Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/25a6cfefa4a0162a3041222bf0cc39/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/aedb306d591d77aa36f30d5e077ea6/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/82/48e85a9b96f2f4a2688ee98fb70506/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/aedb306d591d77aa36f30d5e077ea6/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/25a6cfefa4a0162a3041222bf0cc39/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/25a6cfefa4a0162a3041222bf0cc39/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.SJ.out.tab ==> STAGING COMPLETE (7 inputs) 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Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim Use of uninitialized value $ctat_genome_lib in concatenation (.) or string at /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl line 18. -1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 5754 cancer introns 08:32:33 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim 08:32:33 : INFO : Running: touch /tmp/nxf.YUlUChpjZt/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok 08:32:33 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 08:32:34 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns 08:32:34 : INFO : Running: touch /tmp/nxf.YUlUChpjZt/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok 08:32:34 : INFO : -found 1947 cancer introns 08:32:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 08:32:34 : INFO : Creating the BED File. 08:32:38 : INFO : Saving Bed File as 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 08:32:38 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed 08:32:38 : INFO : Running: touch /tmp/nxf.YUlUChpjZt/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok 08:32:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1 [W::hts_idx_load3] The index file is older than the data file: 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai 08:48:26 : INFO : Execution Time = 15.80 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1 08:48:26 : INFO : Running: touch /tmp/nxf.YUlUChpjZt/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok 08:48:26 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 08:48:27 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam 08:48:27 : INFO : Running: touch /tmp/nxf.YUlUChpjZt/1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok 08:48:27 : INFO : Running: samtools sort -o 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_Q7O_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam