Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/89fb22de8f94be92b005bb24ba0edd/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
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/75/eec97f8d113f13c1d183272c627bfc/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/fb5814cff6051034a00d74cb649e6a/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/fb5814cff6051034a00d74cb649e6a/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/75/eec97f8d113f13c1d183272c627bfc/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/fb5814cff6051034a00d74cb649e6a/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
08:56:14 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10240000], rate=19200000.00/min 08:56:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bst_02_A23WKFTLT4_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.
-BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns: identified 5507 cancer introns
08:56:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer.introns.prelim
08:56:55 : INFO : Running: touch /tmp/nxf.pkEWGiXSfu/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.chckpts/prelim_introns.ok
08:56:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer.introns
08:56:55 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer.introns.prelim --min_total_reads 5 > BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer.introns
08:56:55 : INFO : Running: touch /tmp/nxf.pkEWGiXSfu/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.chckpts/introns_filtered.ok
08:56:55 : INFO : -found 2306 cancer introns
08:56:55 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns --cancer_introns BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns.for_IGV.bed
08:56:55 : INFO : Creating the BED File.
08:57:00 : INFO : Saving Bed File as BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns.for_IGV.bed
08:57:00 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns --cancer_introns BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns.for_IGV.bed
08:57:00 : INFO : Running: touch /tmp/nxf.pkEWGiXSfu/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.chckpts/intron_igv_bed.ok
08:57:00 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
09:14:32 : INFO : Execution Time = 17.54 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.introns.for_IGV.bed --bam BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam --output_prefix BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2
09:14:32 : INFO : Running: touch /tmp/nxf.pkEWGiXSfu/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.chckpts/reads_alignments_extracted.ok
09:14:32 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer_intron_reads.bam
09:14:33 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer_intron_reads.sorted.bam BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.cancer_intron_reads.bam
09:14:33 : INFO : Running: touch /tmp/nxf.pkEWGiXSfu/BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.chckpts/sort_cancer_intron_reads.ok
09:14:33 : INFO : Running: samtools sort -o BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.gene_reads.sorted.bam BVT_FFPE_TRNA_bst_02_A23WKFTLT4_2.gene_reads.bam