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/cf/ceb972680822f8b3f816bbbab7d572/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/495df7c7d87251a4ec09c1d610db54/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/0b22fe6c769c8c652d5c195a60bafb/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/0b22fe6c769c8c652d5c195a60bafb/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/0b22fe6c769c8c652d5c195a60bafb/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/ceb972680822f8b3f816bbbab7d572/.command.run
==> STAGING COMPLETE (7 inputs)
08:48:25 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[12890000], rate=20902702.70/min 08:49:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_CRL_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_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns: identified 7292 cancer introns
08:49:11 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim
08:49:11 : INFO : Running: touch /tmp/nxf.moM6oOaqoD/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/prelim_introns.ok
08:49:11 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
08:49:12 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns
08:49:12 : INFO : Running: touch /tmp/nxf.moM6oOaqoD/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/introns_filtered.ok
08:49:12 : INFO : -found 2504 cancer introns
08:49:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
08:49:12 : INFO : Creating the BED File.
08:49:17 : INFO : Saving Bed File as 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
08:49:18 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns --cancer_introns 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed
08:49:18 : INFO : Running: touch /tmp/nxf.moM6oOaqoD/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/intron_igv_bed.ok
08:49:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1
[W::hts_idx_load3] The index file is older than the data file: 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai
09:07:03 : INFO : Execution Time = 17.76 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.introns.for_IGV.bed --bam 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1
09:07:03 : INFO : Running: touch /tmp/nxf.moM6oOaqoD/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/reads_alignments_extracted.ok
09:07:03 : INFO : Running: samtools sort -o 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
09:07:04 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.sorted.bam 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.cancer_intron_reads.bam
09:07:04 : INFO : Running: touch /tmp/nxf.moM6oOaqoD/1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.chckpts/sort_cancer_intron_reads.ok
09:07:04 : INFO : Running: samtools sort -o 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.sorted.bam 1173_CRL_T1_RNA_SLD_01_A23T55JLT4_1.gene_reads.bam