++ echo USER_NAME=thomasgrnbk,TYPE=sRNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/,FOLDER_NAME=sRNAseq_GEO_format,RUNname=2026-03-11-sRNAseq_GEO_format,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/,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=,DEMUXonly=N,BAM=N,fwADAPTOR=,rvADAPTOR=,N_TRIMM=,rawPAIRED=N,onlyPAIRED=N,FASTQout=N,FASTQoutRAW=N,SUBSAMPLE=,MIN_LENGTH=18,MAX_LENGTH=35,RAW=,TRIMM=,FIRST=1,LAST=1000,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=0,FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA,WIG=,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/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=8,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/files.txt,FOLDER_NAME=sRNAseq_GEO_format,GENOME_VERSION=dm6,subCOLOR=0~0~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=N,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,exportSalmon=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/,newCOLLECTION=N,prepANNOTATIONgff=,prepGENOMEfasta=,prepTRANSCRIPTOMEfasta=,prepCDSfasta=,prepNCRNAfasta=,extraSEQ=,FORCEquant_unstranded=N ++ sed 's/,/\t/g;s/"//g' + VARI='USER_NAME=thomasgrnbk TYPE=sRNAseq SLAM=N BASE_FOLDER=/faststorage/project/PAN_illumina/results/ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/ FOLDER_NAME=sRNAseq_GEO_format RUNname=2026-03-11-sRNAseq_GEO_format TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/ 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= DEMUXonly=N BAM=N fwADAPTOR= rvADAPTOR= N_TRIMM= rawPAIRED=N onlyPAIRED=N FASTQout=N FASTQoutRAW=N SUBSAMPLE= MIN_LENGTH=18 MAX_LENGTH=35 RAW= TRIMM= FIRST=1 LAST=1000 INVERT=N Ychrom=N RANDOMmulti=N MM=0 FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA WIG= WIG_FASTA= spikeINnorm=N noNORM= EXTEND=0 COMPUTING=C GRIDsystem=SLURM keepTMP=N SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/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=8 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/files.txt FOLDER_NAME=sRNAseq_GEO_format GENOME_VERSION=dm6 subCOLOR=0~0~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=N GEO= noSTRANDED= FORCEimport= exportBAM=N exportBAMuncollapsed=N exportSalmon=N RATIOtracks=N GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/ newCOLLECTION=N prepANNOTATIONgff= prepGENOMEfasta= prepTRANSCRIPTOMEfasta= prepCDSfasta= prepNCRNAfasta= extraSEQ= FORCEquant_unstranded=N' + eval 'USER_NAME=thomasgrnbk TYPE=sRNAseq SLAM=N BASE_FOLDER=/faststorage/project/PAN_illumina/results/ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/ FOLDER_NAME=sRNAseq_GEO_format RUNname=2026-03-11-sRNAseq_GEO_format TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/ 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= DEMUXonly=N BAM=N fwADAPTOR= rvADAPTOR= N_TRIMM= rawPAIRED=N onlyPAIRED=N FASTQout=N FASTQoutRAW=N SUBSAMPLE= MIN_LENGTH=18 MAX_LENGTH=35 RAW= TRIMM= FIRST=1 LAST=1000 INVERT=N Ychrom=N RANDOMmulti=N MM=0 FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA WIG= WIG_FASTA= spikeINnorm=N noNORM= EXTEND=0 COMPUTING=C GRIDsystem=SLURM keepTMP=N SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/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=8 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/files.txt FOLDER_NAME=sRNAseq_GEO_format GENOME_VERSION=dm6 subCOLOR=0~0~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=N GEO= noSTRANDED= FORCEimport= exportBAM=N exportBAMuncollapsed=N exportSalmon=N RATIOtracks=N GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/ newCOLLECTION=N prepANNOTATIONgff= prepGENOMEfasta= prepTRANSCRIPTOMEfasta= prepCDSfasta= prepNCRNAfasta= extraSEQ= FORCEquant_unstranded=N' ++ USER_NAME=thomasgrnbk ++ TYPE=sRNAseq ++ SLAM=N ++ BASE_FOLDER=/faststorage/project/PAN_illumina/results/ ++ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/ ++ FOLDER_NAME=sRNAseq_GEO_format ++ RUNname=2026-03-11-sRNAseq_GEO_format ++ TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/ ++ 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= ++ DEMUXonly=N ++ BAM=N ++ fwADAPTOR= ++ rvADAPTOR= ++ N_TRIMM= ++ rawPAIRED=N ++ onlyPAIRED=N ++ FASTQout=N ++ FASTQoutRAW=N ++ SUBSAMPLE= ++ MIN_LENGTH=18 ++ MAX_LENGTH=35 ++ RAW= ++ TRIMM= ++ FIRST=1 ++ LAST=1000 ++ INVERT=N ++ Ychrom=N ++ RANDOMmulti=N ++ MM=0 ++ FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA ++ WIG= ++ WIG_FASTA= ++ spikeINnorm=N ++ noNORM= ++ EXTEND=0 ++ COMPUTING=C ++ GRIDsystem=SLURM ++ keepTMP=N ++ SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/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=8 ++ FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/files.txt ++ FOLDER_NAME=sRNAseq_GEO_format ++ GENOME_VERSION=dm6 ++ subCOLOR=0~0~0 ++ FORCE= ++ SYSTEM=EXTERN ++ LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/LOGs/ ++ prepareREF=no ++ nSPLITS=1000000 ++ SE=N ++ SE2nd= ++ maxCOUNT=1000000 ++ demuxFASTA=N ++ autoViewLimits= ++ only5end= ++ PingPong= ++ DGE=N ++ GEO= ++ noSTRANDED= ++ FORCEimport= ++ exportBAM=N ++ exportBAMuncollapsed=N ++ exportSalmon=N ++ RATIOtracks=N ++ GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/ ++ newCOLLECTION=N ++ prepANNOTATIONgff= ++ prepGENOMEfasta= ++ prepTRANSCRIPTOMEfasta= ++ prepCDSfasta= ++ prepNCRNAfasta= ++ extraSEQ= ++ FORCEquant_unstranded=N + echo USER_NAME=thomasgrnbk,TYPE=sRNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/,FOLDER_NAME=sRNAseq_GEO_format,RUNname=2026-03-11-sRNAseq_GEO_format,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/,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=,DEMUXonly=N,BAM=N,fwADAPTOR=,rvADAPTOR=,N_TRIMM=,rawPAIRED=N,onlyPAIRED=N,FASTQout=N,FASTQoutRAW=N,SUBSAMPLE=,MIN_LENGTH=18,MAX_LENGTH=35,RAW=,TRIMM=,FIRST=1,LAST=1000,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=0,FILTERING_INPUT=rRNA:tRNA:mito:miRNA:pre_miRNA:snRNA:snoRNA:ncRNA,WIG=,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/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=8,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/files.txt,FOLDER_NAME=sRNAseq_GEO_format,GENOME_VERSION=dm6,subCOLOR=0~0~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=N,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,exportSalmon=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/,newCOLLECTION=N,prepANNOTATIONgff=,prepGENOMEfasta=,prepTRANSCRIPTOMEfasta=,prepCDSfasta=,prepNCRNAfasta=,extraSEQ=,FORCEquant_unstranded=N + sed 's/,/\n/g' ++ date +%s + TIME=1773253221 + TIMEx=1773253221 + [[ SLURM == SLURM ]] + CORES=3 + echo 3 + source /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/tools ++ set -a + locTMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + mkdir -p /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + chmod 777 /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + TMPDIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + cd /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + echo /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/ + mkdir /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/files.txt + tr ' ' '\t' + cut -f 2 + rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/annotation_counts.txt ++ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/files.txt ++ awk '{ print $2 }' ++ tr '\n' '\t' + NAMElist='sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ' ++ printf 'annotation\tsRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ' + NAMElistANN='annotation sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ' ++ printf 'length\tsRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ' + NAMElistSIZE='length sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ' + echo annotation sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep2_Ov_XXX_GAACG.pre-processed.fq.gz sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=120747 + Xlist='adaptor_dimer 120747' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_whitesh_rep3_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=21653 + Xlist='adaptor_dimer 120747 21653' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_piwish_rep2_bam_NoHS_GGTAT.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/log.txt ++ grep adaptor_dimer ++ awk '{ print $NF}' + X=19844 + Xlist='adaptor_dimer 120747 21653 19844' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_whitesh_rep1_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=22404 + Xlist='adaptor_dimer 120747 21653 19844 22404' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_whitesh_rep2_bam_NoHS_CAGTG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/log.txt ++ grep adaptor_dimer ++ awk '{ print $NF}' + X=31226 + Xlist='adaptor_dimer 120747 21653 19844 22404 31226' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_piwish_rep3_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=314246 + Xlist='adaptor_dimer 120747 21653 19844 22404 31226 314246' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_piwish_rep1_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=326478 + Xlist='adaptor_dimer 120747 21653 19844 22404 31226 314246 326478' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep1_Ov_XXX_ATGGA.pre-processed.fq.gz sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=84406 + Xlist='adaptor_dimer 120747 21653 19844 22404 31226 314246 326478 84406' + read LINE + echo adaptor_dimer 120747 21653 19844 22404 31226 314246 326478 84406 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep2_Ov_XXX_GAACG.pre-processed.fq.gz sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=4881 + Xlist='artifact_filtered 4881' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_whitesh_rep3_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=2014 + Xlist='artifact_filtered 4881 2014' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_piwish_rep2_bam_NoHS_GGTAT.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=1081 + Xlist='artifact_filtered 4881 2014 1081' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_whitesh_rep1_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=2050 + Xlist='artifact_filtered 4881 2014 1081 2050' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_whitesh_rep2_bam_NoHS_CAGTG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=2867 + Xlist='artifact_filtered 4881 2014 1081 2050 2867' + read LINE ++ tr ' ' '\t' ++ cut -f 2 ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_piwish_rep3_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=939 + Xlist='artifact_filtered 4881 2014 1081 2050 2867 939' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_piwish_rep1_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=564 + Xlist='artifact_filtered 4881 2014 1081 2050 2867 939 564' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep1_Ov_XXX_ATGGA.pre-processed.fq.gz sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/log.txt ++ grep artifact_filtered ++ awk '{ print $NF}' + X=2862 + Xlist='artifact_filtered 4881 2014 1081 2050 2867 939 564 2862' + read LINE + echo artifact_filtered 4881 2014 1081 2050 2867 939 564 2862 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep2_Ov_XXX_GAACG.pre-processed.fq.gz sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=202789 + Xlist='length_filtered_short 202789' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_whitesh_rep3_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=40901 + Xlist='length_filtered_short 202789 40901' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_piwish_rep2_bam_NoHS_GGTAT.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=37982 + Xlist='length_filtered_short 202789 40901 37982' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_whitesh_rep1_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=25374 + Xlist='length_filtered_short 202789 40901 37982 25374' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_whitesh_rep2_bam_NoHS_CAGTG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/log.txt ++ grep length_filtered_short ++ awk '{ print $NF}' + X=77496 + Xlist='length_filtered_short 202789 40901 37982 25374 77496' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_piwish_rep3_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=23048 + Xlist='length_filtered_short 202789 40901 37982 25374 77496 23048' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_piwish_rep1_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=13322 + Xlist='length_filtered_short 202789 40901 37982 25374 77496 23048 13322' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep1_Ov_XXX_ATGGA.pre-processed.fq.gz sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=119881 + Xlist='length_filtered_short 202789 40901 37982 25374 77496 23048 13322 119881' + read LINE + echo length_filtered_short 202789 40901 37982 25374 77496 23048 13322 119881 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep2_Ov_XXX_GAACG.pre-processed.fq.gz sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=597516 + Xlist='length_filtered_long 597516' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_whitesh_rep3_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=212802 + Xlist='length_filtered_long 597516 212802' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_piwish_rep2_bam_NoHS_GGTAT.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=148498 + Xlist='length_filtered_long 597516 212802 148498' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_whitesh_rep1_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/log.txt ++ grep length_filtered_long ++ awk '{ print $NF}' + X=185406 + Xlist='length_filtered_long 597516 212802 148498 185406' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_whitesh_rep2_bam_NoHS_CAGTG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=307556 + Xlist='length_filtered_long 597516 212802 148498 185406 307556' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_piwish_rep3_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=90222 + Xlist='length_filtered_long 597516 212802 148498 185406 307556 90222' + read LINE ++ tr ' ' '\t' ++ cut -f 2 ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_piwish_rep1_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=59895 + Xlist='length_filtered_long 597516 212802 148498 185406 307556 90222 59895' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep1_Ov_XXX_ATGGA.pre-processed.fq.gz sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=337929 + Xlist='length_filtered_long 597516 212802 148498 185406 307556 90222 59895 337929' + read LINE + echo length_filtered_long 597516 212802 148498 185406 307556 90222 59895 337929 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep2_Ov_XXX_GAACG.pre-processed.fq.gz sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/log.txt ++ grep N_filtered ++ awk '{ print $NF}' + X=84606 + Xlist='N_filtered 84606' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_whitesh_rep3_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=40868 + Xlist='N_filtered 84606 40868' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_piwish_rep2_bam_NoHS_GGTAT.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/log.txt ++ grep N_filtered ++ awk '{ print $NF}' + X=31167 + Xlist='N_filtered 84606 40868 31167' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_whitesh_rep1_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=40311 + Xlist='N_filtered 84606 40868 31167 40311' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_whitesh_rep2_bam_NoHS_CAGTG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=75335 + Xlist='N_filtered 84606 40868 31167 40311 75335' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_piwish_rep3_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=14642 + Xlist='N_filtered 84606 40868 31167 40311 75335 14642' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_piwish_rep1_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/log.txt ++ grep N_filtered ++ awk '{ print $NF}' + X=10870 + Xlist='N_filtered 84606 40868 31167 40311 75335 14642 10870' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep1_Ov_XXX_ATGGA.pre-processed.fq.gz sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=50383 + Xlist='N_filtered 84606 40868 31167 40311 75335 14642 10870 50383' + read LINE + echo N_filtered 84606 40868 31167 40311 75335 14642 10870 50383 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep2_Ov_XXX_GAACG.pre-processed.fq.gz sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=34393153 + Xlist='reads_after_filtering 34393153' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_whitesh_rep3_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/log.txt ++ grep reads_after_filtering ++ awk '{ print $NF}' + X=17624595 + Xlist='reads_after_filtering 34393153 17624595' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_piwish_rep2_bam_NoHS_GGTAT.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=12792720 + Xlist='reads_after_filtering 34393153 17624595 12792720' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_whitesh_rep1_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=16769364 + Xlist='reads_after_filtering 34393153 17624595 12792720 16769364' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_whitesh_rep2_bam_NoHS_CAGTG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=31107017 + Xlist='reads_after_filtering 34393153 17624595 12792720 16769364 31107017' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_piwish_rep3_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=6309402 + Xlist='reads_after_filtering 34393153 17624595 12792720 16769364 31107017 6309402' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_piwish_rep1_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=4421291 + Xlist='reads_after_filtering 34393153 17624595 12792720 16769364 31107017 6309402 4421291' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep1_Ov_XXX_ATGGA.pre-processed.fq.gz sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=20586163 + Xlist='reads_after_filtering 34393153 17624595 12792720 16769364 31107017 6309402 4421291 20586163' + read LINE + echo reads_after_filtering 34393153 17624595 12792720 16769364 31107017 6309402 4421291 20586163 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep2_Ov_XXX_GAACG.pre-processed.fq.gz sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=4205941 + Xlist='reads_not_mapped 4205941' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_whitesh_rep3_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/log.txt ++ grep reads_not_mapped ++ awk '{ print $NF}' + X=1931102 + Xlist='reads_not_mapped 4205941 1931102' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_piwish_rep2_bam_NoHS_GGTAT.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=1298855 + Xlist='reads_not_mapped 4205941 1931102 1298855' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_whitesh_rep1_bam_NoHS_GTCAG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=1790046 + Xlist='reads_not_mapped 4205941 1931102 1298855 1790046' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283081_whitesh_rep2_bam_NoHS_CAGTG.pre-processed.fq.gz sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=3115463 + Xlist='reads_not_mapped 4205941 1931102 1298855 1790046 3115463' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283082_piwish_rep3_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC ++ tr ' ' '\t' ++ cut -f 2 + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=732509 + Xlist='reads_not_mapped 4205941 1931102 1298855 1790046 3115463 732509' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283080_piwish_rep1_bam_NoHS_CGTTC.pre-processed.fq.gz sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/log.txt ++ grep reads_not_mapped ++ awk '{ print $NF}' + X=482867 + Xlist='reads_not_mapped 4205941 1931102 1298855 1790046 3115463 732509 482867' + read LINE ++ echo /faststorage/project/PAN_illumina/tmp/2025_Grnbk_Yoth_RAW/smallRNA_R16775_demultiplexed/sRNA_283083_whitesh_rep1_Ov_XXX_ATGGA.pre-processed.fq.gz sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ cut -f 2 ++ tr ' ' '\t' + NAME=sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=2406196 + Xlist='reads_not_mapped 4205941 1931102 1298855 1790046 3115463 732509 482867 2406196' + read LINE + tr ' ' '\t' + echo reads_not_mapped 4205941 1931102 1298855 1790046 3115463 732509 482867 2406196 + 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] } + cut -f 2- + sort -k1,1n }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_annotation_counts.txt ++ read NAME + [[ annotation_counts != annotation_counts ]] + EXT= + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr -s '\t' + tr ' ' '\t' + [[ sRNAseq == CHIPseq ]] + [[ sRNAseq == DNAseq ]] + [[ '' == Y ]] + for CATEGORY in annotation_counts splitup_mRNA splitup_TE + NAMES= + [[ splitup_mRNA != annotation_counts ]] + rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/splitup_mRNA.txt + awk -v 'OFS=\t' '{ X[$1]=X[$1]"\t"$2 Y[$1]+=NR } END { for (i in X) { print Y[i],i,X[i] } + cut -f 2- + sort -k1,1n }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_splitup_mRNA.txt ++ read NAME + [[ splitup_mRNA != annotation_counts ]] + EXT=annotation_ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr ' ' '\t' + tr -s '\t' + [[ sRNAseq == CHIPseq ]] + [[ sRNAseq == DNAseq ]] + [[ '' == Y ]] + for CATEGORY in annotation_counts splitup_mRNA splitup_TE + NAMES= + [[ splitup_TE != annotation_counts ]] + rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/annotation_splitup_TE.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/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_splitup_TE.txt ++ read NAME + [[ splitup_TE != annotation_counts ]] + EXT=annotation_ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr ' ' '\t' + tr -s '\t' + [[ sRNAseq == CHIPseq ]] + [[ sRNAseq == DNAseq ]] + [[ '' == Y ]] + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/ FILE=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/ + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/ FILE=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/ Attaching package: ‘plotly’ The following objects are masked from ‘package:plyr’: arrange, mutate, rename, summarise The following object is masked from ‘package:ggplot2’: last_plot The following object is masked from ‘package:stats’: filter The following object is masked from ‘package:graphics’: layout Using annotation as id variables Warning message: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. Using annotation as id variables + [[ N == Y ]] + [[ dm6 == dm6 ]] + mkdir /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/1kb_tiles + for STRAND in Plus Minus + 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] } + sort -k1,1n ++ read NAME }' /dev/fd/63 ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/WindowCounts_Plus.txt ++ read NAME + echo POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + tr -s '\t' + tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr -s '\t' + tr ' ' '\t' + for STRAND in Plus Minus + cut -f 2- + sort -k1,1n + awk -v 'OFS=\t' ' { if($2==-1){$2=0} X[$1]=X[$1]"\t"$2 Y[$1]+=NR } END { for (i in X) { print Y[i],i,X[i] } }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/WindowCounts_Minus.txt ++ read NAME + echo POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + tr ' ' '\t' + tr -s '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr -s '\t' + 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/sRNAseq/2026-03-11-sRNAseq_GEO_format/1kb_tiles/ + rawFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ + mkdir -p /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ + [[ sRNAseq == sRNAseq ]] + rm -rf '/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/*' + mkdir /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ + for CATEGORY in all filtered TE rRNA miRNA + SWITCH=N + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.817365 + [[ N == N ]] + awk -v 'OFS=\t' -v NORM=0.817365 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT-all.txt + SWITCH=Y + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.06187 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06187 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG-all.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/normalization.txt ++ tail -n 1 ++ tr ' ' '\t' ++ cut -f 1 + NORM=0.12421 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.12421 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT-all.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.084437 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.084437 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG-all.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.155578 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.155578 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG-all.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/normalization.txt ++ tail -n 1 ++ tr ' ' '\t' ++ cut -f 1 + NORM=0.062105 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.062105 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC-all.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.06366 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06366 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC-all.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.42207 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.42207 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA-all.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + echo length sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + tr ' ' '\t' + sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr ' ' '\t' + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=all FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=all FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ Attaching package: ‘plotly’ The following objects are masked from ‘package:plyr’: arrange, mutate, rename, summarise The following object is masked from ‘package:ggplot2’: last_plot The following object is masked from ‘package:stats’: filter The following object is masked from ‘package:graphics’: layout Warning message: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. Saving 7 x 7 in image Saving 7 x 7 in image Warning message: Removed 8 rows containing missing values (`geom_bar()`). + for CATEGORY in all filtered TE rRNA miRNA + SWITCH=N + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.817365 + [[ N == N ]] + awk -v 'OFS=\t' -v NORM=0.817365 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT-filtered.txt + SWITCH=Y + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.06187 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06187 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG-filtered.