++ echo USER_NAME=thomasgrnbk,TYPE=RNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/,FOLDER_NAME=MTD_vs_TOsK_RNAseq,RUNname=2025-10-21-MTD_vs_TOsK_RNAseq,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/,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=Y,FIRST=6,LAST=200,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=2,FILTERING_INPUT=rRNA:tRNA:mito,WIG=Y,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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=20,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/files.txt,FOLDER_NAME=MTD_vs_TOsK_RNAseq,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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/,/\t/g;s/"//g'
+ VARI='USER_NAME=thomasgrnbk	TYPE=RNAseq	SLAM=N	BASE_FOLDER=/faststorage/project/PAN_illumina/results/	FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/	FOLDER_NAME=MTD_vs_TOsK_RNAseq	RUNname=2025-10-21-MTD_vs_TOsK_RNAseq	TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/	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=Y	FIRST=6	LAST=200	INVERT=N	Ychrom=N	RANDOMmulti=N	MM=2	FILTERING_INPUT=rRNA:tRNA:mito	WIG=Y	WIG_FASTA=	spikeINnorm=N	noNORM=	EXTEND=0	COMPUTING=C	GRIDsystem=SLURM	keepTMP=N	SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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=20	FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/files.txt	FOLDER_NAME=MTD_vs_TOsK_RNAseq	GENOME_VERSION=dm6	subCOLOR=0~128~0	FORCE=	SYSTEM=EXTERN	LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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=RNAseq	SLAM=N	BASE_FOLDER=/faststorage/project/PAN_illumina/results/	FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/	FOLDER_NAME=MTD_vs_TOsK_RNAseq	RUNname=2025-10-21-MTD_vs_TOsK_RNAseq	TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/	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=Y	FIRST=6	LAST=200	INVERT=N	Ychrom=N	RANDOMmulti=N	MM=2	FILTERING_INPUT=rRNA:tRNA:mito	WIG=Y	WIG_FASTA=	spikeINnorm=N	noNORM=	EXTEND=0	COMPUTING=C	GRIDsystem=SLURM	keepTMP=N	SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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=20	FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/files.txt	FOLDER_NAME=MTD_vs_TOsK_RNAseq	GENOME_VERSION=dm6	subCOLOR=0~128~0	FORCE=	SYSTEM=EXTERN	LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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=RNAseq
++ SLAM=N
++ BASE_FOLDER=/faststorage/project/PAN_illumina/results/
++ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/
++ FOLDER_NAME=MTD_vs_TOsK_RNAseq
++ RUNname=2025-10-21-MTD_vs_TOsK_RNAseq
++ TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/
++ 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=Y
++ FIRST=6
++ LAST=200
++ INVERT=N
++ Ychrom=N
++ RANDOMmulti=N
++ MM=2
++ FILTERING_INPUT=rRNA:tRNA:mito
++ WIG=Y
++ WIG_FASTA=
++ spikeINnorm=N
++ noNORM=
++ EXTEND=0
++ COMPUTING=C
++ GRIDsystem=SLURM
++ keepTMP=N
++ SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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=20
++ FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/files.txt
++ FOLDER_NAME=MTD_vs_TOsK_RNAseq
++ GENOME_VERSION=dm6
++ subCOLOR=0~128~0
++ FORCE=
++ SYSTEM=EXTERN
++ LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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=RNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/,FOLDER_NAME=MTD_vs_TOsK_RNAseq,RUNname=2025-10-21-MTD_vs_TOsK_RNAseq,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/,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=Y,FIRST=6,LAST=200,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=2,FILTERING_INPUT=rRNA:tRNA:mito,WIG=Y,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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=20,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/files.txt,FOLDER_NAME=MTD_vs_TOsK_RNAseq,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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=1761048887
+ TIMEx=1761048887
+ [[ SLURM == SLURM ]]
+ CORES=3
+ echo 3
+ source /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/script-files/tools
++ set -a
+ locTMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/
+ mkdir -p /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/
+ chmod 777 /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/
+ TMPDIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/
+ cd /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/
+ echo /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/
+ mkdir /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/files.txt
+ cut -f 2
+ tr ' ' '\t'
+ rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/annotation_counts.txt
++ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/files.txt
++ tr '\n' '\t'
++ awk '{ print $2 }'
+ NAMElist='MTD_AubAgo3_C	TOsK_piwi_A	TOsK_white_A	TOsK_piwi_B	TOsK_AubAgo3_A	TOsK_white_B	TOsK_piwi_C	TOsK_PiwiAub_X	MTD_piwi_A	TOsK_AubAgo3_B	TOsK_white_C	MTD_white_A	MTD_piwi_B	TOsK_AubAgo3_C	TOsK_cy_X	MTD_white_B	MTD_piwi_C	MTD_white_C	MTD_AubAgo3_A	MTD_AubAgo3_B	'
++ printf 'annotation\tMTD_AubAgo3_C	TOsK_piwi_A	TOsK_white_A	TOsK_piwi_B	TOsK_AubAgo3_A	TOsK_white_B	TOsK_piwi_C	TOsK_PiwiAub_X	MTD_piwi_A	TOsK_AubAgo3_B	TOsK_white_C	MTD_white_A	MTD_piwi_B	TOsK_AubAgo3_C	TOsK_cy_X	MTD_white_B	MTD_piwi_C	MTD_white_C	MTD_AubAgo3_A	MTD_AubAgo3_B	'
+ NAMElistANN='annotation	MTD_AubAgo3_C	TOsK_piwi_A	TOsK_white_A	TOsK_piwi_B	TOsK_AubAgo3_A	TOsK_white_B	TOsK_piwi_C	TOsK_PiwiAub_X	MTD_piwi_A	TOsK_AubAgo3_B	TOsK_white_C	MTD_white_A	MTD_piwi_B	TOsK_AubAgo3_C	TOsK_cy_X	MTD_white_B	MTD_piwi_C	MTD_white_C	MTD_AubAgo3_A	MTD_AubAgo3_B	'
++ printf 'length\tMTD_AubAgo3_C	TOsK_piwi_A	TOsK_white_A	TOsK_piwi_B	TOsK_AubAgo3_A	TOsK_white_B	TOsK_piwi_C	TOsK_PiwiAub_X	MTD_piwi_A	TOsK_AubAgo3_B	TOsK_white_C	MTD_white_A	MTD_piwi_B	TOsK_AubAgo3_C	TOsK_cy_X	MTD_white_B	MTD_piwi_C	MTD_white_C	MTD_AubAgo3_A	MTD_AubAgo3_B	'
+ NAMElistSIZE='length	MTD_AubAgo3_C	TOsK_piwi_A	TOsK_white_A	TOsK_piwi_B	TOsK_AubAgo3_A	TOsK_white_B	TOsK_piwi_C	TOsK_PiwiAub_X	MTD_piwi_A	TOsK_AubAgo3_B	TOsK_white_C	MTD_white_A	MTD_piwi_B	TOsK_AubAgo3_C	TOsK_cy_X	MTD_white_B	MTD_piwi_C	MTD_white_C	MTD_AubAgo3_A	MTD_AubAgo3_B	'
