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/6b/d68b6018a1796b4a45872ad2e8ad98/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/70597dfe95e15e8b6c8a6ceeba8eef/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/70597dfe95e15e8b6c8a6ceeba8eef/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/70597dfe95e15e8b6c8a6ceeba8eef/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/cefa9fa0826e15a628bc4e2ccff89b/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/d68b6018a1796b4a45872ad2e8ad98/.command.run
==> STAGING COMPLETE (7 inputs)
08:22:42 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[6640000], rate=15323076.92/min 08:23:16 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-b567d0-R1_A23YTGFLT4_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.
-aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns: identified 6517 cancer introns
08:23:17 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns.prelim
08:23:17 : INFO : Running: touch /tmp/nxf.ncmD8sOAz4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok
08:23:17 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns
08:23:17 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns
08:23:17 : INFO : Running: touch /tmp/nxf.ncmD8sOAz4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok
08:23:17 : INFO : -found 2180 cancer introns
08:23:17 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed
08:23:17 : INFO : Creating the BED File.
08:23:23 : INFO : Saving Bed File as aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed
08:23:23 : INFO : Execution Time = 0.09 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed
08:23:23 : INFO : Running: touch /tmp/nxf.ncmD8sOAz4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok
08:23:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-b567d0-R1_A23YTGFLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
08:37:37 : INFO : Execution Time = 14.24 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-b567d0-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-b567d0-R1_A23YTGFLT4_1
08:37:37 : INFO : Running: touch /tmp/nxf.ncmD8sOAz4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok
08:37:37 : INFO : Running: samtools sort -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.bam
08:37:38 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.cancer_intron_reads.bam
08:37:38 : INFO : Running: touch /tmp/nxf.ncmD8sOAz4/aih-tih-sc-b567d0-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok
08:37:38 : INFO : Running: samtools sort -o aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-b567d0-R1_A23YTGFLT4_1.gene_reads.bam
[bam_sort_core] merging from 73 files and 1 in-memory blocks...