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/2f/aa62550f2a5c8714e8bc286cd11eef/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1d/5d86c571d8d65606cf6effcf4c5a87/659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/905f81b694194f2e4c2cae1840a5a2/659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/905f81b694194f2e4c2cae1840a5a2/659_bCu-T1-TRNA-1_B23WHTKLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/905f81b694194f2e4c2cae1840a5a2/659_bCu-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2f/aa62550f2a5c8714e8bc286cd11eef/.command.run
==> STAGING COMPLETE (7 inputs)
07:47:52 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[2710000], rate=14781818.18/min 07:48:09 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bCu-T1-TRNA-1_B23WHTKLT4_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_bCu-T1-TRNA-1_B23WHTKLT4_1.introns: identified 441 cancer introns
07:48:10 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim
07:48:10 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/prelim_introns.ok
07:48:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
07:48:10 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
07:48:10 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/introns_filtered.ok
07:48:10 : INFO : -found 330 cancer introns
07:48:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
07:48:11 : INFO : Creating the BED File.
07:48:13 : INFO : Saving Bed File as 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
07:48:14 : INFO : Execution Time = 0.05 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
07:48:14 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
07:48:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bCu-T1-TRNA-1_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
07:49:49 : INFO : Execution Time = 1.59 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bCu-T1-TRNA-1_B23WHTKLT4_1
07:49:49 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
07:49:49 : INFO : Running: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
07:49:49 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
07:49:49 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
07:49:49 : INFO : Running: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
07:51:26 : INFO : Execution Time = 1.61 minutes. CMD: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
07:51:26 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_gene_reads.ok
07:51:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
Done with chr chr1.
Done with chr chr2.
Done with chr chr3.
Done with chr chr4.
Done with chr chr5.
Done with chr chr6.
Done with chr chr7.
Done with chr chr8.
Done with chr chr9.
Done with chr chr10.
Done with chr chr11.
Done with chr chr12.
Done with chr chr14.
Done with chr chr15.
Done with chr chr16.
Done with chr chr17.
Done with chr chr18.
Done with chr chr19.
Done with chr chr20.
Done with chr chr21.
Done with chr chr22.
07:51:49 : INFO : Execution Time = 0.38 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
07:51:49 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
07:51:49 : INFO : Running: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
07:51:54 : INFO : Execution Time = 0.08 minutes. CMD: samtools sort -o 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
07:51:54 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
07:51:54 : INFO : Running: samtools index 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
07:51:55 : INFO : Execution Time = 0.01 minutes. CMD: samtools index 659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
07:51:55 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bCu-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
07:51:55 : INFO : Running: samtools index 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
07:51:55 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
07:51:55 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bCu-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
07:51:55 : INFO : Running: create_report 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bCu-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bCu-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bCu-T1-TRNA-1_B23WHTKLT4_1'
07:52:37 : INFO : Execution Time = 0.70 minutes. CMD: create_report 659_bCu-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bCu-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bCu-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bCu-T1-TRNA-1_B23WHTKLT4_1'
07:52:37 : INFO : Running: touch /tmp/nxf.vUxCfw0RVo/659_bCu-T1-TRNA-1_B23WHTKLT4_1.chckpts/igv_create_html.ok
07:52:37 : INFO : done.