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/cd/84900063d864f0855f76846c7eee3c/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/6b5f49a5634c30353d0c7c9ef763ee/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/4ae57a790d79b95a1c08daa9f95515/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/6b5f49a5634c30353d0c7c9ef763ee/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/4ae57a790d79b95a1c08daa9f95515/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/18/4ae57a790d79b95a1c08daa9f95515/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
08:47:53 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[14730000], rate=23257894.74/min 08:48:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_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.
-1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.introns: identified 5803 cancer introns
08:48:39 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim
08:48:39 : INFO : Running: touch /tmp/nxf.4Rg6cpCefT/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/prelim_introns.ok
08:48:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns
08:48:39 : INFO : Execution Time = 0.00 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns.prelim --min_total_reads 5 > 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns
08:48:39 : INFO : Running: touch /tmp/nxf.4Rg6cpCefT/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/introns_filtered.ok
08:48:39 : INFO : -found 2110 cancer introns
08:48:39 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
08:48:40 : INFO : Creating the BED File.
08:48:44 : INFO : Saving Bed File as 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
08:48:44 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.introns --cancer_introns 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed
08:48:44 : INFO : Running: touch /tmp/nxf.4Rg6cpCefT/1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.chckpts/intron_igv_bed.ok
08:48:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.introns.for_IGV.bed --bam 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam --output_prefix 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2
[W::hts_idx_load3] The index file is older than the data file: 1173_CRX_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai