++ echo USER_NAME=thomasgrnbk,TYPE=RNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/,FOLDER_NAME=total_RNAseq_SLX-19644_GEO,RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/,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=1000,RAW=,TRIMM=Y,FIRST=6,LAST=200,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=2,FILTERING_INPUT=rRNA:tRNA:mito,WIG=Y,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt,FOLDER_NAME=total_RNAseq_SLX-19644_GEO,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=Y,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=RNAseq SLAM=N BASE_FOLDER=/faststorage/project/PAN_illumina/results/ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ FOLDER_NAME=total_RNAseq_SLX-19644_GEO RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ 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=1000 RAW= TRIMM=Y FIRST=6 LAST=200 INVERT=N Ychrom=N RANDOMmulti=N MM=2 FILTERING_INPUT=rRNA:tRNA:mito WIG=Y WIG_FASTA= spikeINnorm=N noNORM= EXTEND=0 COMPUTING=C GRIDsystem=SLURM keepTMP=N SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt FOLDER_NAME=total_RNAseq_SLX-19644_GEO GENOME_VERSION=dm6 subCOLOR=0~128~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=Y 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=RNAseq SLAM=N BASE_FOLDER=/faststorage/project/PAN_illumina/results/ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ FOLDER_NAME=total_RNAseq_SLX-19644_GEO RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ 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=1000 RAW= TRIMM=Y FIRST=6 LAST=200 INVERT=N Ychrom=N RANDOMmulti=N MM=2 FILTERING_INPUT=rRNA:tRNA:mito WIG=Y WIG_FASTA= spikeINnorm=N noNORM= EXTEND=0 COMPUTING=C GRIDsystem=SLURM keepTMP=N SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt FOLDER_NAME=total_RNAseq_SLX-19644_GEO GENOME_VERSION=dm6 subCOLOR=0~128~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=Y 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=RNAseq ++ SLAM=N ++ BASE_FOLDER=/faststorage/project/PAN_illumina/results/ ++ FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ ++ FOLDER_NAME=total_RNAseq_SLX-19644_GEO ++ RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO ++ TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ ++ 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=1000 ++ RAW= ++ TRIMM=Y ++ FIRST=6 ++ LAST=200 ++ INVERT=N ++ Ychrom=N ++ RANDOMmulti=N ++ MM=2 ++ FILTERING_INPUT=rRNA:tRNA:mito ++ WIG=Y ++ WIG_FASTA= ++ spikeINnorm=N ++ noNORM= ++ EXTEND=0 ++ COMPUTING=C ++ GRIDsystem=SLURM ++ keepTMP=N ++ SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6 ++ FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt ++ FOLDER_NAME=total_RNAseq_SLX-19644_GEO ++ GENOME_VERSION=dm6 ++ subCOLOR=0~128~0 ++ FORCE= ++ SYSTEM=EXTERN ++ LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/ ++ prepareREF=no ++ nSPLITS=1000000 ++ SE=N ++ SE2nd= ++ maxCOUNT=1000000 ++ demuxFASTA=N ++ autoViewLimits= ++ only5end= ++ PingPong= ++ DGE=Y ++ 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=RNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/,FOLDER_NAME=total_RNAseq_SLX-19644_GEO,RUNname=2026-03-18-total_RNAseq_SLX-19644_GEO,TMPdir=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/,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=1000,RAW=,TRIMM=Y,FIRST=6,LAST=200,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=2,FILTERING_INPUT=rRNA:tRNA:mito,WIG=Y,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/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=6,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt,FOLDER_NAME=total_RNAseq_SLX-19644_GEO,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=Y,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=1773841608 + TIMEx=1773841608 + [[ SLURM == SLURM ]] + CORES=3 + echo 3 + source /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/script-files/tools ++ set -a + locTMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ + mkdir -p /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ + chmod 777 /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ + TMPDIR=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ + cd /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ + echo /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/ + mkdir /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt + cut -f 2 + tr ' ' '\t' + rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/annotation_counts.txt ++ cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/files.txt ++ tr '\n' '\t' ++ awk '{ print $2 }' + NAMElist='HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 ' ++ printf 'annotation\tHsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 ' + NAMElistANN='annotation HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 ' ++ printf 'length\tHsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 ' + NAMElistSIZE='length HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 ' + echo annotation HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 + 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/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext03.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext20.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext01.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext05.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext02.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0 0 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext19.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0 0 0 0 0 0' + read LINE + echo adaptor_dimer 0 0 0 0 0 0 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext03.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/log.txt ++ grep artifact_filtered ++ awk '{ print $NF}' + X=484 + Xlist='artifact_filtered 484' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext20.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep2 ++ tr ' ' '\t' ++ cut -f 2 + NAME=HsBam_totalRNAseq_piwiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=1597 + Xlist='artifact_filtered 484 1597' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext01.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=413 + Xlist='artifact_filtered 484 1597 413' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext05.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=776 + Xlist='artifact_filtered 484 1597 413 776' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext02.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=1560 + Xlist='artifact_filtered 484 1597 413 776 1560' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext19.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=1005 + Xlist='artifact_filtered 484 1597 413 776 1560 1005' + read LINE + echo artifact_filtered 484 1597 413 776 1560 1005 + 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/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext03.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/log.txt ++ grep length_filtered_short ++ awk '{ print $NF}' + X=0 + Xlist='length_filtered_short 0' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext20.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=0 + Xlist='length_filtered_short 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext01.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=0 + Xlist='length_filtered_short 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext05.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=0 + Xlist='length_filtered_short 0 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext02.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=0 + Xlist='length_filtered_short 0 0 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext19.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=0 + Xlist='length_filtered_short 0 0 0 0 0 0' + read LINE + echo length_filtered_short 0 0 0 0 0 0 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext03.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=0 + Xlist='length_filtered_long 0' + SWITCH=Y + read LINE ++ tr ' ' '\t' ++ cut -f 2 ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext20.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep2 + NAME=HsBam_totalRNAseq_piwiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=0 + Xlist='length_filtered_long 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext01.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=0 + Xlist='length_filtered_long 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext05.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=0 + Xlist='length_filtered_long 0 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext02.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/log.txt ++ grep length_filtered_long ++ awk '{ print $NF}' + X=0 + Xlist='length_filtered_long 0 0 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext19.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/log.txt ++ grep length_filtered_long ++ awk '{ print $NF}' + X=0 + Xlist='length_filtered_long 0 0 0 0 0 0' + read LINE + echo length_filtered_long 0 0 0 0 0 0 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext03.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=19636 + Xlist='N_filtered 19636' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext20.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=23958 + Xlist='N_filtered 19636 23958' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext01.