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/ea/25a50b1529b18820ba5ec23f253c58/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/3d4917f45a6ef9795185c2789b33ad/tih_rna_sample_00467_B23WHTKLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/13be94662f02b6ae8b8d9ebe164525/tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/25a50b1529b18820ba5ec23f253c58/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/3d4917f45a6ef9795185c2789b33ad/tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/3d4917f45a6ef9795185c2789b33ad/tih_rna_sample_00467_B23WHTKLT4_1.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
08:50:42 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[11870000], rate=12949090.91/min 08:51:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00467_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00467_B23WHTKLT4_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.
-tih_rna_sample_00467_B23WHTKLT4_1.introns: identified 3292 cancer introns
08:51:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00467_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns.prelim
08:51:51 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/prelim_introns.ok
08:51:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns
08:51:52 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns
08:51:52 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/introns_filtered.ok
08:51:52 : INFO : -found 2224 cancer introns
08:51:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00467_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed
08:51:52 : INFO : Creating the BED File.
08:52:05 : INFO : Saving Bed File as tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed
08:52:05 : INFO : Execution Time = 0.22 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00467_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed
08:52:05 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
08:52:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00467_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
09:08:12 : INFO : Execution Time = 16.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00467_B23WHTKLT4_1
09:08:12 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
09:08:12 : INFO : Running: samtools sort -o tih_rna_sample_00467_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00467_B23WHTKLT4_1.cancer_intron_reads.bam
09:08:13 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o tih_rna_sample_00467_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00467_B23WHTKLT4_1.cancer_intron_reads.bam
09:08:13 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
09:08:13 : INFO : Running: samtools sort -o tih_rna_sample_00467_B23WHTKLT4_1.gene_reads.sorted.bam tih_rna_sample_00467_B23WHTKLT4_1.gene_reads.bam
[bam_sort_core] merging from 68 files and 1 in-memory blocks...