/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/ FATAL: Image file already exists: "basicTools.app" - will not overwrite FATAL: Image file already exists: "genome_evaluation.app" - will not overwrite FATAL: Image file already exists: "ragtag.app" - will not overwrite FATAL: Image file already exists: "quast.app" - will not overwrite FATAL: Image file already exists: "AP_R.app" - will not overwrite FATAL: Image file already exists: "deepvariant.app" - will not overwrite FATAL: Image file already exists: "rtg-tools.app" - will not overwrite FATAL: Image file already exists: "sniffles.app" - will not overwrite FATAL: Image file already exists: "busco.app" - will not overwrite FATAL: Image file already exists: "HiC_tools.app" - will not overwrite FATAL: Image file already exists: "repeatmasker.app" - will not overwrite /groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/evaluate_genome.sh: line 359: commitID: unbound variable clip-c2-51.cbe.vbc.ac.at ++ sed 's/,/\t/g;s/"//g' ++ echo OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/,TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/,LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/,COMPUTING=L,DEBUG=Y,FORCE=N,SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/,UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/,APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/,refFASTA=dm6,assemblyNAME=OSC_r1.01,assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,analysisNAME=for_OSC_paper_incl-SiomiData,CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes,ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz,PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz,ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz,STAGE=clusterAnalysis,Ychrom=N,TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa,wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz,OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz,HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz,OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb,CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/,OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/,OSC_RNAseq_PE_NORM=2.5774 + VARI='OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/ TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/ LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/ COMPUTING=L DEBUG=Y FORCE=N SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/ UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/ APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/ refFASTA=dm6 assemblyNAME=OSC_r1.01 assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt analysisNAME=for_OSC_paper_incl-SiomiData CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz STAGE=clusterAnalysis Ychrom=N TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/ OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/ OSC_RNAseq_PE_NORM=2.5774' + eval 'OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/ TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/ LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/ COMPUTING=L DEBUG=Y FORCE=N SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/ UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/ APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/ refFASTA=dm6 assemblyNAME=OSC_r1.01 assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt analysisNAME=for_OSC_paper_incl-SiomiData CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz STAGE=clusterAnalysis Ychrom=N TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/ OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/ OSC_RNAseq_PE_NORM=2.5774' ++ OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/ ++ TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/ ++ LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/ ++ COMPUTING=L ++ DEBUG=Y ++ FORCE=N ++ SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/ ++ UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/ ++ APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/ ++ refFASTA=dm6 ++ assemblyNAME=OSC_r1.01 ++ assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt ++ assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt ++ analysisNAME=for_OSC_paper_incl-SiomiData ++ CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes ++ ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz ++ PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz ++ ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz ++ STAGE=clusterAnalysis ++ Ychrom=N ++ TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa ++ wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz ++ OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz ++ HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz ++ OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb ++ CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/ ++ OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/ ++ OSC_RNAseq_PE_NORM=2.5774 + VARI=OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/,TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/,LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/,COMPUTING=L,DEBUG=Y,FORCE=N,SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/,UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/,APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/,refFASTA=dm6,assemblyNAME=OSC_r1.01,assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,analysisNAME=for_OSC_paper_incl-SiomiData,CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes,ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz,PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz,ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz,STAGE=clusterAnalysis,Ychrom=N,TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa,wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz,OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz,HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz,OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb,CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/,OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/,OSC_RNAseq_PE_NORM=2.5774 + tr , '\n' + echo OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/,TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/,LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/,COMPUTING=L,DEBUG=Y,FORCE=N,SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/,UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/,APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/,refFASTA=dm6,assemblyNAME=OSC_r1.01,assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,analysisNAME=for_OSC_paper_incl-SiomiData,CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes,ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz,PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz,ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz,STAGE=clusterAnalysis,Ychrom=N,TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa,wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz,OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz,HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz,OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb,CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/,OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/,OSC_RNAseq_PE_NORM=2.5774 OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/ TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/ LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/ COMPUTING=L DEBUG=Y FORCE=N SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/ UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/ APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/ refFASTA=dm6 assemblyNAME=OSC_r1.01 assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt analysisNAME=for_OSC_paper_incl-SiomiData CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz STAGE=clusterAnalysis Ychrom=N TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/ OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/ OSC_RNAseq_PE_NORM=2.5774 + locTMP=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/ ++ date +%s + TIME=1759394447 + CORES=6 ++ scontrol show job 22647302 ++ grep TRES ++ awk '{ split($NF, X, /,|=|G/);{print X[5]-5}}' ++ head -n 1 + MEM=15 + source /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/tools ++ set -a ++ set +a + ID= + [[ dm6 == dm6 ]] + [[ ! -s /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/dm6.fa ]] + refFASTA=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/dm6.fa + VARI=OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/,TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/,LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/,COMPUTING=L,DEBUG=Y,FORCE=N,SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/,UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/,APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/,refFASTA=dm6,assemblyNAME=OSC_r1.01,assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,analysisNAME=for_OSC_paper_incl-SiomiData,CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes,ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz,PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz,ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz,STAGE=clusterAnalysis,Ychrom=N,TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa,wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz,OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz,HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz,OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb,CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/,OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/,OSC_RNAseq_PE_NORM=2.5774,refFASTA=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/dm6.fa + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *synteny* ]] + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *busco* ]] + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *quast* ]] + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *gaep* ]] + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *TEcoverage* ]] + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *VARIANTS_ONT* ]] + [[ clusterAnalysis == *VARIANTS_ILLUMINA ]] + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *TEanalysisGENOME* ]] + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *HiC* ]] + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *clusterAnalysis* ]] + COMMAND=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/cluster-analysis.sh + [[ L == C ]] + /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/cluster-analysis.sh OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/,TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/,LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/,COMPUTING=L,DEBUG=Y,FORCE=N,SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/,UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/,APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/,refFASTA=dm6,assemblyNAME=OSC_r1.01,assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,analysisNAME=for_OSC_paper_incl-SiomiData,CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes,ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz,PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz,ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz,STAGE=clusterAnalysis,Ychrom=N,TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa,wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz,OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz,HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz,OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb,CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/,OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/,OSC_RNAseq_PE_NORM=2.5774,refFASTA=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/dm6.fa clip-c2-51.cbe.vbc.ac.at ++ sed 's/,/\t/g;s/"//g' ++ echo OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/,TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/,LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/,COMPUTING=L,DEBUG=Y,FORCE=N,SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/,UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/,APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/,refFASTA=dm6,assemblyNAME=OSC_r1.01,assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt,analysisNAME=for_OSC_paper_incl-SiomiData,CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes,ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz,PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz,ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz,STAGE=clusterAnalysis,Ychrom=N,TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa,wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz,OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz,HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz,OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb,CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/,OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/,OSC_RNAseq_PE_NORM=2.5774,refFASTA=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/dm6.fa + VARI='OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/ TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/ LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/ COMPUTING=L DEBUG=Y FORCE=N SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/ UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/ APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/ refFASTA=dm6 assemblyNAME=OSC_r1.01 assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt analysisNAME=for_OSC_paper_incl-SiomiData CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz STAGE=clusterAnalysis Ychrom=N TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/ OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/ OSC_RNAseq_PE_NORM=2.5774 refFASTA=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/dm6.fa' + eval 'OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/ TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/ LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/ COMPUTING=L DEBUG=Y FORCE=N SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/ UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/ APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/ refFASTA=dm6 assemblyNAME=OSC_r1.01 assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt analysisNAME=for_OSC_paper_incl-SiomiData CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz STAGE=clusterAnalysis Ychrom=N TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/ OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/ OSC_RNAseq_PE_NORM=2.5774 refFASTA=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/dm6.fa' ++ OPENdir=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/ ++ TMPdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/ ++ LOG=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/ ++ COMPUTING=L ++ DEBUG=Y ++ FORCE=N ++ SCRIPTdir=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/ ++ UTILITYdir=/groups/brennecke/handler/scripts/biogenesis-paper/evaluate_genome/utility-files/ ++ APPTAINERdir=/scratch/brennecke/handler/final_annotation/apptainer/ ++ refFASTA=dm6 ++ assemblyNAME=OSC_r1.01 ++ assemblyFASTA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt ++ assemblyFILE=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt ++ analysisNAME=for_OSC_paper_incl-SiomiData ++ CHRsizes=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes ++ ONT_DNA=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/nanopore/assembly/wtOSC/GUPPY_SUPER_5.0.7+2332e8d65_dna_r9.4.1_450bps_sup_31/read-preparation/filtered_reads.fq.gz ++ PacBio_SIOMI=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/SiomiData/SRR29206615_subreads.fastq.gz ++ ILLUMINA_DNAseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/dm6/DNAseq/2024-05-07-OSC+shW/individual-libraries/wtOSC/wtOSC_raw-paired.fq.gz ++ STAGE=clusterAnalysis ++ Ychrom=N ++ TEconsensus=/groups/brennecke/pipelines/utilities/AnnotationPipeline/dmel/dm6/TE_annot_new_WO_DUST.fa ++ wt_sRNA=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/sRNAseq/2025-08-12-sRNA_triplicates/individual-libraries/siLuc_sRNA_Rep1/siLuc_sRNA_Rep1_annotated.fa.gz ++ OSC_RNAseq_PE=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/handler/OSC_r1.01/OSC-paper/AP_runs/RNAseq/2025-08-05-PE_RZ_data_BCfix/individual-libraries/siGFP_RZ_2018_PE125/siGFP_RZ_2018_PE125_raw-paired.fq.gz ++ HiCreads=/scratch-cbe/users/handler/HiC/OSC-HiC_raw-paired.fq.gz ++ OSCuniqueness_100nt=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/annotations/uniqueness/100mer.3MM.bb ++ CHIPdataH3K9=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/data-tracks/CHIPseq_H3K9me3/ ++ OSC_annotations=/appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/final-assemblies/OSC_r1.01_for_paper_2/OSC_r1.01/annotations/ ++ OSC_RNAseq_PE_NORM=2.5774 ++ refFASTA=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/dm6.fa ++ date +%s + TIME=1759394447 + locTMP=/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/ + mkdir /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/ mkdir: cannot create directory ‘/scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/’: File exists + mkdir -p /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/cluster-analysis/ + source /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/script-files/tools ++ set -a ++ set +a + THREADS=6 ++ scontrol show job 22647302 ++ grep TRES ++ awk '{ split($NF, X, /,|=|G/); {print X[5]-5}}' ++ head -n 1 + MEM=15 + cd /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData//LOGs/ + refNAME=dm6 ++ grep -n OSC_r1.01 /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt ++ tr : '\t' ++ cut -f 1 + nOSC=1 ++ sed -n 1p /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation/for_OSC_paper_incl-SiomiData/genome-definition.txt + currASSEMBLYline='/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.fa OSC_r1.01 X_RagTag:22673638-23300000' ++ echo /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.fa OSC_r1.01 X_RagTag:22673638-23300000 ++ tr ' ' '\t' ++ cut -f 1 + ASSEMBLYseq=/appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.fa ++ echo /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.fa OSC_r1.01 X_RagTag:22673638-23300000 ++ tr ' ' '\t' ++ cut -f 2 + ASSEMBLYname=OSC_r1.01 ++ echo /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.fa OSC_r1.01 X_RagTag:22673638-23300000 ++ tr ' ' '\t' ++ cut -f 3 + ASSEMBLYflam=X_RagTag:22673638-23300000 + cp /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.fa /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/OSC.genome.fa + CUTOFF=3 + CUTOFFus=10 + US=1 + bedtools genomecov -ibam /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers_unpaired.bam -split -bg -g /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes -strand + + mawk -v 'OFS=\t' -v NORM=2.5774 '{$4=$4/NORM; print}' + sort -k1,1 -k2,2n + apptainer exec --cleanenv --contain -B /groups -B /scratch -B /scratch-cbe -B /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/:/tmp /scratch/brennecke/handler/final_annotation/apptainer/basicTools.app bedtools genomecov -ibam /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers_unpaired.bam -split -bg -g /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes -strand + + singularity exec /groups/brennecke/singularity-packages/basicTools.simg mawk -v 'OFS=\t' -v NORM=2.5774 '{$4=$4/NORM; print}' ***** *****WARNING: Genome (-g) files are ignored when BAM input is provided. ***** + bedtools genomecov -ibam /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers_unpaired.bam -split -bg -g /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes -strand - + sort -k1,1 -k2,2n + mawk -v 'OFS=\t' -v NORM=2.5774 '{$4=-$4/NORM; print}' + apptainer exec --cleanenv --contain -B /groups -B /scratch -B /scratch-cbe -B /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/:/tmp /scratch/brennecke/handler/final_annotation/apptainer/basicTools.app bedtools genomecov -ibam /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers_unpaired.bam -split -bg -g /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes -strand - + singularity exec /groups/brennecke/singularity-packages/basicTools.simg mawk -v 'OFS=\t' -v NORM=2.5774 '{$4=-$4/NORM; print}' ***** *****WARNING: Genome (-g) files are ignored when BAM input is provided. ***** + bedGraphToBigWig /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.sense_unpaired.bedGraph /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.sense_unpaired.bw + singularity exec /groups/brennecke/singularity-packages/basicTools.simg bedGraphToBigWig /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.sense_unpaired.bedGraph /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.sense_unpaired.bw + bedGraphToBigWig /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.antisense_unpaired.bedGraph /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.antisense_unpaired.bw + singularity exec /groups/brennecke/singularity-packages/basicTools.simg bedGraphToBigWig /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.antisense_unpaired.bedGraph /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.antisense_unpaired.bw + mawk -v 'OFS=\t' -v CUTOFF=3 ' { if($4>CUTOFF){ print $1,$2,$3,NR,0,"+" } }' /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.sense_unpaired.bedGraph + sort -k1,1 -k2,2n + singularity exec /groups/brennecke/singularity-packages/basicTools.simg mawk -v 'OFS=\t' -v CUTOFF=3 ' { if($4>CUTOFF){ print $1,$2,$3,NR,0,"+" } }' /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.sense_unpaired.bedGraph + bedToBigBed /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/analyzable-regions_for_spliceAnalysis.sense.bed /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/cluster-analysis/analyzable-regions_for_spliceAnalysis.sense.bb + apptainer exec --cleanenv --contain -B /groups -B /scratch -B /scratch-cbe -B /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/:/tmp /scratch/brennecke/handler/final_annotation/apptainer/basicTools.app bedToBigBed /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/analyzable-regions_for_spliceAnalysis.sense.bed /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/cluster-analysis/analyzable-regions_for_spliceAnalysis.sense.bb pass1 - making usageList (11 chroms): 992 millis pass2 - checking and writing primary data (5768026 records, 6 fields): 8197 millis + mawk -v 'OFS=\t' -v CUTOFF=10 ' { if(-$4>CUTOFF){ print $1,$2,$3,NR,0,"-" } }' /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.antisense_unpaired.bedGraph + sort -k1,1 -k2,2n + singularity exec /groups/brennecke/singularity-packages/basicTools.simg mawk -v 'OFS=\t' -v CUTOFF=10 ' { if(-$4>CUTOFF){ print $1,$2,$3,NR,0,"-" } }' /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.antisense_unpaired.bedGraph + bedToBigBed /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.antisense_unpaired.filtered.antisense.bedGraph /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/cluster-analysis/analyzable-regions_for_spliceAnalysis.antisense.bb + apptainer exec --cleanenv --contain -B /groups -B /scratch -B /scratch-cbe -B /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/:/tmp /scratch/brennecke/handler/final_annotation/apptainer/basicTools.app bedToBigBed /scratch-cbe/users/handler/genome_evaluation/for_OSC_paper_incl-SiomiData/cluster-analysis/unique_mappers.antisense_unpaired.filtered.antisense.bedGraph /appdata/vbc-static-extern/brennecke/tmp/AnnotationPipeline/ASSEMBLIES/OSC_r1.01/OSC_r1.01/OSC_r1.01.chrom.sizes /appdata/vbc-static-extern/brennecke/tmp/dominik_XA12B/YB_paper_for-figures/genome_evaluation//for_OSC_paper_incl-SiomiData/cluster-analysis/analyzable-regions_for_spliceAnalysis.antisense.bb pass1 - making usageList (7 chroms): 814 millis pass2 - checking and writing primary data (4769461 records, 6 fields): 6854 millis + exit + [[ -z clusterAnalysis ]] + [[ clusterAnalysis == *misc* ]]