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.12421 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.12421 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT-filtered.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/normalization.txt ++ tail -n 1 ++ tr ' ' '\t' ++ cut -f 1 + NORM=0.084437 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.084437 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG-filtered.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.155578 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.155578 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG-filtered.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.062105 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.062105 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC-filtered.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.06366 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06366 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC-filtered.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.42207 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.42207 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA-filtered.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + echo length sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + tr ' ' '\t' + sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr ' ' '\t' + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=filtered FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=filtered FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ Attaching package: ‘plotly’ The following objects are masked from ‘package:plyr’: arrange, mutate, rename, summarise The following object is masked from ‘package:ggplot2’: last_plot The following object is masked from ‘package:stats’: filter The following object is masked from ‘package:graphics’: layout Warning message: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. Saving 7 x 7 in image Saving 7 x 7 in image Warning message: Removed 8 rows containing missing values (`geom_bar()`). + for CATEGORY in all filtered TE rRNA miRNA + SWITCH=N + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.817365 + [[ N == N ]] + awk -v 'OFS=\t' -v NORM=0.817365 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT-TE.txt + SWITCH=Y + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/normalization.txt ++ cut -f 1 ++ tail -n 1 ++ tr ' ' '\t' + NORM=0.06187 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06187 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG-TE.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.12421 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.12421 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT-TE.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/normalization.txt ++ cut -f 1 ++ tail -n 1 ++ tr ' ' '\t' + NORM=0.084437 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.084437 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG-TE.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.155578 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.155578 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG-TE.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/normalization.txt ++ tail -n 1 ++ tr ' ' '\t' ++ cut -f 1 + NORM=0.062105 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.062105 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC-TE.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.06366 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06366 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC-TE.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.42207 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.42207 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA-TE.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + echo length sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + tr ' ' '\t' + sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr ' ' '\t' + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=TE FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=TE FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ Attaching package: ‘plotly’ The following objects are masked from ‘package:plyr’: arrange, mutate, rename, summarise The following object is masked from ‘package:ggplot2’: last_plot The following object is masked from ‘package:stats’: filter The following object is masked from ‘package:graphics’: layout Warning message: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. Saving 7 x 7 in image Saving 7 x 7 in image Warning message: Removed 8 rows containing missing values (`geom_bar()`). + for CATEGORY in all filtered TE rRNA miRNA + SWITCH=N + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.817365 + [[ N == N ]] + awk -v 'OFS=\t' -v NORM=0.817365 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT-rRNA.txt + SWITCH=Y + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.06187 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06187 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG-rRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.12421 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.12421 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT-rRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.084437 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.084437 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG-rRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/normalization.txt ++ tr ' ' '\t' ++ tail -n 1 ++ cut -f 1 + NORM=0.155578 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.155578 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG-rRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.062105 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.062105 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC-rRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/normalization.txt ++ tail -n 1 ++ cut -f 1 ++ tr ' ' '\t' + NORM=0.06366 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06366 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC-rRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.42207 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.42207 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA-rRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + echo length sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + tr ' ' '\t' + sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr ' ' '\t' + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=rRNA FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=rRNA FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ Attaching package: ‘plotly’ The following objects are masked from ‘package:plyr’: arrange, mutate, rename, summarise The following object is masked from ‘package:ggplot2’: last_plot The following object is masked from ‘package:stats’: filter The following object is masked from ‘package:graphics’: layout Warning message: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. Saving 7 x 7 in image Saving 7 x 7 in image Warning message: Removed 8 rows containing missing values (`geom_bar()`). + for CATEGORY in all filtered TE rRNA miRNA + SWITCH=N + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.817365 + [[ N == N ]] + awk -v 'OFS=\t' -v NORM=0.817365 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/size-profiles/size-profile_sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT-miRNA.txt + SWITCH=Y + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.06187 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06187 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG-miRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.12421 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.12421 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT-miRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.084437 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.084437 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG-miRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/normalization.txt ++ tail -n 1 ++ tr ' ' '\t' ++ cut -f 1 + NORM=0.155578 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.155578 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/size-profiles/size-profile_sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG-miRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.062105 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.062105 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC-miRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/normalization.txt ++ tr ' ' '\t' ++ cut -f 1 ++ tail -n 1 + NORM=0.06366 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.06366 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/size-profiles/size-profile_sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC-miRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/ ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/normalization.txt ++ cut -f 1 ++ tr ' ' '\t' ++ tail -n 1 + NORM=0.42207 + [[ Y == N ]] + awk -v 'OFS=\t' -v NORM=0.42207 '{ print $1,$2/NORM }' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/size-profiles/size-profile_sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA-miRNA.txt + join /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMPnorm.txt + mv /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP2.txt /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + read NAME + echo length sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA + tr ' ' '\t' + sort -k1,1n /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr ' ' '\t' + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=miRNA FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_compound-size-profile.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ CATEGORY=miRNA FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/ PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/size-profiles/ Attaching package: ‘plotly’ The following objects are masked from ‘package:plyr’: arrange, mutate, rename, summarise The following object is masked from ‘package:ggplot2’: last_plot The following object is masked from ‘package:stats’: filter The following object is masked from ‘package:graphics’: layout Warning message: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. Saving 7 x 7 in image Saving 7 x 7 in image Warning message: Removed 8 rows containing missing values (`geom_bar()`). + [[ sRNAseq == sRNAseq ]] + CATEGORIES='TE_RPKM_sense-salmon TE_RPKM_antisense-salmon TE_RPKM_sense-bowtie TE_RPKM_antisense-bowtie TE_counts_sense-bowtie TE_counts_antisense-bowtie' + [[ N == Y ]] + [[ sRNAseq == sRNAseq ]] + for CATEGORY in $CATEGORIES + [[ TE_RPKM_sense-salmon == \T\E\_\G\e\T\M\M ]] + [[ TE_RPKM_sense-salmon == GeTMM_gene ]] + [[ TE_RPKM_sense-salmon == TE_GeTMM_unistrand ]] + NAMES=TE + awk -v 'OFS=\t' '{ X[$1]=X[$1]"\t"$2 } END { for (i in X) { print i,X[i] } }' /dev/fd/63 + cut --complement -f 1 + sort -k1,1 + awk -v 'OFS=\t' '{ X=$1 gsub("_AS","",X) print X,$0 }' ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/TE_RPKM_sense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/TE_RPKM_sense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/TE_RPKM_sense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/TE_RPKM_sense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/TE_RPKM_sense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/TE_RPKM_sense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/TE_RPKM_sense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/TE_RPKM_sense-salmon.txt ++ read NAME ++ echo TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr ' ' '\t' + tr -s '\t' + sed 's/::/\t/g' + for CATEGORY in $CATEGORIES + [[ TE_RPKM_antisense-salmon == \T\E\_\G\e\T\M\M ]] + [[ TE_RPKM_antisense-salmon == GeTMM_gene ]] + [[ TE_RPKM_antisense-salmon == TE_GeTMM_unistrand ]] + NAMES=TE + awk -v 'OFS=\t' '{ X[$1]=X[$1]"\t"$2 } END { for (i in X) { print i,X[i] } }' /dev/fd/63 + cut --complement -f 1 + sort -k1,1 + awk -v 'OFS=\t' '{ X=$1 gsub("_AS","",X) print X,$0 }' ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/TE_RPKM_antisense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/TE_RPKM_antisense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/TE_RPKM_antisense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/TE_RPKM_antisense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/TE_RPKM_antisense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/TE_RPKM_antisense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/TE_RPKM_antisense-salmon.