+ tr ' ' '\t'
+ echo annotation MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B
+ 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/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294242/294242_S28_R1_001.fastq.gz MTD_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
+ [[ N == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0'
+ SWITCH=Y
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294222/294222_S8_R1_001.fastq.gz TOsK_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294221/294221_S7_R1_001.fastq.gz TOsK_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294233/294233_S19_R1_001.fastq.gz TOsK_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294225/294225_S11_R1_001.fastq.gz TOsK_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294232/294232_S18_R1_001.fastq.gz TOsK_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294244/294244_S30_R1_001.fastq.gz TOsK_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314942/314942_S50_R1_001.fastq.gz TOsK_PiwiAub_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_PiwiAub_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294217/294217_S3_R1_001.fastq.gz MTD_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294236/294236_S22_R1_001.fastq.gz TOsK_AubAgo3_B
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294243/294243_S29_R1_001.fastq.gz TOsK_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294216/294216_S2_R1_001.fastq.gz MTD_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294228/294228_S14_R1_001.fastq.gz MTD_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294247/294247_S33_R1_001.fastq.gz TOsK_AubAgo3_C
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314943/314943_S51_R1_001.fastq.gz TOsK_cy_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_cy_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294227/294227_S13_R1_001.fastq.gz MTD_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294239/294239_S25_R1_001.fastq.gz MTD_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/log.txt
++ grep adaptor_dimer
++ awk '{ print $NF}'
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294238/294238_S24_R1_001.fastq.gz MTD_white_C
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/log.txt
++ grep adaptor_dimer
++ awk '{ print $NF}'
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294220/294220_S6_R1_001.fastq.gz MTD_AubAgo3_A
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/log.txt
++ grep adaptor_dimer
++ awk '{ print $NF}'
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294231/294231_S17_R1_001.fastq.gz MTD_AubAgo3_B
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/log.txt
++ awk '{ print $NF}'
++ grep adaptor_dimer
+ X=0
+ Xlist='adaptor_dimer 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
+ tr ' ' '\t'
+ echo adaptor_dimer 0 0 0 0 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
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294242/294242_S28_R1_001.fastq.gz MTD_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
+ [[ N == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/log.txt
++ grep artifact_filtered
++ awk '{ print $NF}'
+ X=474
+ Xlist='artifact_filtered 474'
+ SWITCH=Y
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294222/294222_S8_R1_001.fastq.gz TOsK_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=2307
+ Xlist='artifact_filtered 474 2307'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294221/294221_S7_R1_001.fastq.gz TOsK_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=5526
+ Xlist='artifact_filtered 474 2307 5526'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294233/294233_S19_R1_001.fastq.gz TOsK_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=803
+ Xlist='artifact_filtered 474 2307 5526 803'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294225/294225_S11_R1_001.fastq.gz TOsK_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=5175
+ Xlist='artifact_filtered 474 2307 5526 803 5175'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294232/294232_S18_R1_001.fastq.gz TOsK_white_B
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=1881
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294244/294244_S30_R1_001.fastq.gz TOsK_piwi_C
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=1291
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314942/314942_S50_R1_001.fastq.gz TOsK_PiwiAub_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_PiwiAub_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=320
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294217/294217_S3_R1_001.fastq.gz MTD_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=1189
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294236/294236_S22_R1_001.fastq.gz TOsK_AubAgo3_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=1786
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294243/294243_S29_R1_001.fastq.gz TOsK_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=1029
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294216/294216_S2_R1_001.fastq.gz MTD_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=1974
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294228/294228_S14_R1_001.fastq.gz MTD_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/log.txt
++ grep artifact_filtered
++ awk '{ print $NF}'
+ X=788
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974 788'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294247/294247_S33_R1_001.fastq.gz TOsK_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=1541
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974 788 1541'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314943/314943_S51_R1_001.fastq.gz TOsK_cy_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_cy_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=495
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974 788 1541 495'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294227/294227_S13_R1_001.fastq.gz MTD_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=933
