++ echo USER_NAME=my,TYPE=RNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/,FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1,RUNname=2025-01-27-RNAseq_Thomas_PolyA_Bam1,TMPdir=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/,LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/,SINGULARITYdir=/home/my/AP_singu/,downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/,DEBUG=N,VERSION=r6.40,asmHUBpath=,ASMdir=,ASMname=,BAM=N,fwADAPTOR=,rvADAPTOR=,N_TRIMM=,rawPAIRED=N,onlyPAIRED=N,FASTQout=N,FASTQoutRAW=N,SUBSAMPLE=,MIN_LENGTH=18,MAX_LENGTH=1000,RAW=,TRIMM=Y,FIRST=6,LAST=200,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=2,FILTERING_INPUT=rRNA:tRNA:mito,WIG=Y,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/,BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/,UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/,RELEASE=,VERSION=r6.40,UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/,nFILES=4,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/files.txt,FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=N,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//my/dm6/,newCOLLECTION=N ++ sed 's/,/\t/g;s/"//g' + VARI='USER_NAME=my TYPE=RNAseq SLAM=N BASE_FOLDER=/faststorage/project/PAN_illumina/results/ FOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/ FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1 RUNname=2025-01-27-RNAseq_Thomas_PolyA_Bam1 TMPdir=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/ LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/ SINGULARITYdir=/home/my/AP_singu/ downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/ DEBUG=N VERSION=r6.40 asmHUBpath= ASMdir= ASMname= BAM=N fwADAPTOR= rvADAPTOR= N_TRIMM= rawPAIRED=N onlyPAIRED=N FASTQout=N FASTQoutRAW=N SUBSAMPLE= MIN_LENGTH=18 MAX_LENGTH=1000 RAW= TRIMM=Y FIRST=6 LAST=200 INVERT=N Ychrom=N RANDOMmulti=N MM=2 FILTERING_INPUT=rRNA:tRNA:mito WIG=Y WIG_FASTA= spikeINnorm=N noNORM= EXTEND=0 COMPUTING=C GRIDsystem=SLURM keepTMP=N SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/ BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/ UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/ RELEASE= VERSION=r6.40 UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/ nFILES=4 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/files.txt FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1 GENOME_VERSION=dm6 subCOLOR=0~128~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=N GEO= noSTRANDED= FORCEimport= exportBAM=N exportBAMuncollapsed=N RATIOtracks=N GENOMEdir=/faststorage/project/PAN_illumina/results//my/dm6/ newCOLLECTION=N' + eval 'USER_NAME=my TYPE=RNAseq SLAM=N BASE_FOLDER=/faststorage/project/PAN_illumina/results/ FOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/ FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1 RUNname=2025-01-27-RNAseq_Thomas_PolyA_Bam1 TMPdir=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/ LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/ SINGULARITYdir=/home/my/AP_singu/ downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/ DEBUG=N VERSION=r6.40 asmHUBpath= ASMdir= ASMname= BAM=N fwADAPTOR= rvADAPTOR= N_TRIMM= rawPAIRED=N onlyPAIRED=N FASTQout=N FASTQoutRAW=N SUBSAMPLE= MIN_LENGTH=18 MAX_LENGTH=1000 RAW= TRIMM=Y FIRST=6 LAST=200 INVERT=N Ychrom=N RANDOMmulti=N MM=2 FILTERING_INPUT=rRNA:tRNA:mito WIG=Y WIG_FASTA= spikeINnorm=N noNORM= EXTEND=0 COMPUTING=C GRIDsystem=SLURM keepTMP=N SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/ BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/ UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/ RELEASE= VERSION=r6.40 UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/ nFILES=4 FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/files.txt FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1 GENOME_VERSION=dm6 subCOLOR=0~128~0 FORCE= SYSTEM=EXTERN LOGs=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/LOGs/ prepareREF=no nSPLITS=1000000 SE=N SE2nd= maxCOUNT=1000000 demuxFASTA=N autoViewLimits= only5end= PingPong= DGE=N GEO= noSTRANDED= FORCEimport= exportBAM=N exportBAMuncollapsed=N RATIOtracks=N GENOMEdir=/faststorage/project/PAN_illumina/results//my/dm6/ newCOLLECTION=N' ++ USER_NAME=my ++ TYPE=RNAseq ++ SLAM=N ++ BASE_FOLDER=/faststorage/project/PAN_illumina/results/ ++ FOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/ ++ FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1 ++ RUNname=2025-01-27-RNAseq_Thomas_PolyA_Bam1 ++ TMPdir=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/ ++ LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/ ++ SINGULARITYdir=/home/my/AP_singu/ ++ downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/ ++ DEBUG=N ++ VERSION=r6.40 ++ asmHUBpath= ++ ASMdir= ++ ASMname= ++ BAM=N ++ fwADAPTOR= ++ rvADAPTOR= ++ N_TRIMM= ++ rawPAIRED=N ++ onlyPAIRED=N ++ FASTQout=N ++ FASTQoutRAW=N ++ SUBSAMPLE= ++ MIN_LENGTH=18 ++ MAX_LENGTH=1000 ++ RAW= ++ TRIMM=Y ++ FIRST=6 ++ LAST=200 ++ INVERT=N ++ Ychrom=N ++ RANDOMmulti=N ++ MM=2 ++ FILTERING_INPUT=rRNA:tRNA:mito ++ WIG=Y ++ WIG_FASTA= ++ spikeINnorm=N ++ noNORM= ++ EXTEND=0 ++ COMPUTING=C ++ GRIDsystem=SLURM ++ keepTMP=N ++ SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/ ++ BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/ ++ UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/ ++ RELEASE= ++ VERSION=r6.40 ++ UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/ ++ nFILES=4 ++ FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/files.txt ++ FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1 ++ GENOME_VERSION=dm6 ++ subCOLOR=0~128~0 ++ FORCE= ++ SYSTEM=EXTERN ++ LOGs=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/LOGs/ ++ prepareREF=no ++ nSPLITS=1000000 ++ SE=N ++ SE2nd= ++ maxCOUNT=1000000 ++ demuxFASTA=N ++ autoViewLimits= ++ only5end= ++ PingPong= ++ DGE=N ++ GEO= ++ noSTRANDED= ++ FORCEimport= ++ exportBAM=N ++ exportBAMuncollapsed=N ++ RATIOtracks=N ++ GENOMEdir=/faststorage/project/PAN_illumina/results//my/dm6/ ++ newCOLLECTION=N + echo USER_NAME=my,TYPE=RNAseq,SLAM=N,BASE_FOLDER=/faststorage/project/PAN_illumina/results/,FOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/,FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1,RUNname=2025-01-27-RNAseq_Thomas_PolyA_Bam1,TMPdir=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/,LIB_STORAGE_FOLDER=/faststorage/project/PAN_illumina/data/libSTORAGE/,SINGULARITYdir=/home/my/AP_singu/,downDIR=/faststorage/project/PAN_illumina/tmp//NGS_downloads/,DEBUG=N,VERSION=r6.40,asmHUBpath=,ASMdir=,ASMname=,BAM=N,fwADAPTOR=,rvADAPTOR=,N_TRIMM=,rawPAIRED=N,onlyPAIRED=N,FASTQout=N,FASTQoutRAW=N,SUBSAMPLE=,MIN_LENGTH=18,MAX_LENGTH=1000,RAW=,TRIMM=Y,FIRST=6,LAST=200,INVERT=N,Ychrom=N,RANDOMmulti=N,MM=2,FILTERING_INPUT=rRNA:tRNA:mito,WIG=Y,WIG_FASTA=,spikeINnorm=N,noNORM=,EXTEND=0,COMPUTING=C,GRIDsystem=SLURM,keepTMP=N,SCRIPT_DIR=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/,BASE_UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/,UTILITY_LOCATION=/faststorage/project/PAN_illumina/utilities/AnnotationPipeline/dmel/dm6/,RELEASE=,VERSION=r6.40,UTILITY_DIR=/faststorage/project/PAN_illumina/backup/scripts/AnnotationPipeline/utility-files/,nFILES=4,FILE_CONTAINING_LIBRARIES=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/files.txt,FOLDER_NAME=RNAseq_Thomas_PolyA_Bam1,GENOME_VERSION=dm6,subCOLOR=0~128~0,FORCE=,SYSTEM=EXTERN,LOGs=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/LOGs/,prepareREF=no,nSPLITS=1000000,SE=N,SE2nd=,maxCOUNT=1000000,demuxFASTA=N,autoViewLimits=,only5end=,PingPong=,DGE=N,GEO=,noSTRANDED=,FORCEimport=,exportBAM=N,exportBAMuncollapsed=N,RATIOtracks=N,GENOMEdir=/faststorage/project/PAN_illumina/results//my/dm6/,newCOLLECTION=N + sed 's/,/\n/g' ++ date +%s + TIME=1737992843 + TIMEx=1737992843 + [[ SLURM == SLURM ]] + CORES=2 + echo 2 + source /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/tools ++ set -a + locTMP=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ + mkdir -p /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ + chmod 777 /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ + TMPDIR=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ + cd /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ + echo /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/ + mkdir /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots + cat /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/files.txt + cut -f 2 + tr ' ' '\t' + rm -rf /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/annotation_counts.txt ++ cat /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/files.txt ++ tr '\n' '\t' ++ awk '{ print $2 }' + NAMElist='HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A ' ++ printf 'annotation\tHsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A ' + NAMElistANN='annotation HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A ' ++ printf 'length\tHsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A ' + NAMElistSIZE='length HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A ' + echo annotation HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324079/324079_S2_R1_001.fastq.gz HsBam_polyA_piwiKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_piwiKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324087/324087_S10_R1_001.fastq.gz Ov_polyA_whiteKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_whiteKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324088/324088_S11_R1_001.fastq.gz Ov_polyA_piwiKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_piwiKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324078/324078_S1_R1_001.fastq.gz HsBam_polyA_whiteKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_whiteKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep adaptor_dimer + X=0 + Xlist='adaptor_dimer 0 0 0 0' + read LINE + echo adaptor_dimer 0 0 0 0 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324079/324079_S2_R1_001.fastq.gz HsBam_polyA_piwiKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_piwiKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=151011 + Xlist='artifact_filtered 151011' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324087/324087_S10_R1_001.fastq.gz Ov_polyA_whiteKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_whiteKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/log.txt ++ grep artifact_filtered ++ awk '{ print $NF}' + X=9490 + Xlist='artifact_filtered 151011 9490' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324088/324088_S11_R1_001.fastq.gz Ov_polyA_piwiKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_piwiKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=11392 + Xlist='artifact_filtered 151011 9490 11392' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324078/324078_S1_R1_001.fastq.gz HsBam_polyA_whiteKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_whiteKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep artifact_filtered + X=19536 + Xlist='artifact_filtered 151011 9490 11392 19536' + read LINE + echo artifact_filtered 151011 9490 11392 19536 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324079/324079_S2_R1_001.fastq.gz HsBam_polyA_piwiKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_piwiKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=0 + Xlist='length_filtered_short 0' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324087/324087_S10_R1_001.fastq.gz Ov_polyA_whiteKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_whiteKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=0 + Xlist='length_filtered_short 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324088/324088_S11_R1_001.fastq.gz Ov_polyA_piwiKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_piwiKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=0 + Xlist='length_filtered_short 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324078/324078_S1_R1_001.fastq.gz HsBam_polyA_whiteKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_whiteKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_short + X=0 + Xlist='length_filtered_short 0 0 0 0' + read LINE + echo length_filtered_short 0 0 0 0 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324079/324079_S2_R1_001.fastq.gz HsBam_polyA_piwiKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_piwiKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=0 + Xlist='length_filtered_long 0' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324087/324087_S10_R1_001.fastq.gz Ov_polyA_whiteKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_whiteKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=0 + Xlist='length_filtered_long 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324088/324088_S11_R1_001.fastq.gz Ov_polyA_piwiKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_piwiKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=0 + Xlist='length_filtered_long 0 0 0' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324078/324078_S1_R1_001.fastq.gz HsBam_polyA_whiteKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_whiteKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep length_filtered_long + X=0 + Xlist='length_filtered_long 0 0 0 0' + read LINE + echo length_filtered_long 0 0 0 0 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324079/324079_S2_R1_001.fastq.gz