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/TE_RPKM_antisense-salmon.txt ++ read NAME ++ echo TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr -s '\t' + tr ' ' '\t' + sed 's/::/\t/g' + for CATEGORY in $CATEGORIES + [[ TE_RPKM_sense-bowtie == \T\E\_\G\e\T\M\M ]] + [[ TE_RPKM_sense-bowtie == GeTMM_gene ]] + [[ TE_RPKM_sense-bowtie == TE_GeTMM_unistrand ]] + NAMES=TE + awk -v 'OFS=\t' '{ X[$1]=X[$1]"\t"$2 } END { for (i in X) { print i,X[i] } + cut --complement -f 1 + sort -k1,1 + awk -v 'OFS=\t' '{ X=$1 gsub("_AS","",X) print X,$0 }' ++ read NAME }' /dev/fd/63 ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/TE_RPKM_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/TE_RPKM_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/TE_RPKM_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/TE_RPKM_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/TE_RPKM_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/TE_RPKM_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/TE_RPKM_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/TE_RPKM_sense-bowtie.txt ++ read NAME ++ echo TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr -s '\t' + tr ' ' '\t' + sed 's/::/\t/g' + for CATEGORY in $CATEGORIES + [[ TE_RPKM_antisense-bowtie == \T\E\_\G\e\T\M\M ]] + [[ TE_RPKM_antisense-bowtie == GeTMM_gene ]] + [[ TE_RPKM_antisense-bowtie == TE_GeTMM_unistrand ]] + NAMES=TE + awk -v 'OFS=\t' '{ X[$1]=X[$1]"\t"$2 } END { for (i in X) { print i,X[i] } + cut --complement -f 1 + sort -k1,1 + awk -v 'OFS=\t' '{ X=$1 gsub("_AS","",X) print X,$0 }' ++ read NAME }' /dev/fd/63 ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/TE_RPKM_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/TE_RPKM_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/TE_RPKM_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/TE_RPKM_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/TE_RPKM_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/TE_RPKM_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/TE_RPKM_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/TE_RPKM_antisense-bowtie.txt ++ read NAME ++ echo TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr -s '\t' + tr ' ' '\t' + sed 's/::/\t/g' + for CATEGORY in $CATEGORIES + [[ TE_counts_sense-bowtie == \T\E\_\G\e\T\M\M ]] + [[ TE_counts_sense-bowtie == GeTMM_gene ]] + [[ TE_counts_sense-bowtie == TE_GeTMM_unistrand ]] + NAMES=TE + awk -v 'OFS=\t' '{ X[$1]=X[$1]"\t"$2 } END { for (i in X) { print i,X[i] } + cut --complement -f 1 + sort -k1,1 + awk -v 'OFS=\t' '{ X=$1 gsub("_AS","",X) print X,$0 ++ read NAME }' /dev/fd/63 }' ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/TE_counts_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/TE_counts_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/TE_counts_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/TE_counts_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/TE_counts_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/TE_counts_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/TE_counts_sense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/TE_counts_sense-bowtie.txt ++ read NAME ++ echo TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + sed 's/::/\t/g' + tr ' ' '\t' + tr -s '\t' + for CATEGORY in $CATEGORIES + [[ TE_counts_antisense-bowtie == \T\E\_\G\e\T\M\M ]] + [[ TE_counts_antisense-bowtie == GeTMM_gene ]] + [[ TE_counts_antisense-bowtie == TE_GeTMM_unistrand ]] + NAMES=TE + awk -v 'OFS=\t' '{ X[$1]=X[$1]"\t"$2 } END { for (i in X) { print i,X[i] } }' /dev/fd/63 + cut --complement -f 1 + sort -k1,1 + awk -v 'OFS=\t' '{ X=$1 gsub("_AS","",X) print X,$0 }' ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/TE_counts_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/TE_counts_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/TE_counts_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/TE_counts_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/TE_counts_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/TE_counts_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/TE_counts_antisense-bowtie.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES='TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/TE_counts_antisense-bowtie.txt ++ read NAME ++ echo TE sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP.txt + tr ' ' '\t' + sed 's/::/\t/g' + tr -s '\t' + [[ N == Y ]] + [[ '' == Y ]] + [[ sRNAseq == RNAseq ]] + [[ sRNAseq == sRNAseq ]] + [[ sRNAseq == CHIPseq ]] + [[ sRNAseq == DNAseq ]] + [[ '' == Y ]] + CATEGORIES='sense antisense' + [[ sRNAseq == sRNAseq ]] + CLASSES='man man.21mer' + [[ sRNAseq == sRNAseq ]] + STRINGENCYvec='normal all' + for STRINGENCY in $STRINGENCYvec + [[ normal == all ]] + STRINGENCYext= + FOLDERext=stringent-no-interTE-alignments + for CATEGORY in $CATEGORIES + for currCLASS in $CLASSES + NAMES= + sort -k2,2n ++ read NAME + 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 ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_TE-sense_man.bg ++ read NAME ++ echo TE POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' ++ tr '~' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP_TEhist_man.txt + tr ' ' '\t' + tr '~' '\t' + sort -k2,2n + for currCLASS in $CLASSES + NAMES= + sort -k2,2n + awk -v 'OFS=\t' '{ NAME=$1"~"$2 if(NAME in X) { X[NAME]=X[NAME]"\t"$3 }else{ X[NAME]=$3 } } END { for (i in X) { print i,X[i] } }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_TE-sense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_TE-sense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_TE-sense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_TE-sense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_TE-sense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_TE-sense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_TE-sense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_TE-sense_man.21mer.bg ++ read NAME ++ echo TE POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' ++ tr '~' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP_TEhist_man.21mer.txt + tr ' ' '\t' + tr '~' '\t' + sort -k2,2n + for CATEGORY in $CATEGORIES + for currCLASS in $CLASSES + NAMES= + sort -k2,2n + awk -v 'OFS=\t' '{ NAME=$1"~"$2 if(NAME in X) { X[NAME]=X[NAME]"\t"$3 }else{ X[NAME]=$3 } } END { for (i in X) { print i,X[i] } }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_TE-antisense_man.bg ++ read NAME ++ echo TE POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr '~' '\t' ++ tr ' ' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP_TEhist_man.txt + tr ' ' '\t' + sort -k2,2n + tr '~' '\t' + for currCLASS in $CLASSES + NAMES= + sort -k2,2n + awk -v 'OFS=\t' '{ NAME=$1"~"$2 if(NAME in X) { X[NAME]=X[NAME]"\t"$3 }else{ X[NAME]=$3 } } END { for (i in X) { print i,X[i] } }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_TE-antisense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_TE-antisense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_TE-antisense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_TE-antisense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_TE-antisense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_TE-antisense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_TE-antisense_man.21mer.