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974 788 1541 495 933'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294239/294239_S25_R1_001.fastq.gz MTD_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=286
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974 788 1541 495 933 286'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294238/294238_S24_R1_001.fastq.gz MTD_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/log.txt
++ grep artifact_filtered
++ awk '{ print $NF}'
+ X=1839
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974 788 1541 495 933 286 1839'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294220/294220_S6_R1_001.fastq.gz MTD_AubAgo3_A
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/log.txt
++ awk '{ print $NF}'
++ grep artifact_filtered
+ X=2088
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974 788 1541 495 933 286 1839 2088'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294231/294231_S17_R1_001.fastq.gz MTD_AubAgo3_B
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/log.txt
++ grep artifact_filtered
++ awk '{ print $NF}'
+ X=3320
+ Xlist='artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974 788 1541 495 933 286 1839 2088 3320'
+ read LINE
+ tr ' ' '\t'
+ echo artifact_filtered 474 2307 5526 803 5175 1881 1291 320 1189 1786 1029 1974 788 1541 495 933 286 1839 2088 3320
+ 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/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294242/294242_S28_R1_001.fastq.gz MTD_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
+ [[ N == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/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/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294222/294222_S8_R1_001.fastq.gz TOsK_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_short
+ X=0
+ Xlist='length_filtered_short 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294221/294221_S7_R1_001.fastq.gz TOsK_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/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/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294233/294233_S19_R1_001.fastq.gz TOsK_piwi_B
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/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/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294225/294225_S11_R1_001.fastq.gz TOsK_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/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/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294232/294232_S18_R1_001.fastq.gz TOsK_white_B
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/log.txt
++ grep length_filtered_short
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294244/294244_S30_R1_001.fastq.gz TOsK_piwi_C
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/log.txt
++ grep length_filtered_short
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314942/314942_S50_R1_001.fastq.gz TOsK_PiwiAub_X
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_PiwiAub_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_short
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294217/294217_S3_R1_001.fastq.gz MTD_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_short
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294236/294236_S22_R1_001.fastq.gz TOsK_AubAgo3_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/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'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294243/294243_S29_R1_001.fastq.gz TOsK_white_C
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/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'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294216/294216_S2_R1_001.fastq.gz MTD_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/log.txt
++ grep length_filtered_short
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294228/294228_S14_R1_001.fastq.gz MTD_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/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 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294247/294247_S33_R1_001.fastq.gz TOsK_AubAgo3_C
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/log.txt
++ grep length_filtered_short
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_short 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314943/314943_S51_R1_001.fastq.gz TOsK_cy_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_cy_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/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 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294227/294227_S13_R1_001.fastq.gz MTD_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/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 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294239/294239_S25_R1_001.fastq.gz MTD_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/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 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294238/294238_S24_R1_001.fastq.gz MTD_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/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 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294220/294220_S6_R1_001.fastq.gz MTD_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/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 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294231/294231_S17_R1_001.fastq.gz MTD_AubAgo3_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/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 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 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
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294242/294242_S28_R1_001.fastq.gz MTD_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
+ [[ N == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0'
+ SWITCH=Y
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294222/294222_S8_R1_001.fastq.gz TOsK_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294221/294221_S7_R1_001.fastq.gz TOsK_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294233/294233_S19_R1_001.fastq.gz TOsK_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/log.txt
++ grep length_filtered_long
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_long 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294225/294225_S11_R1_001.fastq.gz TOsK_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294232/294232_S18_R1_001.fastq.gz TOsK_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294244/294244_S30_R1_001.fastq.gz TOsK_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314942/314942_S50_R1_001.fastq.gz TOsK_PiwiAub_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_PiwiAub_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294217/294217_S3_R1_001.fastq.gz MTD_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294236/294236_S22_R1_001.fastq.gz TOsK_AubAgo3_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294243/294243_S29_R1_001.fastq.gz TOsK_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294216/294216_S2_R1_001.fastq.gz MTD_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294228/294228_S14_R1_001.fastq.gz MTD_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ 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/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294247/294247_S33_R1_001.fastq.gz TOsK_AubAgo3_C
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/log.txt
++ grep length_filtered_long
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314943/314943_S51_R1_001.fastq.gz TOsK_cy_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_cy_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/log.txt
++ grep length_filtered_long
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294227/294227_S13_R1_001.fastq.gz MTD_white_B
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/log.txt
++ grep length_filtered_long
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294239/294239_S25_R1_001.fastq.gz MTD_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/log.txt
++ grep length_filtered_long
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294238/294238_S24_R1_001.fastq.gz MTD_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/log.txt
++ awk '{ print $NF}'
++ grep length_filtered_long
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294220/294220_S6_R1_001.fastq.gz MTD_AubAgo3_A
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/log.txt
++ grep length_filtered_long
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294231/294231_S17_R1_001.fastq.gz MTD_AubAgo3_B
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/log.txt
++ grep length_filtered_long
++ awk '{ print $NF}'
+ X=0
+ Xlist='length_filtered_long 0 0 0 0 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 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
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294242/294242_S28_R1_001.fastq.gz MTD_AubAgo3_C
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
+ [[ N == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/log.txt
++ grep N_filtered
++ awk '{ print $NF}'
+ X=218552
+ Xlist='N_filtered 218552'
+ SWITCH=Y
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294222/294222_S8_R1_001.fastq.gz TOsK_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=236159
+ Xlist='N_filtered 218552 236159'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294221/294221_S7_R1_001.fastq.gz TOsK_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=247439
+ Xlist='N_filtered 218552 236159 247439'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294233/294233_S19_R1_001.fastq.gz TOsK_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/log.txt
++ grep N_filtered
++ awk '{ print $NF}'
+ X=139254
+ Xlist='N_filtered 218552 236159 247439 139254'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294225/294225_S11_R1_001.fastq.gz TOsK_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=288960
+ Xlist='N_filtered 218552 236159 247439 139254 288960'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294232/294232_S18_R1_001.fastq.gz TOsK_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=274684
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294244/294244_S30_R1_001.fastq.gz TOsK_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=231899
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314942/314942_S50_R1_001.fastq.gz TOsK_PiwiAub_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_PiwiAub_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=170986
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294217/294217_S3_R1_001.fastq.gz MTD_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=183626
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294236/294236_S22_R1_001.fastq.gz TOsK_AubAgo3_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=211779
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294243/294243_S29_R1_001.fastq.gz TOsK_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=228640
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294216/294216_S2_R1_001.fastq.gz MTD_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=213900
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294228/294228_S14_R1_001.fastq.gz MTD_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/log.txt
++ grep N_filtered
++ awk '{ print $NF}'
+ X=105275
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900 105275'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294247/294247_S33_R1_001.fastq.gz TOsK_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/log.txt
++ grep N_filtered
++ awk '{ print $NF}'
+ X=292556
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900 105275 292556'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314943/314943_S51_R1_001.fastq.gz TOsK_cy_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_cy_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=201070
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900 105275 292556 201070'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294227/294227_S13_R1_001.fastq.gz MTD_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
+ [[ Y == N ]]
++ awk '{ print $NF}'
++ grep N_filtered
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/log.txt
+ X=194417
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900 105275 292556 201070 194417'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294239/294239_S25_R1_001.fastq.gz MTD_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=181676
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900 105275 292556 201070 194417 181676'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294238/294238_S24_R1_001.fastq.gz MTD_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=293837
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900 105275 292556 201070 194417 181676 293837'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294220/294220_S6_R1_001.fastq.gz MTD_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=202903
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900 105275 292556 201070 194417 181676 293837 202903'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294231/294231_S17_R1_001.fastq.gz MTD_AubAgo3_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/log.txt
++ awk '{ print $NF}'
++ grep N_filtered
+ X=245069
+ Xlist='N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900 105275 292556 201070 194417 181676 293837 202903 245069'
+ read LINE
+ tr ' ' '\t'
+ echo N_filtered 218552 236159 247439 139254 288960 274684 231899 170986 183626 211779 228640 213900 105275 292556 201070 194417 181676 293837 202903 245069
+ 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/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294242/294242_S28_R1_001.fastq.gz MTD_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
+ [[ N == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=17336625
+ Xlist='reads_after_filtering 17336625'
+ SWITCH=Y
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294222/294222_S8_R1_001.fastq.gz TOsK_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=18552015
+ Xlist='reads_after_filtering 17336625 18552015'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294221/294221_S7_R1_001.fastq.gz TOsK_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=19715046
+ Xlist='reads_after_filtering 17336625 18552015 19715046'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294233/294233_S19_R1_001.fastq.gz TOsK_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=11030732
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294225/294225_S11_R1_001.fastq.gz TOsK_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=22580897
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294232/294232_S18_R1_001.fastq.gz TOsK_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=21524930
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294244/294244_S30_R1_001.fastq.gz TOsK_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=18127500
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314942/314942_S50_R1_001.fastq.gz TOsK_PiwiAub_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_PiwiAub_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=17643238
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294217/294217_S3_R1_001.fastq.gz MTD_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/log.txt
++ grep reads_after_filtering
++ awk '{ print $NF}'
+ X=14468381
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294236/294236_S22_R1_001.fastq.gz TOsK_AubAgo3_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=16793594
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294243/294243_S29_R1_001.fastq.gz TOsK_white_C
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=18032918
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294216/294216_S2_R1_001.fastq.gz MTD_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=17005484
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294228/294228_S14_R1_001.fastq.gz MTD_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=8214174
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484 8214174'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294247/294247_S33_R1_001.fastq.gz TOsK_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=23007640
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484 8214174 23007640'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314943/314943_S51_R1_001.fastq.gz TOsK_cy_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_cy_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=20864054
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484 8214174 23007640 20864054'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294227/294227_S13_R1_001.fastq.gz MTD_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=15481703
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484 8214174 23007640 20864054 15481703'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294239/294239_S25_R1_001.fastq.gz MTD_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/log.txt
++ grep reads_after_filtering
++ awk '{ print $NF}'
+ X=14305042
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484 8214174 23007640 20864054 15481703 14305042'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294238/294238_S24_R1_001.fastq.gz MTD_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=22880507
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484 8214174 23007640 20864054 15481703 14305042 22880507'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294220/294220_S6_R1_001.fastq.gz MTD_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=15847103
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484 8214174 23007640 20864054 15481703 14305042 22880507 15847103'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294231/294231_S17_R1_001.fastq.gz MTD_AubAgo3_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/log.txt
++ awk '{ print $NF}'
++ grep reads_after_filtering
+ X=19099807
+ Xlist='reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484 8214174 23007640 20864054 15481703 14305042 22880507 15847103 19099807'
+ read LINE
+ tr ' ' '\t'
+ echo reads_after_filtering 17336625 18552015 19715046 11030732 22580897 21524930 18127500 17643238 14468381 16793594 18032918 17005484 8214174 23007640 20864054 15481703 14305042 22880507 15847103 19099807
+ 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/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294242/294242_S28_R1_001.fastq.gz MTD_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
+ [[ N == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=2839381
+ Xlist='reads_not_mapped 2839381'
+ SWITCH=Y
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294222/294222_S8_R1_001.fastq.gz TOsK_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=4521625
+ Xlist='reads_not_mapped 2839381 4521625'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294221/294221_S7_R1_001.fastq.gz TOsK_white_A
++ tr ' ' '\t'
++ cut -f 2
+ NAME=TOsK_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=4347588
+ Xlist='reads_not_mapped 2839381 4521625 4347588'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294233/294233_S19_R1_001.fastq.gz TOsK_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=1600897
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294225/294225_S11_R1_001.fastq.gz TOsK_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=5378167
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294232/294232_S18_R1_001.fastq.gz TOsK_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=3113404
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294244/294244_S30_R1_001.fastq.gz TOsK_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=2535212
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314942/314942_S50_R1_001.fastq.gz TOsK_PiwiAub_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_PiwiAub_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=2027828
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294217/294217_S3_R1_001.fastq.gz MTD_piwi_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=3354759
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294236/294236_S22_R1_001.fastq.gz TOsK_AubAgo3_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=2344009
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294243/294243_S29_R1_001.fastq.gz TOsK_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/log.txt
++ grep reads_not_mapped
++ awk '{ print $NF}'
+ X=2545443
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294216/294216_S2_R1_001.fastq.gz MTD_white_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=3646997
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294228/294228_S14_R1_001.fastq.gz MTD_piwi_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/log.txt
++ grep reads_not_mapped
++ awk '{ print $NF}'
+ X=1440969
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997 1440969'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294247/294247_S33_R1_001.fastq.gz TOsK_AubAgo3_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_AubAgo3_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=3293890
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997 1440969 3293890'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_08_27_RNAseq_sRNAseq_MY_AE_22MYG2LT3_2_R17585/demultiplexed/314943/314943_S51_R1_001.fastq.gz TOsK_cy_X
++ cut -f 2
++ tr ' ' '\t'
+ NAME=TOsK_cy_X
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=2452827
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997 1440969 3293890 2452827'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294227/294227_S13_R1_001.fastq.gz MTD_white_B
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=2489888
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997 1440969 3293890 2452827 2489888'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294239/294239_S25_R1_001.fastq.gz MTD_piwi_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_piwi_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=2736954
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997 1440969 3293890 2452827 2489888 2736954'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294238/294238_S24_R1_001.fastq.gz MTD_white_C
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_white_C
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/log.txt
++ awk '{ print $NF}'
++ grep reads_not_mapped
+ X=5313779
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997 1440969 3293890 2452827 2489888 2736954 5313779'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294220/294220_S6_R1_001.fastq.gz MTD_AubAgo3_A
++ cut -f 2
++ tr ' ' '\t'
+ NAME=MTD_AubAgo3_A
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/log.txt
++ grep reads_not_mapped
++ awk '{ print $NF}'
+ X=3900407
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997 1440969 3293890 2452827 2489888 2736954 5313779 3900407'
+ read LINE
++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2024_05_THG_RNAseq_22KHJ7LT3_7_R17202_20240530/22KHJ7LT3_7_R17202_20240530/demultiplexed/294231/294231_S17_R1_001.fastq.gz MTD_AubAgo3_B
++ tr ' ' '\t'
++ cut -f 2
+ NAME=MTD_AubAgo3_B
+ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
+ [[ Y == N ]]
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/log.txt
++ grep reads_not_mapped
++ awk '{ print $NF}'
+ X=4406259
+ Xlist='reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997 1440969 3293890 2452827 2489888 2736954 5313779 3900407 4406259'
+ read LINE
+ tr ' ' '\t'
+ echo reads_not_mapped 2839381 4521625 4347588 1600897 5378167 3113404 2535212 2027828 3354759 2344009 2545443 3646997 1440969 3293890 2452827 2489888 2736954 5313779 3900407 4406259
+ for CATEGORY in annotation_counts splitup_mRNA splitup_TE
+ NAMES=
+ [[ annotation_counts != annotation_counts ]]
+ awk -v 'OFS=\t' '{
    X[$1]=X[$1]"\t"$2
    Y[$1]+=NR
  }
  END {
    for (i in X) {
      print Y[i],i,X[i]
    }
+ sort -k1,1n
+ cut -f 2-
  }' /dev/fd/63
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/MTD_AubAgo3_C_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/TOsK_piwi_A_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/TOsK_white_A_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/TOsK_piwi_B_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/TOsK_AubAgo3_A_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/TOsK_white_B_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/TOsK_piwi_C_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/TOsK_PiwiAub_X_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/MTD_piwi_A_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/TOsK_AubAgo3_B_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/TOsK_white_C_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/MTD_white_A_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/MTD_piwi_B_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/TOsK_AubAgo3_C_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/TOsK_cy_X_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/MTD_white_B_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/MTD_piwi_C_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/MTD_white_C_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/MTD_AubAgo3_A_annotation_counts.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/MTD_AubAgo3_B_annotation_counts.txt
++ read NAME
+ [[ annotation_counts != annotation_counts ]]
+ EXT=
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/TMP.txt
+ tr ' ' '\t'
+ tr -s '\t'
+ [[ RNAseq == CHIPseq ]]
+ [[ RNAseq == 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/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/splitup_mRNA.txt
+ cut -f 2-
+ awk -v 'OFS=\t' '{
    X[$1]=X[$1]"\t"$2
    Y[$1]+=NR
  }
  END {
    for (i in X) {
      print Y[i],i,X[i]
    }
+ sort -k1,1n
++ read NAME
  }' /dev/fd/63
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/MTD_AubAgo3_C_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/TOsK_piwi_A_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/TOsK_white_A_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/TOsK_piwi_B_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/TOsK_AubAgo3_A_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/TOsK_white_B_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/TOsK_piwi_C_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/TOsK_PiwiAub_X_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/MTD_piwi_A_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/TOsK_AubAgo3_B_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/TOsK_white_C_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/MTD_white_A_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/MTD_piwi_B_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/TOsK_AubAgo3_C_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/TOsK_cy_X_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/MTD_white_B_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/MTD_piwi_C_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/MTD_white_C_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/MTD_AubAgo3_A_splitup_mRNA.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/MTD_AubAgo3_B_splitup_mRNA.txt
++ read NAME
+ [[ splitup_mRNA != annotation_counts ]]
+ EXT=annotation_
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/TMP.txt
+ tr ' ' '\t'
+ tr -s '\t'
+ [[ RNAseq == CHIPseq ]]
+ [[ RNAseq == 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/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/annotation_splitup_TE.txt
+ 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
+ cut -f 2-
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/MTD_AubAgo3_C_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/TOsK_piwi_A_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/TOsK_white_A_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/TOsK_piwi_B_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/TOsK_AubAgo3_A_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/TOsK_white_B_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/TOsK_piwi_C_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/TOsK_PiwiAub_X_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/MTD_piwi_A_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/TOsK_AubAgo3_B_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/TOsK_white_C_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/MTD_white_A_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/MTD_piwi_B_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/TOsK_AubAgo3_C_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/TOsK_cy_X_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/MTD_white_B_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/MTD_piwi_C_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/MTD_white_C_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/MTD_AubAgo3_A_splitup_TE.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/MTD_AubAgo3_B_splitup_TE.txt
++ read NAME
+ [[ splitup_TE != annotation_counts ]]
+ EXT=annotation_
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/TMP.txt
+ tr ' ' '\t'
+ tr -s '\t'
+ [[ RNAseq == CHIPseq ]]
+ [[ RNAseq == DNAseq ]]
+ [[ '' == Y ]]
+ Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/ FILE=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/
+ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/ FILE=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/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/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/1kb_tiles
+ for STRAND in Plus Minus
+ sort -k1,1n
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
+ 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]
      }
+ cut -f 2-
++ NAMES=' MTD_AubAgo3_C'
    }' /dev/fd/63
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/WindowCounts_Plus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/WindowCounts_Plus.txt
++ read NAME
+ tr ' ' '\t'
+ echo POS MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B
+ tr -s '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/TMP.txt
+ tr -s '\t'
+ tr ' ' '\t'
+ for STRAND in Plus Minus
+ sort -k1,1n
+ cut -f 2-
+ 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/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/WindowCounts_Minus.txt
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/WindowCounts_Minus.txt
++ read NAME
+ echo POS MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B
+ tr -s '\t'
+ tr ' ' '\t'
+ tr -s '\t'
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/TMP.txt
+ tr ' ' '\t'
+ 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/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/1kb_tiles/
+ rawFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/raw-data/
+ mkdir -p /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/raw-data/
+ [[ RNAseq == sRNAseq ]]
+ [[ RNAseq == CLIPseq ]]
+ [[ RNAseq == sRNAseqIP ]]
+ [[ RNAseq == SLAMseq ]]
+ [[ RNAseq == GROseq ]]
+ [[ RNAseq == sRNAseq ]]
+ [[ RNAseq == sRNAseqIP ]]
+ [[ RNAseq == CLIPseq ]]
