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/63/42183caf74233a9797ff684b8de8af/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/1611e612de2a72d4d0b522c005bebb/GM24385_0001_RNA_0001_23H5VFLT4_s08.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/1611e612de2a72d4d0b522c005bebb/GM24385_0001_RNA_0001_23H5VFLT4_s08.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/8da13709480ffe33bf68c093bb80a4/GM24385_0001_RNA_0001_23H5VFLT4_s08.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/42183caf74233a9797ff684b8de8af/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/1611e612de2a72d4d0b522c005bebb/GM24385_0001_RNA_0001_23H5VFLT4_s08.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
08:29:47 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[12150000], rate=12355932.20/min 08:30:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file GM24385_0001_RNA_0001_23H5VFLT4_s08.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > GM24385_0001_RNA_0001_23H5VFLT4_s08.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.
-GM24385_0001_RNA_0001_23H5VFLT4_s08.introns: identified 4728 cancer introns
08:30:56 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file GM24385_0001_RNA_0001_23H5VFLT4_s08.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer.introns.prelim
08:30:56 : INFO : Running: touch /tmp/nxf.sdciXDBu53/GM24385_0001_RNA_0001_23H5VFLT4_s08.chckpts/prelim_introns.ok
08:30:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer.introns.prelim --min_total_reads 5 > GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer.introns
08:30:56 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer.introns.prelim --min_total_reads 5 > GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer.introns
08:30:56 : INFO : Running: touch /tmp/nxf.sdciXDBu53/GM24385_0001_RNA_0001_23H5VFLT4_s08.chckpts/introns_filtered.ok
08:30:56 : INFO : -found 2401 cancer introns
08:30:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GM24385_0001_RNA_0001_23H5VFLT4_s08.introns --cancer_introns GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed GM24385_0001_RNA_0001_23H5VFLT4_s08.introns.for_IGV.bed
08:30:57 : INFO : Creating the BED File.
08:31:06 : INFO : Saving Bed File as GM24385_0001_RNA_0001_23H5VFLT4_s08.introns.for_IGV.bed
08:31:06 : INFO : Execution Time = 0.17 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns GM24385_0001_RNA_0001_23H5VFLT4_s08.introns --cancer_introns GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed GM24385_0001_RNA_0001_23H5VFLT4_s08.introns.for_IGV.bed
08:31:06 : INFO : Running: touch /tmp/nxf.sdciXDBu53/GM24385_0001_RNA_0001_23H5VFLT4_s08.chckpts/intron_igv_bed.ok
08:31:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed GM24385_0001_RNA_0001_23H5VFLT4_s08.introns.for_IGV.bed --bam GM24385_0001_RNA_0001_23H5VFLT4_s08.Aligned.sortedByCoord.out.bam --output_prefix GM24385_0001_RNA_0001_23H5VFLT4_s08
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s08.Aligned.sortedByCoord.out.bam.bai
08:48:16 : INFO : Execution Time = 17.16 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed GM24385_0001_RNA_0001_23H5VFLT4_s08.introns.for_IGV.bed --bam GM24385_0001_RNA_0001_23H5VFLT4_s08.Aligned.sortedByCoord.out.bam --output_prefix GM24385_0001_RNA_0001_23H5VFLT4_s08
08:48:16 : INFO : Running: touch /tmp/nxf.sdciXDBu53/GM24385_0001_RNA_0001_23H5VFLT4_s08.chckpts/reads_alignments_extracted.ok
08:48:16 : INFO : Running: samtools sort -o GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer_intron_reads.sorted.bam GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer_intron_reads.bam
08:48:17 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer_intron_reads.sorted.bam GM24385_0001_RNA_0001_23H5VFLT4_s08.cancer_intron_reads.bam
08:48:17 : INFO : Running: touch /tmp/nxf.sdciXDBu53/GM24385_0001_RNA_0001_23H5VFLT4_s08.chckpts/sort_cancer_intron_reads.ok
08:48:17 : INFO : Running: samtools sort -o GM24385_0001_RNA_0001_23H5VFLT4_s08.gene_reads.sorted.bam GM24385_0001_RNA_0001_23H5VFLT4_s08.gene_reads.bam