ RAW=
++ TRIMM=
++ FIRST=1
++ LAST=1000
++ INVERT=N
++ Ychrom=N
++ RANDOMmulti=N
++ MM=0
++ FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA
++ WIG=
++ WIG_FASTA=
++ spikeINnorm=N
++ noNORM=
++ EXTEND=0
++ COMPUTING=C
++ GRIDsystem=SLURM
++ keepTMP=N
++ SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/
++ BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/
++ UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/
++ RELEASE=
++ VERSION=r6.63
++ UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/
++ nFILES=16
++ FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/files.txt
++ FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA
++ GENOME_VERSION=dm6
++ subCOLOR=0~0~0
++ FORCE=
++ SYSTEM=EXTERN
++ LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/LOGs/
++ prepareREF=no
++ nSPLITS=1000000
++ SE=N
++ SE2nd=
++ maxCOUNT=1000000
++ demuxFASTA=N
++ autoViewLimits=
++ only5end=
++ PingPong=
++ DGE=N
++ GEO=
++ noSTRANDED=
++ FORCEimport=
++ exportBAM=N
++ exportBAMuncollapsed=N
++ RATIOtracks=N
++ GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/
++ newCOLLECTION=N
++ prepANNOTATIONgff=
++ prepGENOMEfasta=
++ prepTRANSCRIPTOMEfasta=
++ prepCDSfasta=
++ prepNCRNAfasta=
+ sed 's/,/\n/g'
+ echo USER_NAME=thomasgrnbk,TYPE=sRNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/,FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA,RUNname=2025-11-25-sRNAseq_HsBam_fullov_exclrepA,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/,LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/,SINGULARITYdir=/home/thomasgrnbk/AP_singu/,downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/,DEBUG=N,VERSION=r6.63,asmHUBpath=,ASMdir=,ASMname=,BAM=N,fwADAPTOR=,rvADAPTOR=,N_TRIMM=,rawPAIRED=N,onlyPAIRED=N,FASTQout=N,FASTQoutRAW=N,SUBSAMPLE=,MIN_LENGTH=18,MAX_LENGTH=1000,RAW=,TRIMM=,FIRST=1,LAST=1000,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=0,FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA,WIG=,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/,BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/,UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/,RELEASE=,VERSION=r6.63,UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/,nFILES=16,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/files.txt,FOLDER_NAME=sRNAseq_HsBam_fullov_exclrepA,GENOME_VERSION=dm6,subCOLOR=0~0~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=N,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/,newCOLLECTION=N,prepANNOTATIONgff=,prepGENOMEfasta=,prepTRANSCRIPTOMEfasta=,prepCDSfasta=,prepNCRNAfasta=
++ date +%s
+ TIME=1764086610
+ TIMEx=1764086610
+ [[ SLURM == SLURM ]]
+ CORES=3
+ echo 3
+ source /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/tools
++ set -a
+ locTMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
+ mkdir -p /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
+ chmod 777 /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
+ TMPDIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
+ cd /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
+ echo /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/
+ mkdir /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots
+ cut -f 2
+ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/files.txt
+ rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/annotation_counts.txt
++ tr '\n' '\t'
++ awk '{ print $2 }'
++ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/files.txt
+ NAMElist='sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT	sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA	sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG	sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG	sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA	sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT	'
++ printf 'annotation\tsRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT	sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA	sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG	sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG	sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA	sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT	'
+ NAMElistANN='annotation	sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT	sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA	sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG	sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG	sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA	sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT	'
++ printf 'length\tsRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT	sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA	sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG	sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG	sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA	sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT	'
+ NAMElistSIZE='length	sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT	sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA	sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA	sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC	sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG	sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG	sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA	sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG	sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT	sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT	'
+ tr ' ' '\t'
+ echo annotation sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped
+ SWITCH=N
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
+ [[ N == N ]]
++ grep adaptor_dimer
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/log.txt
+ X=0
+ Xlist='adaptor_dimer 0'
+ SWITCH=Y
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_AGCAA.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_TACCA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_GAACG.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ACGAG.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
+ [[ Y == N ]]
++ grep adaptor_dimer
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ATGGA.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_CAGTG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_GGTAT.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
+ [[ Y == N ]]
++ grep adaptor_dimer
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_CTGAT.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep adaptor_dimer
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/log.txt
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
+ echo adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ tr ' ' '\t'
+ for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped
+ SWITCH=N
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
+ [[ N == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/log.txt
+ X=5790
+ Xlist='artifact_filtered 5790'
+ SWITCH=Y
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_AGCAA.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/log.txt
+ X=2149
+ Xlist='artifact_filtered 5790 2149'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/log.txt
+ X=1091
+ Xlist='artifact_filtered 5790 2149 1091'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/log.txt
+ X=2160
+ Xlist='artifact_filtered 5790 2149 1091 2160'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_TACCA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
+ [[ Y == N ]]
++ grep artifact_filtered
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/log.txt
+ X=1140
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/log.txt
+ X=1010
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
++ tr ' ' '\t'
++ cut -f 2
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/log.txt
+ X=587
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_GAACG.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/log.txt
+ X=5268
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/log.txt
+ X=645
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268 645'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
+ [[ Y == N ]]
++ grep artifact_filtered
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/log.txt
+ X=2175
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268 645 2175'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/log.txt
+ X=5537
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268 645 2175 5537'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ACGAG.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/log.txt
+ X=919
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268 645 2175 5537 919'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ATGGA.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
+ [[ Y == N ]]
++ grep artifact_filtered
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/log.txt
+ X=3135
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268 645 2175 5537 919 3135'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_CAGTG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep artifact_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/log.txt
