Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/a74f49ecbea6f0c2811763254a0353/659_Mt-T1-TRNA-1_B23MHV2LT4_1.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/20/070e8fb0d9f89e00ebaa9e0e7d095c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/91b9d2780652ac37d7c19e2b7cf63f/659_Mt-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/91b9d2780652ac37d7c19e2b7cf63f/659_Mt-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/91b9d2780652ac37d7c19e2b7cf63f/659_Mt-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/070e8fb0d9f89e00ebaa9e0e7d095c/.command.run
==> STAGING COMPLETE (7 inputs)
08:36:55 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[9050000], rate=11804347.83/min 08:37:50 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_Mt-T1-TRNA-1_B23MHV2LT4_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.
-659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns: identified 5533 cancer introns
08:37:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim
08:37:51 : INFO : Running: touch /tmp/nxf.4asoi1h8Y8/659_Mt-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok
08:37:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer.introns
08:37:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer.introns
08:37:51 : INFO : Running: touch /tmp/nxf.4asoi1h8Y8/659_Mt-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok
08:37:51 : INFO : -found 2082 cancer introns
08:37:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:37:52 : INFO : Creating the BED File.
08:37:59 : INFO : Saving Bed File as 659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:37:59 : INFO : Execution Time = 0.13 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed
08:37:59 : INFO : Running: touch /tmp/nxf.4asoi1h8Y8/659_Mt-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok
08:37:59 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_Mt-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_Mt-T1-TRNA-1_B23MHV2LT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_Mt-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
09:08:24 : INFO : Execution Time = 30.42 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_Mt-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_Mt-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_Mt-T1-TRNA-1_B23MHV2LT4_1
09:08:24 : INFO : Running: touch /tmp/nxf.4asoi1h8Y8/659_Mt-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok
09:08:24 : INFO : Running: samtools sort -o 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam
09:08:25 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_Mt-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam
09:08:25 : INFO : Running: touch /tmp/nxf.4asoi1h8Y8/659_Mt-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok
09:08:25 : INFO : Running: samtools sort -o 659_Mt-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_Mt-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam