Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/18fe20dd395ab631b4f57a91fcdb12/659_buD-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/18fe20dd395ab631b4f57a91fcdb12/659_buD-T1-TRNA-1_A23MVY2LT4_2.SJ.out.tab
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/6bcb027cf8773d4ad1bc7ca26c9438/.command.sh
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Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/6bcb027cf8773d4ad1bc7ca26c9438/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/366e253fa972ac1ca727bbadf75240/659_buD-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (7 inputs)
08:43:03 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[8150000], rate=20375000.00/min 08:43:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_buD-T1-TRNA-1_A23MVY2LT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_buD-T1-TRNA-1_A23MVY2LT4_2.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.
-659_buD-T1-TRNA-1_A23MVY2LT4_2.introns: identified 6580 cancer introns
08:43:35 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_buD-T1-TRNA-1_A23MVY2LT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer.introns.prelim
08:43:35 : INFO : Running: touch /tmp/nxf.fzBbiqQ2Dx/659_buD-T1-TRNA-1_A23MVY2LT4_2.chckpts/prelim_introns.ok
08:43:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer.introns.prelim --min_total_reads 5 > 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer.introns
08:43:36 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer.introns.prelim --min_total_reads 5 > 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer.introns
08:43:36 : INFO : Running: touch /tmp/nxf.fzBbiqQ2Dx/659_buD-T1-TRNA-1_A23MVY2LT4_2.chckpts/introns_filtered.ok
08:43:36 : INFO : -found 2859 cancer introns
08:43:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_buD-T1-TRNA-1_A23MVY2LT4_2.introns --cancer_introns 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_buD-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed
08:43:36 : INFO : Creating the BED File.
08:43:41 : INFO : Saving Bed File as 659_buD-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed
08:43:41 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_buD-T1-TRNA-1_A23MVY2LT4_2.introns --cancer_introns 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_buD-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed
08:43:41 : INFO : Running: touch /tmp/nxf.fzBbiqQ2Dx/659_buD-T1-TRNA-1_A23MVY2LT4_2.chckpts/intron_igv_bed.ok
08:43:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_buD-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed --bam 659_buD-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam --output_prefix 659_buD-T1-TRNA-1_A23MVY2LT4_2
[W::hts_idx_load3] The index file is older than the data file: 659_buD-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam.bai
08:59:13 : INFO : Execution Time = 15.53 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_buD-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed --bam 659_buD-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam --output_prefix 659_buD-T1-TRNA-1_A23MVY2LT4_2
08:59:13 : INFO : Running: touch /tmp/nxf.fzBbiqQ2Dx/659_buD-T1-TRNA-1_A23MVY2LT4_2.chckpts/reads_alignments_extracted.ok
08:59:13 : INFO : Running: samtools sort -o 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.bam
08:59:13 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam 659_buD-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.bam
08:59:13 : INFO : Running: touch /tmp/nxf.fzBbiqQ2Dx/659_buD-T1-TRNA-1_A23MVY2LT4_2.chckpts/sort_cancer_intron_reads.ok
08:59:13 : INFO : Running: samtools sort -o 659_buD-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.bam 659_buD-T1-TRNA-1_A23MVY2LT4_2.gene_reads.bam
[bam_sort_core] merging from 88 files and 1 in-memory blocks...