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=16398 + Xlist='N_filtered 19636 23958 16398' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext05.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=24561 + Xlist='N_filtered 19636 23958 16398 24561' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext02.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/log.txt ++ grep N_filtered ++ awk '{ print $NF}' + X=25484 + Xlist='N_filtered 19636 23958 16398 24561 25484' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext19.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=19469 + Xlist='N_filtered 19636 23958 16398 24561 25484 19469' + read LINE + tr ' ' '\t' + echo N_filtered 19636 23958 16398 24561 25484 19469 + 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/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext03.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=12029051 + Xlist='reads_after_filtering 12029051' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext20.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=14488533 + Xlist='reads_after_filtering 12029051 14488533' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext01.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=9829763 + Xlist='reads_after_filtering 12029051 14488533 9829763' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext05.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_whiteKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=15099258 + Xlist='reads_after_filtering 12029051 14488533 9829763 15099258' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext02.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=15360493 + Xlist='reads_after_filtering 12029051 14488533 9829763 15099258 15360493' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext19.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=11798282 + Xlist='reads_after_filtering 12029051 14488533 9829763 15099258 15360493 11798282' + read LINE + echo reads_after_filtering 12029051 14488533 9829763 15099258 15360493 11798282 + 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/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext03.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/log.txt ++ grep reads_not_mapped ++ awk '{ print $NF}' + X=3689149 + Xlist='reads_not_mapped 3689149' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext20.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_piwiKD_00h_rep2 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_piwiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=4627016 + Xlist='reads_not_mapped 3689149 4627016' + read LINE ++ cut -f 2 ++ tr ' ' '\t' ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext01.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep1 + NAME=HsBam_totalRNAseq_whiteKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ + [[ Y == N ]] ++ grep reads_not_mapped ++ awk '{ print $NF}' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/log.txt + X=2521775 + Xlist='reads_not_mapped 3689149 4627016 2521775' + read LINE ++ tr ' ' '\t' ++ cut -f 2 ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext05.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_whiteKD_00h_rep2 + NAME=HsBam_totalRNAseq_whiteKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ + [[ Y == N ]] ++ grep reads_not_mapped ++ awk '{ print $NF}' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/log.txt + X=3756078 + Xlist='reads_not_mapped 3689149 4627016 2521775 3756078' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext02.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep1 ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_totalRNAseq_rhiKD_00h_rep1 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ + [[ Y == N ]] ++ awk '{ print $NF}' ++ grep reads_not_mapped ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/log.txt + X=3779156 + Xlist='reads_not_mapped 3689149 4627016 2521775 3756078 3779156' + read LINE ++ echo /faststorage/project/PAN_illumina/data/libSTORAGE/2023_02_THG_HSbam_RNAseq/ftp1.cruk.cam.ac.uk/SLX-19644.NEBNext19.HW7MTDRX2.s_2.r_1.fq.gz HsBam_totalRNAseq_rhiKD_00h_rep2 ++ tr ' ' '\t' ++ cut -f 2 + NAME=HsBam_totalRNAseq_rhiKD_00h_rep2 + libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=3875640 + Xlist='reads_not_mapped 3689149 4627016 2521775 3756078 3779156 3875640' + read LINE + echo reads_not_mapped 3689149 4627016 2521775 3756078 3779156 3875640 + tr ' ' '\t' + 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] } }' /dev/fd/63 + cut -f 2- ++ read NAME + sort -k1,1n ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/HsBam_totalRNAseq_piwiKD_00h_rep1_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/HsBam_totalRNAseq_piwiKD_00h_rep2_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/HsBam_totalRNAseq_whiteKD_00h_rep1_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/HsBam_totalRNAseq_whiteKD_00h_rep2_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/HsBam_totalRNAseq_rhiKD_00h_rep1_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/HsBam_totalRNAseq_rhiKD_00h_rep2_annotation_counts.txt ++ read NAME + [[ annotation_counts != annotation_counts ]] + EXT= + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/TMP.txt + tr -s '\t' + tr ' ' '\t' + [[ RNAseq == CHIPseq ]] + [[ RNAseq == DNAseq ]] + [[ '' == Y ]] + for CATEGORY in annotation_counts splitup_mRNA splitup_TE + NAMES= + [[ splitup_mRNA != annotation_counts ]] + rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/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] } }' /dev/fd/63 + cut -f 2- + sort -k1,1n ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/HsBam_totalRNAseq_piwiKD_00h_rep1_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/HsBam_totalRNAseq_piwiKD_00h_rep2_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/HsBam_totalRNAseq_whiteKD_00h_rep1_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/HsBam_totalRNAseq_whiteKD_00h_rep2_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/HsBam_totalRNAseq_rhiKD_00h_rep1_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/HsBam_totalRNAseq_rhiKD_00h_rep2_splitup_mRNA.txt ++ read NAME + [[ splitup_mRNA != annotation_counts ]] + EXT=annotation_ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/TMP.txt + tr -s '\t' + tr ' ' '\t' + [[ RNAseq == CHIPseq ]] + [[ RNAseq == DNAseq ]] + [[ '' == Y ]] + for CATEGORY in annotation_counts splitup_mRNA splitup_TE + NAMES= + [[ splitup_TE != annotation_counts ]] + rm -rf /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/annotation_splitup_TE.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/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/HsBam_totalRNAseq_piwiKD_00h_rep1_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/HsBam_totalRNAseq_piwiKD_00h_rep2_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/HsBam_totalRNAseq_whiteKD_00h_rep1_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/HsBam_totalRNAseq_whiteKD_00h_rep2_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/HsBam_totalRNAseq_rhiKD_00h_rep1_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/HsBam_totalRNAseq_rhiKD_00h_rep2_splitup_TE.txt ++ read NAME + [[ splitup_TE != annotation_counts ]] + EXT=annotation_ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/TMP.txt + tr -s '\t' + tr ' ' '\t' + [[ RNAseq == CHIPseq ]] + [[ RNAseq == DNAseq ]] + [[ '' == Y ]] + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/ FILE=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/ + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/ FILE=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/ Attaching package: ‘plotly’ The following objects are masked from ‘package:plyr’: arrange, mutate, rename, summarise The following object is masked from ‘package:ggplot2’: last_plot The following object is masked from ‘package:stats’: filter The following object is masked from ‘package:graphics’: layout Using annotation as id variables Warning message: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0. ℹ Please use the `linewidth` argument instead. Using annotation as id variables + [[ N == Y ]] + [[ dm6 == dm6 ]] + mkdir /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/1kb_tiles + for STRAND in Plus Minus + awk -v 'OFS=\t' ' { if($2==-1){$2=0} X[$1]=X[$1]"\t"$2 Y[$1]+=NR } END { for (i in X) { print Y[i],i,X[i] } + cut -f 2- + sort -k1,1n }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/WindowCounts_Plus.txt ++ read NAME + echo POS HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 + tr ' ' '\t' + tr -s '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/TMP.txt + tr ' ' '\t' + tr -s '\t' + for STRAND in Plus Minus + 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 + cut -f 2- + sort -k1,1n ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/WindowCounts_Minus.txt ++ read NAME + echo POS HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 + tr -s '\t' + tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/TMP.txt + tr ' ' '\t' + tr -s '\t' + cp /faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files//dmel/dm6/1kb_tile/kbWindows_mainchr_genes_tss_dm6.txt /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/1kb_tiles/ + rawFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/raw-data/ + mkdir -p /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/raw-data/ + [[ RNAseq == sRNAseq ]] + [[ RNAseq == CLIPseq ]] + [[ RNAseq == sRNAseqIP ]] + [[ RNAseq == SLAMseq ]] + [[ RNAseq == GROseq ]] + [[ RNAseq == sRNAseq ]] + [[ RNAseq == sRNAseqIP ]] + [[ RNAseq == CLIPseq ]] + [[ RNAseq = RNAseq ]] + CATEGORIES='TE_GeTMM GeTMM_gene' + [[ RNAseq == sRNAseq ]] + [[ RNAseq == sRNAseqIP ]] + [[ RNAseq == CLIPseq ]] + [[ RNAseq = RNAseq ]] + for CATEGORY in $CATEGORIES + [[ TE_GeTMM == \T\E\_\G\e\T\M\M ]] + head -n 1 /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep '^TE:' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep -v _AS + head -n 1 /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep '^TE:' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/gene-expression/GeTMM_normalized.txt + grep _AS + tr ' ' '\t' + for CATEGORY in $CATEGORIES + [[ GeTMM_gene == \T\E\_\G\e\T\M\M ]] + [[ GeTMM_gene == GeTMM_gene ]] + head -n 1 /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep -v '^TE:' /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + [[ N == Y ]] + [[ '' == Y ]] + [[ RNAseq == RNAseq ]] + [[ RNAseq == CHIPseq ]] + [[ RNAseq == DNAseq ]] + [[ '' == Y ]] + CATEGORIES='sense antisense' + [[ RNAseq == sRNAseq ]] + [[ RNAseq == sRNAseqIP ]] + CLASSES=man + [[ RNAseq == sRNAseq ]] + [[ RNAseq == sRNAseqIP ]] + STRINGENCYvec=normal + for STRINGENCY in $STRINGENCYvec + [[ normal == all ]] + STRINGENCYext= + FOLDERext=stringent-no-interTE-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] } ++ read NAME }' /dev/fd/63 ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/HsBam_totalRNAseq_piwiKD_00h_rep1_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/HsBam_totalRNAseq_piwiKD_00h_rep2_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/HsBam_totalRNAseq_whiteKD_00h_rep1_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/HsBam_totalRNAseq_whiteKD_00h_rep2_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/HsBam_totalRNAseq_rhiKD_00h_rep1_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/HsBam_totalRNAseq_rhiKD_00h_rep2_TE-sense_man.bg ++ read NAME ++ echo TE POS HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 ++ tr '~' '\t' ++ tr ' ' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/TMP_TEhist_man.txt + sort -k2,2n + tr ' ' '\t' + tr '~' '\t' + for CATEGORY in $CATEGORIES + for currCLASS in $CLASSES + NAMES= + sort -k2,2n + awk -v 'OFS=\t' '{ NAME=$1"~"$2 if(NAME in X) { X[NAME]=X[NAME]"\t"$3 }else{ X[NAME]=$3 } } END { for (i in X) { print i,X[i] } }' /dev/fd/63 ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep1/HsBam_totalRNAseq_piwiKD_00h_rep1_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_piwiKD_00h_rep2/HsBam_totalRNAseq_piwiKD_00h_rep2_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep1/HsBam_totalRNAseq_whiteKD_00h_rep1_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_whiteKD_00h_rep2/HsBam_totalRNAseq_whiteKD_00h_rep2_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep1/HsBam_totalRNAseq_rhiKD_00h_rep1_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/ ++ NAMES=' HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2' ++ cat /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO//individual-libraries/HsBam_totalRNAseq_rhiKD_00h_rep2/HsBam_totalRNAseq_rhiKD_00h_rep2_TE-antisense_man.bg ++ read NAME ++ echo TE POS HsBam_totalRNAseq_piwiKD_00h_rep1 HsBam_totalRNAseq_piwiKD_00h_rep2 HsBam_totalRNAseq_whiteKD_00h_rep1 HsBam_totalRNAseq_whiteKD_00h_rep2 HsBam_totalRNAseq_rhiKD_00h_rep1 HsBam_totalRNAseq_rhiKD_00h_rep2 ++ tr '~' '\t' ++ tr ' ' '\t' + echo /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ + cat /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/TMP_TEhist_man.txt + tr ' ' '\t' + sort -k2,2n + tr '~' '\t' + mkdir -p /faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/TEhist_stringent-no-interTE-alignments/html-dependencies/ + Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/TEhist_stringent-no-interTE-alignments/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/raw-data/TE_hist TYPE=RNAseq STRINGENCYext=.txt + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/:/tmp /home/thomasgrnbk/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/TEhist_stringent-no-interTE-alignments/ INPUT=/faststorage/project/PAN_illumina/results//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/plots/raw-data/TE_hist TYPE=RNAseq 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 + rm -rf /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/Rscripts.pdf + [[ N != Y ]] + rm -rf /faststorage/project/PAN_illumina/tmp//thomasgrnbk/dm6/RNAseq/2026-03-18-total_RNAseq_SLX-19644_GEO/TMP/ ++ awk '{ print ($1-$2)/60 }' +++ date +%s ++ echo -e 1773841690 1773841608 + PROCESSED_TIME=1.36667 + echo 'collect-numbers - processing_time=' 1.36667 + exit