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/c6/e70849769b0bd9ac79501d8ad54fc4/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/ee962920b4c920a2ad9202321cdc6d/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/9c3b58ad3ad1c96a56aaf93e7daab6/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/9c3b58ad3ad1c96a56aaf93e7daab6/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/e70849769b0bd9ac79501d8ad54fc4/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bd/9c3b58ad3ad1c96a56aaf93e7daab6/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
08:51:45 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[11670000], rate=25007142.86/min 08:52:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_brn_01_A23WKFTLT4_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.
-BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns: identified 3913 cancer introns
08:52:20 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer.introns.prelim
08:52:20 : INFO : Running: touch /tmp/nxf.5zibIG9c1n/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.chckpts/prelim_introns.ok
08:52:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer.introns
08:52:20 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer.introns
08:52:20 : INFO : Running: touch /tmp/nxf.5zibIG9c1n/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.chckpts/introns_filtered.ok
08:52:20 : INFO : -found 2190 cancer introns
08:52:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns --cancer_introns BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns.for_IGV.bed
08:52:21 : INFO : Creating the BED File.
08:52:25 : INFO : Saving Bed File as BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns.for_IGV.bed
08:52:25 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns --cancer_introns BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns.for_IGV.bed
08:52:25 : INFO : Running: touch /tmp/nxf.5zibIG9c1n/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.chckpts/intron_igv_bed.ok
08:52:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns.for_IGV.bed --bam BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
09:04:02 : INFO : Execution Time = 11.62 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.introns.for_IGV.bed --bam BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1
09:04:02 : INFO : Running: touch /tmp/nxf.5zibIG9c1n/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.chckpts/reads_alignments_extracted.ok
09:04:02 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer_intron_reads.bam
09:04:02 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.cancer_intron_reads.bam
09:04:02 : INFO : Running: touch /tmp/nxf.5zibIG9c1n/BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.chckpts/sort_cancer_intron_reads.ok
09:04:02 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gene_reads.sorted.bam BVT_FFPE_TRNA_brn_01_A23WKFTLT4_1.gene_reads.bam
[bam_sort_core] merging from 75 files and 1 in-memory blocks...