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_TE-antisense_man.21mer.bg ++ read NAME ++ echo TE POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' ++ tr '~' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP_TEhist_man.21mer.txt + tr ' ' '\t' + sort -k2,2n + tr '~' '\t' + mkdir -p /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/TEhist_stringent-no-interTE-alignments/html-dependencies/ + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/TEhist_stringent-no-interTE-alignments/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/TE_hist TYPE=sRNAseq STRINGENCYext=.txt + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/TEhist_stringent-no-interTE-alignments/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/TE_hist TYPE=sRNAseq STRINGENCYext=.txt ── 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 () 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 + for STRINGENCY in $STRINGENCYvec + [[ all == all ]] + STRINGENCYext=.all + FOLDERext=all-alignments + for CATEGORY in $CATEGORIES + for currCLASS in $CLASSES + NAMES= + sort -k2,2n + awk -v 'OFS=\t' '{ NAME=$1"~"$2 if(NAME in X) { X[NAME]=X[NAME]"\t"$3 }else{ X[NAME]=$3 } } END { for (i in X) { print i,X[i] } }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_TE-sense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_TE-sense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_TE-sense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_TE-sense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_TE-sense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_TE-sense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_TE-sense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_TE-sense_man.all.bg ++ read NAME ++ echo TE POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr '~' '\t' ++ tr ' ' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP_TEhist_man.all.txt + tr ' ' '\t' + tr '~' '\t' + sort -k2,2n + for currCLASS in $CLASSES + NAMES= + sort -k2,2n + awk -v 'OFS=\t' '{ NAME=$1"~"$2 if(NAME in X) { X[NAME]=X[NAME]"\t"$3 }else{ X[NAME]=$3 } } END { for (i in X) { print i,X[i] } }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_TE-sense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_TE-sense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_TE-sense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_TE-sense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_TE-sense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_TE-sense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_TE-sense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_TE-sense_man.21mer.all.bg ++ read NAME ++ echo TE POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr ' ' '\t' ++ tr '~' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP_TEhist_man.21mer.all.txt + tr ' ' '\t' + tr '~' '\t' + sort -k2,2n + for CATEGORY in $CATEGORIES + for currCLASS in $CLASSES + NAMES= + sort -k2,2n + awk -v 'OFS=\t' '{ NAME=$1"~"$2 if(NAME in X) { X[NAME]=X[NAME]"\t"$3 }else{ X[NAME]=$3 } } END { for (i in X) { print i,X[i] } }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_TE-antisense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_TE-antisense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_TE-antisense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_TE-antisense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_TE-antisense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_TE-antisense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_TE-antisense_man.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_TE-antisense_man.all.bg ++ read NAME ++ echo TE POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr '~' '\t' ++ tr ' ' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP_TEhist_man.all.txt + tr ' ' '\t' + sort -k2,2n + tr '~' '\t' + for currCLASS in $CLASSES + NAMES= + sort -k2,2n + awk -v 'OFS=\t' '{ NAME=$1"~"$2 if(NAME in X) { X[NAME]=X[NAME]"\t"$3 }else{ X[NAME]=$3 } } END { for (i in X) { print i,X[i] } ++ read NAME }' /dev/fd/63 ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT/sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT_TE-antisense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG_TE-antisense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT/sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT_TE-antisense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG/sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG_TE-antisense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG/sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG_TE-antisense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC_TE-antisense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC/sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC_TE-antisense_man.21mer.all.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/ ++ NAMES=' sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format//individual-libraries/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA/sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA_TE-antisense_man.21mer.all.bg ++ read NAME ++ echo TE POS sRNAseq_Ovaries_MTD_PiwiKD_rep2_283083_sRBC_CTGAT sRNAseq_HsBam_ControlKD_0hAHS_rep3_283082_sRBC_GTCAG sRNAseq_HsBam_PiwiKD_0hAHS_rep2_283081_sRBC_GGTAT sRNAseq_HsBam_ControlKD_0hAHS_rep1_283080_sRBC_GTCAG sRNAseq_HsBam_ControlKD_0hAHS_rep2_283081_sRBC_CAGTG sRNAseq_HsBam_PiwiKD_0hAHS_rep3_283082_sRBC_CGTTC sRNAseq_HsBam_PiwiKD_0hAHS_rep1_283080_sRBC_CGTTC sRNAseq_Ovaries_MTD_ControlKD_rep1_283083_sRBC_ATGGA ++ tr '~' '\t' ++ tr ' ' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/TMP_TEhist_man.21mer.all.txt + tr ' ' '\t' + tr '~' '\t' + sort -k2,2n + mkdir -p /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/TEhist_all-alignments/html-dependencies/ + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/TEhist_all-alignments/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/TE_hist TYPE=sRNAseq STRINGENCYext=.all.txt + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/TEhist_all-alignments/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/plots/raw-data/TE_hist TYPE=sRNAseq STRINGENCYext=.all.txt ── 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 () 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/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/Rscripts.pdf + [[ N != Y ]] + rm -rf /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/sRNAseq/2026-03-11-sRNAseq_GEO_format/TMP/ ++ awk '{ print ($1-$2)/60 }' +++ date +%s ++ echo -e 1773253673 1773253221 + PROCESSED_TIME=7.53333 + echo 'collect-numbers - processing_time=' 7.53333 + exit