HsBam_polyA_piwiKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_piwiKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/log.txt ++ grep N_filtered ++ awk '{ print $NF}' + X=89485 + Xlist='N_filtered 89485' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324087/324087_S10_R1_001.fastq.gz Ov_polyA_whiteKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_whiteKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=78148 + Xlist='N_filtered 89485 78148' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324088/324088_S11_R1_001.fastq.gz Ov_polyA_piwiKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_piwiKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=60341 + Xlist='N_filtered 89485 78148 60341' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324078/324078_S1_R1_001.fastq.gz HsBam_polyA_whiteKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_whiteKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep N_filtered + X=131813 + Xlist='N_filtered 89485 78148 60341 131813' + read LINE + echo N_filtered 89485 78148 60341 131813 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324079/324079_S2_R1_001.fastq.gz HsBam_polyA_piwiKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_piwiKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=26439718 + Xlist='reads_after_filtering 26439718' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324087/324087_S10_R1_001.fastq.gz Ov_polyA_whiteKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_whiteKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=23101098 + Xlist='reads_after_filtering 26439718 23101098' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324088/324088_S11_R1_001.fastq.gz Ov_polyA_piwiKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_piwiKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=17831816 + Xlist='reads_after_filtering 26439718 23101098 17831816' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324078/324078_S1_R1_001.fastq.gz HsBam_polyA_whiteKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_whiteKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep reads_after_filtering + X=38869928 + Xlist='reads_after_filtering 26439718 23101098 17831816 38869928' + read LINE + echo reads_after_filtering 26439718 23101098 17831816 38869928 + tr ' ' '\t' + for CATEGORY in adaptor_dimer artifact_filtered length_filtered_short length_filtered_long N_filtered reads_after_filtering reads_not_mapped + SWITCH=N + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324079/324079_S2_R1_001.fastq.gz HsBam_polyA_piwiKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_piwiKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ + [[ N == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=2874507 + Xlist='reads_not_mapped 2874507' + SWITCH=Y + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324087/324087_S10_R1_001.fastq.gz Ov_polyA_whiteKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_whiteKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=2243936 + Xlist='reads_not_mapped 2874507 2243936' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324088/324088_S11_R1_001.fastq.gz Ov_polyA_piwiKD_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=Ov_polyA_piwiKD_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=1888651 + Xlist='reads_not_mapped 2874507 2243936 1888651' + read LINE ++ echo /faststorage/project/PAN_illumina/backup/data/libSTORAGE/2025_01_25_RNAseq_MY_22VCLJLT3_1_R18168/demultiplexed/324078/324078_S1_R1_001.fastq.gz HsBam_polyA_whiteKD_00h_A ++ cut -f 2 ++ tr ' ' '\t' + NAME=HsBam_polyA_whiteKD_00h_A + libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ + [[ Y == N ]] ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/log.txt ++ awk '{ print $NF}' ++ grep reads_not_mapped + X=4351133 + Xlist='reads_not_mapped 2874507 2243936 1888651 4351133' + read LINE + echo reads_not_mapped 2874507 2243936 1888651 4351133 + tr ' ' '\t' + for CATEGORY in annotation_counts splitup_mRNA splitup_TE + NAMES= + [[ annotation_counts != annotation_counts ]] + 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] } }' /dev/fd/63 + sort -k1,1n ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/HsBam_polyA_piwiKD_00h_A_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/Ov_polyA_whiteKD_A_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/Ov_polyA_piwiKD_A_annotation_counts.