+ [[ RNAseq = RNAseq ]]
+ CATEGORIES='TE_GeTMM TE_GeTMM GeTMM_gene'
+ [[ RNAseq == sRNAseq ]]
+ [[ RNAseq == sRNAseqIP ]]
+ [[ RNAseq == CLIPseq ]]
+ [[ RNAseq = RNAseq ]]
+ for CATEGORY in $CATEGORIES
+ [[ TE_GeTMM == *\T\E\_\G\e\T\M\M* ]]
+ head -n 1 /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ tr ' ' '\t'
+ grep '^TE:' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ grep -v _AS
+ tr ' ' '\t'
+ head -n 1 /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ tr ' ' '\t'
+ grep '^TE:' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ grep _AS
+ tr ' ' '\t'
+ for CATEGORY in $CATEGORIES
+ [[ TE_GeTMM == *\T\E\_\G\e\T\M\M* ]]
+ tr ' ' '\t'
+ head -n 1 /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ grep '^TE:' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ tr ' ' '\t'
+ grep -v _AS
+ tr ' ' '\t'
+ head -n 1 /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ grep '^TE:' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ grep _AS
+ tr ' ' '\t'
+ for CATEGORY in $CATEGORIES
+ [[ GeTMM_gene == *\T\E\_\G\e\T\M\M* ]]
+ [[ GeTMM_gene == GeTMM_gene ]]
+ head -n 1 /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ tr ' ' '\t'
+ tr ' ' '\t'
+ grep -v '^TE:' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/gene-expression/GeTMM_normalized.txt
+ [[ N == Y ]]
+ [[ '' == Y ]]
+ [[ RNAseq == RNAseq ]]
+ [[ RNAseq == CHIPseq ]]
+ [[ RNAseq == DNAseq ]]
+ [[ '' == Y ]]
+ CATEGORIES='sense antisense'
+ [[ RNAseq == sRNAseq ]]
+ [[ RNAseq == sRNAseqIP ]]
+ CLASSES=man
+ 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/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/MTD_AubAgo3_C_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/TOsK_piwi_A_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/TOsK_white_A_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/TOsK_piwi_B_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/TOsK_AubAgo3_A_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/TOsK_white_B_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/TOsK_piwi_C_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/TOsK_PiwiAub_X_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/MTD_piwi_A_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/TOsK_AubAgo3_B_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/TOsK_white_C_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/MTD_white_A_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/MTD_piwi_B_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/TOsK_AubAgo3_C_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/TOsK_cy_X_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/MTD_white_B_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/MTD_piwi_C_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/MTD_white_C_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/MTD_AubAgo3_A_TE-sense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/MTD_AubAgo3_B_TE-sense_man.bg
++ read NAME
++ echo TE POS MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B
++ tr '~' '\t'
++ tr ' ' '\t'
+ echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/TMP_TEhist_man.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/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_C/MTD_AubAgo3_C_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_A/TOsK_piwi_A_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_A/TOsK_white_A_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_B/TOsK_piwi_B_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_A/TOsK_AubAgo3_A_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_B/TOsK_white_B_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_piwi_C/TOsK_piwi_C_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_PiwiAub_X/TOsK_PiwiAub_X_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_A/MTD_piwi_A_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_B/TOsK_AubAgo3_B_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_white_C/TOsK_white_C_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_A/MTD_white_A_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_B/MTD_piwi_B_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_AubAgo3_C/TOsK_AubAgo3_C_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/TOsK_cy_X/TOsK_cy_X_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_B/MTD_white_B_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_piwi_C/MTD_piwi_C_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_white_C/MTD_white_C_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_A/MTD_AubAgo3_A_TE-antisense_man.bg
++ read NAME
++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/
++ NAMES=' MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B'
++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq//individual-libraries/MTD_AubAgo3_B/MTD_AubAgo3_B_TE-antisense_man.bg
++ read NAME
++ echo TE POS MTD_AubAgo3_C TOsK_piwi_A TOsK_white_A TOsK_piwi_B TOsK_AubAgo3_A TOsK_white_B TOsK_piwi_C TOsK_PiwiAub_X MTD_piwi_A TOsK_AubAgo3_B TOsK_white_C MTD_white_A MTD_piwi_B TOsK_AubAgo3_C TOsK_cy_X MTD_white_B MTD_piwi_C MTD_white_C MTD_AubAgo3_A MTD_AubAgo3_B
++ tr '~' '\t'
++ tr ' ' '\t'
+ echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/
+ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/TMP_TEhist_man.txt
+ tr '~' '\t'
+ tr ' ' '\t'
+ sort -k2,2n
+ mkdir -p /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/TEhist/html-dependencies/
+ Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/TEhist/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/raw-data/TE_hist TYPE=RNAseq
+ singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/TEhist/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/plots/raw-data/TE_hist TYPE=RNAseq
── 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’

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

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/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/Rscripts.pdf
+ [[ N != Y ]]
+ rm -rf /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2025-10-21-MTD_vs_TOsK_RNAseq/TMP/
++ awk '{ print ($1-$2)/60 }'
+++ date +%s
++ echo -e 1761049464 1761048887
+ PROCESSED_TIME=9.61667
+ echo 'collect-numbers - processing_time=' 9.61667
+ exit