+ X=3105
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268 645 2175 5537 919 3135 3105'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_GGTAT.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
+ [[ Y == N ]]
++ grep artifact_filtered
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/log.txt
+ X=1178
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268 645 2175 5537 919 3135 3105 1178'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_CTGAT.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/log.txt
++ grep artifact_filtered
++ awk '{ print $NF}'
+ X=1635
+ Xlist='artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268 645 2175 5537 919 3135 3105 1178 1635'
+ read LINE
+ echo artifact_filtered 5790 2149 1091 2160 1140 1010 587 5268 645 2175 5537 919 3135 3105 1178 1635
+ tr ' ' '\t'
+ for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped
+ SWITCH=N
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
++ tr ' ' '\t'
++ cut -f 2
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
+ [[ N == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/log.txt
++ grep length_filtered_short
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_short 0'
+ SWITCH=Y
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_AGCAA.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
++ tr ' ' '\t'
++ cut -f 2
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/log.txt
++ grep length_filtered_short
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_short 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_short
+ X=0
+ Xlist='length_filtered_short 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_short
+ X=0
+ Xlist='length_filtered_short 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_TACCA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_short
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_short
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_short
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_GAACG.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_short
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/log.txt
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_short
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/log.txt
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
+ [[ Y == N ]]
++ grep length_filtered_short
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/log.txt
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_short
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/log.txt
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ACGAG.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_short
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ATGGA.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_short
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/log.txt
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_CAGTG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
+ [[ Y == N ]]
++ grep length_filtered_short
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/log.txt
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_GGTAT.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_short
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/log.txt
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_CTGAT.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_short
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/log.txt
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
+ echo length_filtered_short 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ tr ' ' '\t'
+ for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped
+ SWITCH=N
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
+ [[ N == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/log.txt
+ X=0
+ Xlist='length_filtered_long 0'
+ SWITCH=Y
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_AGCAA.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
+ [[ Y == N ]]
++ grep length_filtered_long
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_TACCA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_GAACG.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
+ [[ Y == N ]]
++ grep length_filtered_long
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ACGAG.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ATGGA.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
+ [[ Y == N ]]
++ grep length_filtered_long
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_CAGTG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_GGTAT.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_CTGAT.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep length_filtered_long
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/log.txt
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
+ tr ' ' '\t'
+ echo length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped
+ SWITCH=N
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
+ [[ N == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/log.txt
+ X=111000
+ Xlist='N_filtered 111000'
+ SWITCH=Y
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_AGCAA.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/log.txt
+ X=76332
+ Xlist='N_filtered 111000 76332'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/log.txt
+ X=14950
+ Xlist='N_filtered 111000 76332 14950'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/log.txt
+ X=41628
+ Xlist='N_filtered 111000 76332 14950 41628'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_TACCA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/log.txt
+ X=26620
+ Xlist='N_filtered 111000 76332 14950 41628 26620'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/log.txt
+ X=16635
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/log.txt
+ X=8689
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_GAACG.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/log.txt
+ X=86220
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689 86220'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/log.txt
+ X=11111
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689 86220 11111'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/log.txt
+ X=40983
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689 86220 11111 40983'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/log.txt
+ X=95431
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689 86220 11111 40983 95431'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ACGAG.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/log.txt
+ X=27045
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689 86220 11111 40983 95431 27045'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ATGGA.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/log.txt
+ X=51374
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689 86220 11111 40983 95431 27045 51374'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_CAGTG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/log.txt
+ X=76755
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689 86220 11111 40983 95431 27045 51374 76755'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_GGTAT.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/log.txt
+ X=31782
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689 86220 11111 40983 95431 27045 51374 76755 31782'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_CTGAT.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
+ [[ Y == N ]]
++ grep N_filtered
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/log.txt
+ X=24729
+ Xlist='N_filtered 111000 76332 14950 41628 26620 16635 8689 86220 11111 40983 95431 27045 51374 76755 31782 24729'
+ read LINE
+ echo N_filtered 111000 76332 14950 41628 26620 16635 8689 86220 11111 40983 95431 27045 51374 76755 31782 24729
+ tr ' ' '\t'
+ for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped
+ SWITCH=N
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
+ [[ N == N ]]
++ grep reads_after_filtering
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/log.txt
+ X=45558391
+ Xlist='reads_after_filtering 45558391'
+ SWITCH=Y
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_AGCAA.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
++ tr ' ' '\t'
++ cut -f 2
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
+ [[ Y == N ]]
++ grep reads_after_filtering
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/log.txt
+ X=31095446
+ Xlist='reads_after_filtering 45558391 31095446'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/log.txt
+ X=6393616
+ Xlist='reads_after_filtering 45558391 31095446 6393616'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/log.txt
++ grep reads_after_filtering
++ awk '{ print $NF}'
+ X=17814614
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_TACCA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/log.txt
+ X=10748767
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/log.txt
+ X=7075012
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
++ tr ' ' '\t'
++ cut -f 2
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/log.txt
+ X=3589222
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_GAACG.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/log.txt
+ X=34763177
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/log.txt
+ X=4471050
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177 4471050'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
++ tr ' ' '\t'
++ cut -f 2
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
+ [[ Y == N ]]
++ grep reads_after_filtering
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/log.txt
+ X=16928632
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177 4471050 16928632'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
+ [[ Y == N ]]
++ grep reads_after_filtering
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/log.txt
+ X=40898343
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177 4471050 16928632 40898343'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ACGAG.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/log.txt
+ X=10965213
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177 4471050 16928632 40898343 10965213'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ATGGA.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/log.txt
+ X=20817568
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177 4471050 16928632 40898343 10965213 20817568'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_CAGTG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/log.txt
+ X=31442870
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177 4471050 16928632 40898343 10965213 20817568 31442870'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_GGTAT.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
+ [[ Y == N ]]
++ grep reads_after_filtering
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/log.txt
+ X=12939835
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177 4471050 16928632 40898343 10965213 20817568 31442870 12939835'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_CTGAT.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_after_filtering
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/log.txt
+ X=10011668
+ Xlist='reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177 4471050 16928632 40898343 10965213 20817568 31442870 12939835 10011668'
+ read LINE
+ tr ' ' '\t'
+ echo reads_after_filtering 45558391 31095446 6393616 17814614 10748767 7075012 3589222 34763177 4471050 16928632 40898343 10965213 20817568 31442870 12939835 10011668
+ for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped
+ SWITCH=N
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
+ [[ N == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/log.txt
+ X=5701599
+ Xlist='reads_not_mapped 5701599'
+ SWITCH=Y
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_AGCAA.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/log.txt
+ X=3547983
+ Xlist='reads_not_mapped 5701599 3547983'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
+ [[ Y == N ]]
++ grep reads_not_mapped
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/log.txt
+ X=758662
+ Xlist='reads_not_mapped 5701599 3547983 758662'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
++ cut -f 2
++ tr ' ' '\t'
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=1978198
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_TACCA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/log.txt
+ X=1148097
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097'
+ read LINE
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
++ tr ' ' '\t'
++ cut -f 2
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
+ [[ Y == N ]]
++ grep reads_not_mapped
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/log.txt
+ X=782779
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_ATGGA.fasta.gz sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ NAME=sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/log.txt
+ X=381958
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_GAACG.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/log.txt
+ X=4285416
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_CGTTC.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/log.txt
+ X=497515
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416 497515'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283080_S8_R1_001_GTCAG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/log.txt
+ X=1828032
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416 497515 1828032'
+ read LINE
++ tr ' ' '\t'
++ cut -f 2
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283082_S10_R1_001_TGACT.fasta.gz sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ NAME=sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
+ [[ Y == N ]]
++ grep reads_not_mapped
++ awk '{ print $NF}'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/log.txt
+ X=4632085
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416 497515 1828032 4632085'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ACGAG.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/log.txt
+ X=1428375
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416 497515 1828032 4632085 1428375'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_ATGGA.fasta.gz sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ NAME=sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/log.txt
+ X=2461293
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416 497515 1828032 4632085 1428375 2461293'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_CAGTG.fasta.gz sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ NAME=sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/log.txt
+ X=3190905
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416 497515 1828032 4632085 1428375 2461293 3190905'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283081_S9_R1_001_GGTAT.fasta.gz sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ NAME=sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/log.txt
+ X=1332947
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416 497515 1828032 4632085 1428375 2461293 3190905 1332947'
+ read LINE
++ cut -f 2
++ tr ' ' '\t'
++ echo /faststorage/project/PAN_illumina/tmp/sRBC_trimmed/283083_S11_R1_001_CTGAT.fasta.gz sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ NAME=sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep reads_not_mapped
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/log.txt
+ X=1362557
+ Xlist='reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416 497515 1828032 4632085 1428375 2461293 3190905 1332947 1362557'
+ read LINE
+ tr ' ' '\t'
+ echo reads_not_mapped 5701599 3547983 758662 1978198 1148097 782779 381958 4285416 497515 1828032 4632085 1428375 2461293 3190905 1332947 1362557
+ for CATEGORY in annotation_counts splitup_mRNA splitup_TE
+ NAMES=
+ [[ annotation_counts != annotation_counts ]]
+ cut -f 2-
++ read NAME
+ sort -k1,1n
+ awk -v 'OFS=\t' '{
    X[$1]=X[$1]"\t"$2
    Y[$1]+=NR
  }
  END {
    for (i in X) {
      print Y[i],i,X[i]
    }
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
  }' /dev/fd/63
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT_annotation_counts.txt
++ read NAME
+ [[ annotation_counts != annotation_counts ]]
+ EXT=
+ tr -s '\t'
+ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ [[ sRNAseq == CHIPseq ]]
+ [[ sRNAseq == DNAseq ]]
+ [[ '' == Y ]]
+ for CATEGORY in annotation_counts splitup_mRNA splitup_TE
+ NAMES=
+ [[ splitup_mRNA != annotation_counts ]]
+ rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/splitup_mRNA.txt
+ cut -f 2-
+ sort -k1,1n
+ awk -v 'OFS=\t' '{
    X[$1]=X[$1]"\t"$2
    Y[$1]+=NR
  }
  END {
    for (i in X) {
      print Y[i],i,X[i]
    }
  }' /dev/fd/63
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT_splitup_mRNA.txt
++ read NAME
+ [[ splitup_mRNA != annotation_counts ]]
+ EXT=annotation_
+ tr -s '\t'
+ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ [[ sRNAseq == CHIPseq ]]
+ [[ sRNAseq == DNAseq ]]
+ [[ '' == Y ]]
+ for CATEGORY in annotation_counts splitup_mRNA splitup_TE
+ NAMES=
+ [[ splitup_TE != annotation_counts ]]
+ rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/annotation_splitup_TE.txt
+ cut -f 2-
+ sort -k1,1n
+ awk -v 'OFS=\t' '{
    X[$1]=X[$1]"\t"$2
    Y[$1]+=NR
  }
  END {
    for (i in X) {
      print Y[i],i,X[i]
    }
  }' /dev/fd/63
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT_splitup_TE.txt
++ read NAME
+ [[ splitup_TE != annotation_counts ]]
+ EXT=annotation_
+ tr -s '\t'
+ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ [[ sRNAseq == CHIPseq ]]
+ [[ sRNAseq == DNAseq ]]
+ [[ '' == Y ]]
+ Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/ FILE=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/
+ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/ FILE=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/

Attaching package: ‘plotly’

The following objects are masked from ‘package:plyr’:

    arrange, mutate, rename, summarise

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

Using annotation as id variables
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 
Using annotation as id variables
+ [[ N == Y ]]
+ [[ dm6 == dm6 ]]
+ mkdir /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/1kb_tiles
+ for STRAND in Plus Minus
+ cut -f 2-
+ sort -k1,1n
+ awk -v 'OFS=\t' '
    {
      if($2==-1){$2=0}

      X[$1]=X[$1]"\t"$2
      Y[$1]+=NR
    }
    END {
      for (i in X) {
        print Y[i],i,X[i]
      }
    }' /dev/fd/63
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/WindowCounts_Plus.txt
++ read NAME
+ tr -s '\t'
+ tr ' ' '\t'
+ echo POS sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ tr -s '\t'
+ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ for STRAND in Plus Minus
+ cut -f 2-
+ sort -k1,1n
+ awk -v 'OFS=\t' '
    {
      if($2==-1){$2=0}

      X[$1]=X[$1]"\t"$2
      Y[$1]+=NR
    }
    END {
      for (i in X) {
        print Y[i],i,X[i]
      }
    }' /dev/fd/63
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/WindowCounts_Minus.txt
++ read NAME
+ tr -s '\t'
+ tr ' ' '\t'
+ echo POS sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ tr -s '\t'
+ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ cp /faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files//dmel/dm6/1kb_tile/kbWindows_mainchr_genes_tss_dm6.txt /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/1kb_tiles/
+ rawFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/
+ mkdir -p /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/
+ [[ sRNAseq == sRNAseq ]]
+ rm -rf '/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/*'
+ mkdir /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/
+ for CATEGORY in all filtered TE rRNA miRNA
+ SWITCH=N
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.20746
+ [[ N == N ]]
+ awk -v 'OFS=\t' -v NORM=0.20746 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT-all.txt
+ SWITCH=Y
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.106004
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.106004 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.062835
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062835 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/normalization.txt
++ cut -f 1
++ tr ' ' '\t'
++ tail -n 1
+ NORM=0.062486
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062486 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/normalization.txt
++ cut -f 1
++ tr ' ' '\t'
++ tail -n 1
+ NORM=0.077875
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.077875 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.056136
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.056136 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.040006
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.040006 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/normalization.txt
++ tail -n 1
++ cut -f 1
++ tr ' ' '\t'
+ NORM=0.825623
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.825623 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.064261
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.064261 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.085161
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.085161 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.131917
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.131917 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/normalization.txt
++ tr ' ' '\t'
++ tail -n 1
++ cut -f 1
+ NORM=0.382409
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.382409 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.426394
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.426394 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/normalization.txt
++ tail -n 1
++ cut -f 1
++ tr ' ' '\t'
+ NORM=0.157178
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.157178 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/normalization.txt
++ tail -n 1
++ cut -f 1
++ tr ' ' '\t'
+ NORM=0.125547
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.125547 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.311344
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.311344 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT-all.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ tr ' ' '\t'
+ echo length sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ tr ' ' '\t'
+ Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=all FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/
+ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=all FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/

Attaching package: ‘plotly’

The following objects are masked from ‘package:plyr’:

    arrange, mutate, rename, summarise

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 
Saving 7 x 7 in image
Warning message:
Removed 15440 rows containing missing values (`geom_step()`). 
Saving 7 x 7 in image
Warning messages:
1: Removed 15440 rows containing missing values (`position_stack()`). 
2: Removed 16 rows containing missing values (`geom_bar()`). 
Warning message:
Removed 15440 rows containing missing values (`position_stack()`). 
+ for CATEGORY in all filtered TE rRNA miRNA
+ SWITCH=N
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/normalization.txt
++ tail -n 1
++ cut -f 1
++ tr ' ' '\t'
+ NORM=0.20746
+ [[ N == N ]]
+ awk -v 'OFS=\t' -v NORM=0.20746 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT-filtered.txt
+ SWITCH=Y
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/normalization.txt
++ cut -f 1
++ tail -n 1
++ tr ' ' '\t'
+ NORM=0.106004
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.106004 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.062835
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062835 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.062486
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062486 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/normalization.txt
++ cut -f 1
++ tr ' ' '\t'
++ tail -n 1
+ NORM=0.077875
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.077875 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.056136
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.056136 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.040006
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.040006 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.825623
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.825623 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/normalization.txt
++ cut -f 1
++ tr ' ' '\t'
++ tail -n 1
+ NORM=0.064261
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.064261 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.085161
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.085161 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.131917
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.131917 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.382409
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.382409 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/normalization.txt
++ cut -f 1
++ tail -n 1
++ tr ' ' '\t'
+ NORM=0.426394
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.426394 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.157178
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.157178 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.125547
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.125547 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.311344
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.311344 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT-filtered.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ echo length sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ tr ' ' '\t'
+ tr ' ' '\t'
+ sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=filtered FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/
+ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=filtered FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/

Attaching package: ‘plotly’

The following objects are masked from ‘package:plyr’:

    arrange, mutate, rename, summarise

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 
Saving 7 x 7 in image
Warning message:
Removed 15440 rows containing missing values (`geom_step()`). 
Saving 7 x 7 in image
Warning messages:
1: Removed 15440 rows containing missing values (`position_stack()`). 
2: Removed 16 rows containing missing values (`geom_bar()`). 
Warning message:
Removed 15440 rows containing missing values (`position_stack()`). 
+ for CATEGORY in all filtered TE rRNA miRNA
+ SWITCH=N
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.20746
+ [[ N == N ]]
+ awk -v 'OFS=\t' -v NORM=0.20746 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT-TE.txt
+ SWITCH=Y
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.106004
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.106004 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.062835
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062835 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.062486
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062486 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.077875
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.077875 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.056136
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.056136 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.040006
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.040006 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.825623
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.825623 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.064261
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.064261 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.085161
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.085161 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.131917
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.131917 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.382409
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.382409 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.426394
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.426394 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.157178
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.157178 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.125547
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.125547 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.311344
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.311344 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT-TE.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ echo length sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ tr ' ' '\t'
+ sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ tr ' ' '\t'
+ Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=TE FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/
+ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=TE FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/

Attaching package: ‘plotly’

The following objects are masked from ‘package:plyr’:

    arrange, mutate, rename, summarise

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 
Saving 7 x 7 in image
Warning message:
Removed 15440 rows containing missing values (`geom_step()`). 
Saving 7 x 7 in image
Warning messages:
1: Removed 15440 rows containing missing values (`position_stack()`). 
2: Removed 16 rows containing missing values (`geom_bar()`). 
Warning message:
Removed 15440 rows containing missing values (`position_stack()`). 
+ for CATEGORY in all filtered TE rRNA miRNA
+ SWITCH=N
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.20746
+ [[ N == N ]]
+ awk -v 'OFS=\t' -v NORM=0.20746 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT-rRNA.txt
+ SWITCH=Y
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/normalization.txt
++ tr ' ' '\t'
++ tail -n 1
++ cut -f 1
+ NORM=0.106004
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.106004 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.062835
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062835 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.062486
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062486 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.077875
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.077875 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.056136
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.056136 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.040006
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.040006 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.825623
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.825623 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/normalization.txt
++ tr ' ' '\t'
++ tail -n 1
++ cut -f 1
+ NORM=0.064261
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.064261 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.085161
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.085161 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.131917
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.131917 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.382409
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.382409 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.426394
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.426394 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/normalization.txt
++ tail -n 1
++ cut -f 1
++ tr ' ' '\t'
+ NORM=0.157178
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.157178 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.125547
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.125547 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/normalization.txt
++ tail -n 1
++ tr ' ' '\t'
++ cut -f 1
+ NORM=0.311344
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.311344 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT-rRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ echo length sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ tr ' ' '\t'
+ sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ tr ' ' '\t'
+ Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=rRNA FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/
+ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=rRNA FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/

Attaching package: ‘plotly’

The following objects are masked from ‘package:plyr’:

    arrange, mutate, rename, summarise

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 
Saving 7 x 7 in image
Warning message:
Removed 15440 rows containing missing values (`geom_step()`). 
Saving 7 x 7 in image
Warning messages:
1: Removed 15440 rows containing missing values (`position_stack()`). 
2: Removed 16 rows containing missing values (`geom_bar()`). 
Warning message:
Removed 15440 rows containing missing values (`position_stack()`). 
+ for CATEGORY in all filtered TE rRNA miRNA
+ SWITCH=N
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/normalization.txt
++ tail -n 1
++ cut -f 1
++ tr ' ' '\t'
+ NORM=0.20746
+ [[ N == N ]]
+ awk -v 'OFS=\t' -v NORM=0.20746 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT-miRNA.txt
+ SWITCH=Y
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.106004
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.106004 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.062835
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062835 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/normalization.txt
++ tr ' ' '\t'
++ tail -n 1
++ cut -f 1
+ NORM=0.062486
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.062486 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.077875
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.077875 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.056136
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.056136 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.040006
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.040006 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.825623
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.825623 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.064261
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.064261 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.085161
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.085161 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.131917
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.131917 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.382409
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.382409 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.426394
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.426394 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.157178
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.157178 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.125547
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.125547 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/normalization.txt
++ tr ' ' '\t'
++ cut -f 1
++ tail -n 1
+ NORM=0.311344
+ [[ Y == N ]]
+ awk -v 'OFS=\t' -v NORM=0.311344 '{
          print $1,$2/NORM
        }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT-miRNA.txt
+ join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMPnorm.txt
+ mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ read NAME
+ echo length sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
+ tr ' ' '\t'
+ sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ tr ' ' '\t'
+ Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=miRNA FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/
+ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/ CATEGORY=miRNA FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/size-profiles/

Attaching package: ‘plotly’

The following objects are masked from ‘package:plyr’:

    arrange, mutate, rename, summarise

The following object is masked from ‘package:ggplot2’:

    last_plot

The following object is masked from ‘package:stats’:

    filter

The following object is masked from ‘package:graphics’:

    layout

Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead. 
Saving 7 x 7 in image
Warning message:
Removed 15440 rows containing missing values (`geom_step()`). 
Saving 7 x 7 in image
Warning messages:
1: Removed 15440 rows containing missing values (`position_stack()`). 
2: Removed 16 rows containing missing values (`geom_bar()`). 
Warning message:
Removed 15440 rows containing missing values (`position_stack()`). 
+ [[ sRNAseq == sRNAseq ]]
+ CATEGORIES='TE_RPKM_sense-salmon TE_RPKM_antisense-salmon TE_RPKM_sense-bowtie TE_RPKM_antisense-bowtie TE_counts_sense-bowtie TE_counts_antisense-bowtie'
+ [[ N == Y ]]
+ [[ sRNAseq == sRNAseq ]]
+ for CATEGORY in $CATEGORIES
+ [[ TE_RPKM_sense-salmon == *\T\E\_\G\e\T\M\M* ]]
+ [[ TE_RPKM_sense-salmon == GeTMM_gene ]]
+ NAMES=TE
+ awk -v 'OFS=\t' '{
        X[$1]=X[$1]"\t"$2
      }
      END {
        for (i in X) {
        print i,X[i]
        }
      }' /dev/fd/63
+ sort -k1,1
+ cut --complement -f 1
+ awk -v 'OFS=\t' '{
          X=$1
          gsub("_AS","",X)
          print X,$0
        }'
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/TE_RPKM_sense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/TE_RPKM_sense-salmon.txt
++ read NAME
++ echo TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ tr -s '\t'
+ tr ' ' '\t'
+ sed 's/::/\t/g'
+ for CATEGORY in $CATEGORIES
+ [[ TE_RPKM_antisense-salmon == *\T\E\_\G\e\T\M\M* ]]
+ [[ TE_RPKM_antisense-salmon == GeTMM_gene ]]
+ NAMES=TE
+ awk -v 'OFS=\t' '{
        X[$1]=X[$1]"\t"$2
      }
      END {
        for (i in X) {
        print i,X[i]
        }
+ sort -k1,1
+ awk -v 'OFS=\t' '{
          X=$1
          gsub("_AS","",X)
          print X,$0
        }'
++ read NAME
+ cut --complement -f 1
      }' /dev/fd/63
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/TE_RPKM_antisense-salmon.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/TE_RPKM_antisense-salmon.txt
++ read NAME
++ echo TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ tr ' ' '\t'
+ tr -s '\t'
+ sed 's/::/\t/g'
+ for CATEGORY in $CATEGORIES
+ [[ TE_RPKM_sense-bowtie == *\T\E\_\G\e\T\M\M* ]]
+ [[ TE_RPKM_sense-bowtie == GeTMM_gene ]]
+ NAMES=TE
+ awk -v 'OFS=\t' '{
        X[$1]=X[$1]"\t"$2
      }
      END {
        for (i in X) {
        print i,X[i]
        }
      }' /dev/fd/63
+ sort -k1,1
+ cut --complement -f 1
+ awk -v 'OFS=\t' '{
          X=$1
          gsub("_AS","",X)
          print X,$0
        }'
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/TE_RPKM_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/TE_RPKM_sense-bowtie.txt
++ read NAME
++ echo TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ tr ' ' '\t'
+ tr -s '\t'
+ sed 's/::/\t/g'
+ for CATEGORY in $CATEGORIES
+ [[ TE_RPKM_antisense-bowtie == *\T\E\_\G\e\T\M\M* ]]
+ [[ TE_RPKM_antisense-bowtie == GeTMM_gene ]]
+ NAMES=TE
+ cut --complement -f 1
+ awk -v 'OFS=\t' '{
        X[$1]=X[$1]"\t"$2
      }
      END {
        for (i in X) {
        print i,X[i]
        }
      }' /dev/fd/63
+ awk -v 'OFS=\t' '{
          X=$1
          gsub("_AS","",X)
          print X,$0
        }'
+ sort -k1,1
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/TE_RPKM_antisense-bowtie.txt
++ read NAME
++ echo TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ tr ' ' '\t'
+ tr -s '\t'
+ sed 's/::/\t/g'
+ for CATEGORY in $CATEGORIES
+ [[ TE_counts_sense-bowtie == *\T\E\_\G\e\T\M\M* ]]
+ [[ TE_counts_sense-bowtie == GeTMM_gene ]]
+ NAMES=TE
+ awk -v 'OFS=\t' '{
        X[$1]=X[$1]"\t"$2
      }
      END {
        for (i in X) {
        print i,X[i]
        }
      }' /dev/fd/63
+ sort -k1,1
+ cut --complement -f 1
+ awk -v 'OFS=\t' '{
          X=$1
          gsub("_AS","",X)
          print X,$0
        }'
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/TE_counts_sense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/TE_counts_sense-bowtie.txt
++ read NAME
++ echo TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ sed 's/::/\t/g'
+ tr -s '\t'
+ tr ' ' '\t'
+ for CATEGORY in $CATEGORIES
+ [[ TE_counts_antisense-bowtie == *\T\E\_\G\e\T\M\M* ]]
+ [[ TE_counts_antisense-bowtie == GeTMM_gene ]]
+ NAMES=TE
+ awk -v 'OFS=\t' '{
          X=$1
          gsub("_AS","",X)
          print X,$0
+ cut --complement -f 1
+ awk -v 'OFS=\t' '{
        X[$1]=X[$1]"\t"$2
      }
      END {
        for (i in X) {
        print i,X[i]
        }
      }' /dev/fd/63
        }'
+ sort -k1,1
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/TE_counts_antisense-bowtie.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES='TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/TE_counts_antisense-bowtie.txt
++ read NAME
++ echo TE sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr ' ' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP.txt
+ tr ' ' '\t'
+ tr -s '\t'
+ sed 's/::/\t/g'
+ [[ N == Y ]]
+ [[ '' == Y ]]
+ [[ sRNAseq == RNAseq ]]
+ [[ sRNAseq == sRNAseq ]]
+ [[ sRNAseq == CHIPseq ]]
+ [[ sRNAseq == DNAseq ]]
+ [[ '' == Y ]]
+ CATEGORIES='sense antisense'
+ [[ sRNAseq == sRNAseq ]]
+ CLASSES='man man.21mer'
+ for CATEGORY in $CATEGORIES
+ for currCLASS in $CLASSES
+ NAMES=
+ sort -k2,2n
+ awk -v 'OFS=\t' '{
          
          NAME=$1"~"$2
          if(NAME in X) {
            X[NAME]=X[NAME]"\t"$3
          }else{
            X[NAME]=$3
          }
        }
        END {
          for (i in X) {
            print i,X[i]
          }
        }' /dev/fd/63
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT_TE-sense_man.bg
++ read NAME
++ echo TE POS sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr '~' '\t'
++ tr ' ' '\t'
+ echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
+ tr '~' '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP_TEhist_man.txt
+ sort -k2,2n
+ tr ' ' '\t'
+ for currCLASS in $CLASSES
+ NAMES=
+ sort -k2,2n
+ awk -v 'OFS=\t' '{
          
          NAME=$1"~"$2
          if(NAME in X) {
            X[NAME]=X[NAME]"\t"$3
          }else{
            X[NAME]=$3
          }
        }
        END {
          for (i in X) {
            print i,X[i]
          }
        }' /dev/fd/63
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT_TE-sense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT_TE-sense_man.21mer.bg
++ read NAME
++ echo TE POS sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr '~' '\t'
++ tr ' ' '\t'
+ echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP_TEhist_man.21mer.txt
+ tr ' ' '\t'
+ tr '~' '\t'
+ sort -k2,2n
+ for CATEGORY in $CATEGORIES
+ for currCLASS in $CLASSES
+ NAMES=
+ sort -k2,2n
+ awk -v 'OFS=\t' '{
          
          NAME=$1"~"$2
          if(NAME in X) {
            X[NAME]=X[NAME]"\t"$3
          }else{
            X[NAME]=$3
          }
        }
        END {
          for (i in X) {
            print i,X[i]
          }
        }' /dev/fd/63
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT_TE-antisense_man.bg
++ read NAME
++ echo TE POS sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr '~' '\t'
++ tr ' ' '\t'
+ echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP_TEhist_man.txt
+ tr ' ' '\t'
+ sort -k2,2n
+ tr '~' '\t'
+ for currCLASS in $CLASSES
+ NAMES=
+ awk -v 'OFS=\t' '{
          
          NAME=$1"~"$2
          if(NAME in X) {
            X[NAME]=X[NAME]"\t"$3
          }else{
            X[NAME]=$3
          }
        }
        END {
          for (i in X) {
            print i,X[i]
          }
        }' /dev/fd/63
+ sort -k2,2n
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA/sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA/sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG/sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT/sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG/sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG/sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT/sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT_TE-antisense_man.21mer.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/
++ NAMES=' sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT_TE-antisense_man.21mer.bg
++ read NAME
++ echo TE POS sRNAseq_HsBam_nos_ControlKD_68hAHS_repB_283080_sRBC_TGACT sRNAseq_HsBam_nos_ControlKD_68hAHS_repC_283081_sRBC_AGCAA sRNAseq_HsBam_nos_PiwiKD_00hAHS_repD_283082_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repD_283082_sRBC_GTCAG sRNAseq_HsBam_nos_PiwiKD_68hAHS_repC_283081_sRBC_TACCA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repD_283082_sRBC_ATGGA sRNAseq_HsBam_nos_PiwiKD_68hAHS_repB_283080_sRBC_ATGGA sRNAseq_Ovaries_MTD_ControlKD_ov_repF_283083_sRBC_GAACG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repB_283080_sRBC_CGTTC sRNAseq_HsBam_nos_ControlKD_00hAHS_repB_283080_sRBC_GTCAG sRNAseq_HsBam_nos_ControlKD_68hAHS_repD_283082_sRBC_TGACT sRNAseq_Ovaries_MTD_PiwiKD_ov_repE_283083_sRBC_ACGAG sRNAseq_Ovaries_MTD_ControlKD_ov_repE_283083_sRBC_ATGGA sRNAseq_HsBam_nos_ControlKD_00hAHS_repC_283081_sRBC_CAGTG sRNAseq_HsBam_nos_PiwiKD_00hAHS_repC_283081_sRBC_GGTAT sRNAseq_Ovaries_MTD_PiwiKD_ov_repF_283083_sRBC_CTGAT
++ tr '~' '\t'
++ tr ' ' '\t'
+ echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/TMP_TEhist_man.21mer.txt
+ tr ' ' '\t'
+ sort -k2,2n
+ tr '~' '\t'
+ mkdir -p /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/TEhist/html-dependencies/
+ Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/TEhist/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/TE_hist TYPE=sRNAseq
+ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/TEhist/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/plots/raw-data/TE_hist TYPE=sRNAseq
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.3     ✔ readr     2.1.4
✔ forcats   1.0.0     ✔ stringr   1.5.0
✔ ggplot2   3.4.4     ✔ tibble    3.2.1
✔ lubridate 1.9.3     ✔ tidyr     1.3.0
✔ purrr     1.0.2     
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Attaching package: ‘cowplot’

The following object is masked from ‘package:lubridate’:

    stamp


Attaching package: ‘plotly’

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    filter

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    layout

Loading required package: foreach

Attaching package: ‘foreach’

The following objects are masked from ‘package:purrr’:

    accumulate, when

Loading required package: iterators
Loading required package: parallel
+ rm -rf /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/Rscripts.pdf
+ [[ N != Y ]]
+ rm -rf /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2025-11-25-sRNAseq_HsBam_fullov_exclrepA/TMP/
++ awk '{ print ($1-$2)/60 }'
+++ date +%s
++ echo -e 1764087390 1764086610
+ PROCESSED_TIME=13
+ echo 'collect-numbers - processing_time=' 13
+ exit