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/HsBam_polyA_whiteKD_00h_A_annotation_counts.txt ++ read NAME + [[ annotation_counts != annotation_counts ]] + EXT= + cat /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/TMP.txt + tr ' ' '\t' + tr -s '\t' + [[ RNAseq == CHIPseq ]] + [[ RNAseq == DNAseq ]] + [[ '' == Y ]] + for CATEGORY in annotation_counts splitup_mRNA splitup_TE + NAMES= + [[ splitup_mRNA != annotation_counts ]] + rm -rf /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/splitup_mRNA.txt + cut -f 2- + awk -v 'OFS=\t' '{ X[$1]=X[$1]"\t"$2 Y[$1]+=NR } END { for (i in X) { print Y[i],i,X[i] } + sort -k1,1n ++ read NAME }' /dev/fd/63 ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/HsBam_polyA_piwiKD_00h_A_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/Ov_polyA_whiteKD_A_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/Ov_polyA_piwiKD_A_splitup_mRNA.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/HsBam_polyA_whiteKD_00h_A_splitup_mRNA.txt ++ read NAME + [[ splitup_mRNA != annotation_counts ]] + EXT=annotation_ + cat /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/TMP.txt + tr ' ' '\t' + tr -s '\t' + [[ RNAseq == CHIPseq ]] + [[ RNAseq == DNAseq ]] + [[ '' == Y ]] + for CATEGORY in annotation_counts splitup_mRNA splitup_TE + NAMES= + [[ splitup_TE != annotation_counts ]] + rm -rf /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/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//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/HsBam_polyA_piwiKD_00h_A_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/Ov_polyA_whiteKD_A_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/Ov_polyA_piwiKD_A_splitup_TE.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/HsBam_polyA_whiteKD_00h_A_splitup_TE.txt ++ read NAME + [[ splitup_TE != annotation_counts ]] + EXT=annotation_ + cat /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/TMP.txt + tr ' ' '\t' + tr -s '\t' + [[ RNAseq == CHIPseq ]] + [[ RNAseq == DNAseq ]] + [[ '' == Y ]] + Rscript /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/ FILE=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/ + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/:/tmp /home/my/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/plot_annotations.R TMP=/faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ OUTdir=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/ FILE=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/annotation_counts.txt PLOTdir=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/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 Using annotation as id variables + [[ N == Y ]] + [[ dm6 == dm6 ]] + mkdir /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/1kb_tiles + for STRAND in Plus Minus + cut -f 3- + 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//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/WindowCounts_Plus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/WindowCounts_Plus.txt ++ read NAME + echo HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A + tr -s '\t' + tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/TMP.txt + tr ' ' '\t' + tr -s '\t' + for STRAND in Plus Minus + cut -f 3- + 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//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/WindowCounts_Minus.txt ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/WindowCounts_Minus.txt ++ read NAME + echo HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A + tr -s '\t' + tr ' ' '\t' + cat /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/TMP.txt + tr -s '\t' + tr ' ' '\t' + echo HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A + 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//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/1kb_tiles/ + rawFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/raw-data/ + mkdir -p /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/raw-data/ + [[ RNAseq == sRNAseq ]] + [[ RNAseq == CLIPseq ]] + [[ RNAseq == sRNAseqIP ]] + [[ RNAseq == SLAMseq ]] + [[ RNAseq == GROseq ]] + [[ RNAseq == sRNAseq ]] + [[ RNAseq == sRNAseqIP ]] + [[ RNAseq == CLIPseq ]] + [[ RNAseq = RNAseq ]] + CATEGORIES='TE_GeTMM TE_GeTMM GeTMM_gene' + [[ RNAseq == sRNAseq ]] + [[ RNAseq == sRNAseqIP ]] + [[ RNAseq == CLIPseq ]] + [[ RNAseq = RNAseq ]] + for CATEGORY in $CATEGORIES + [[ TE_GeTMM == *\T\E\_\G\e\T\M\M* ]] + head -n 1 /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep '^TE:' /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep -v _AS + head -n 1 /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep '^TE:' /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep _AS + for CATEGORY in $CATEGORIES + [[ TE_GeTMM == *\T\E\_\G\e\T\M\M* ]] + head -n 1 /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep '^TE:' /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep -v _AS + head -n 1 /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep '^TE:' /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep _AS + 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//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + grep -v '^TE:' /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/gene-expression/GeTMM_normalized.txt + tr ' ' '\t' + [[ N == Y ]] + [[ RNAseq == CHIPseq ]] + [[ RNAseq == DNAseq ]] + [[ '' == Y ]] + CATEGORIES='sense antisense' + for CATEGORY in $CATEGORIES + NAMES= + awk -v 'OFS=\t' '{ NAME=$1"~"$2 if(NAME in X) { X[NAME]=X[NAME]"\t"$3 }else{ X[NAME]=$3 } } END { for (i in X) { print i,X[i] } }' /dev/fd/63 + sort -k2,2n ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/HsBam_polyA_piwiKD_00h_A_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/Ov_polyA_whiteKD_A_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/Ov_polyA_piwiKD_A_TE-sense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/HsBam_polyA_whiteKD_00h_A_TE-sense_man.bg ++ read NAME ++ echo TE POS HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A ++ tr '~' '\t' ++ tr ' ' '\t' + echo /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ + cat /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/TMP_TEhist.txt + tr ' ' '\t' + sort -k2,2n + tr '~' '\t' + for CATEGORY in $CATEGORIES + 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//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_piwiKD_00h_A/HsBam_polyA_piwiKD_00h_A_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_whiteKD_A/Ov_polyA_whiteKD_A_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/Ov_polyA_piwiKD_A/Ov_polyA_piwiKD_A_TE-antisense_man.bg ++ read NAME ++ libFOLDER=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/ ++ NAMES=' HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A' ++ cat /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1//individual-libraries/HsBam_polyA_whiteKD_00h_A/HsBam_polyA_whiteKD_00h_A_TE-antisense_man.bg ++ read NAME ++ tr '~' '\t' ++ tr ' ' '\t' ++ echo TE POS HsBam_polyA_piwiKD_00h_A Ov_polyA_whiteKD_A Ov_polyA_piwiKD_A HsBam_polyA_whiteKD_00h_A + echo /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ + cat /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/TMP_TEhist.txt + tr '~' '\t' + tr ' ' '\t' + sort -k2,2n + mkdir -p /faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/TEhist/ + Rscript /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/TEhist/ inSENSE=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/raw-data/TE_hist_sense.txt inANTISENSE=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/raw-data/TE_hist_antisense.txt inALL=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/raw-data/TE_hist_all.txt TYPE=RNAseq + singularity exec --cleanenv -B /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/:/tmp /home/my/AP_singu/R.simg Rscript /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/script-files/plot_TEhist.R OPENdir=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/TEhist/ inSENSE=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/raw-data/TE_hist_sense.txt inANTISENSE=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/raw-data/TE_hist_antisense.txt inALL=/faststorage/project/PAN_illumina/results//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/plots/raw-data/TE_hist_all.txt TYPE=RNAseq ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ── ✔ ggplot2 3.3.4.9000 ✔ purrr 0.3.4 ✔ tibble 3.1.2 ✔ dplyr 1.0.7 ✔ tidyr 1.1.3 ✔ stringr 1.4.0 ✔ readr 1.4.0 ✔ forcats 0.5.1 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() 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 + rm -rf /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/Rscripts.pdf + [[ N != Y ]] + rm -rf /faststorage/project/PAN_illumina/tmp//my/dm6/RNAseq/2025-01-27-RNAseq_Thomas_PolyA_Bam1/TMP/ ++ awk '{ print ($1-$2)/60 }' +++ date +%s ++ echo -e 1737992938 1737992843 + PROCESSED_TIME=1.58333 + echo 'collect-numbers - processing_time=' 1.58333 + exit