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/d8/7a4937ae3b06d3c886525c75e06ef9/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/08e79a31961c6496a3da353d388b5c/659_cVw-T1-TRNA-1_A23MVY2LT4_2.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/08e79a31961c6496a3da353d388b5c/659_cVw-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/55d645b0c751ebe6c8621c66ec73d8/659_cVw-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d8/7a4937ae3b06d3c886525c75e06ef9/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/08e79a31961c6496a3da353d388b5c/659_cVw-T1-TRNA-1_A23MVY2LT4_2.SJ.out.tab
==> STAGING COMPLETE (7 inputs)
09:27:16 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10470000], rate=11852830.19/min
[10480000], rate=11864150.94/min
[10490000], rate=11655555.56/min
[10500000], rate=11666666.67/min
[10510000], rate=11677777.78/min
[10520000], rate=11688888.89/min
[10530000], rate=11700000.00/min
[10540000], rate=11711111.11/min
[10550000], rate=11722222.22/min 09:28:23 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_cVw-T1-TRNA-1_A23MVY2LT4_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.
-659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns: identified 7252 cancer introns
09:28:24 : INFO : Execution Time = 0.02 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer.introns.prelim
09:28:24 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/prelim_introns.ok
09:28:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer.introns.prelim --min_total_reads 5 > 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer.introns
09:28:25 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer.introns.prelim --min_total_reads 5 > 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer.introns
09:28:25 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/introns_filtered.ok
09:28:25 : INFO : -found 3712 cancer introns
09:28:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns --cancer_introns 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed
09:28:25 : INFO : Creating the BED File.
09:28:36 : INFO : Saving Bed File as 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed
09:28:37 : INFO : Execution Time = 0.20 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns --cancer_introns 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed
09:28:37 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/intron_igv_bed.ok
09:28:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed --bam 659_cVw-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam --output_prefix 659_cVw-T1-TRNA-1_A23MVY2LT4_2
[W::hts_idx_load3] The index file is older than the data file: 659_cVw-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam.bai
10:02:02 : INFO : Execution Time = 33.41 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed --bam 659_cVw-T1-TRNA-1_A23MVY2LT4_2.Aligned.sortedByCoord.out.bam --output_prefix 659_cVw-T1-TRNA-1_A23MVY2LT4_2
10:02:02 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/reads_alignments_extracted.ok
10:02:02 : INFO : Running: samtools sort -o 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.bam
10:02:02 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.bam
10:02:02 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/sort_cancer_intron_reads.ok
10:02:02 : INFO : Running: samtools sort -o 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.bam 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.bam
[bam_sort_core] merging from 133 files and 1 in-memory blocks...
10:30:48 : INFO : Execution Time = 28.77 minutes. CMD: samtools sort -o 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.bam 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.bam
10:30:48 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/sort_gene_reads.ok
10:30:48 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_cVw-T1-TRNA-1_A23MVY2LT4_2.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 chr13.
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.
10:39:43 : INFO : Execution Time = 8.92 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.bam
10:39:43 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp.ok
10:39:43 : INFO : Running: samtools sort -o 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 4 files and 1 in-memory blocks...
10:40:45 : INFO : Execution Time = 1.03 minutes. CMD: samtools sort -o 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmp
10:40:45 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:40:45 : INFO : Running: samtools index 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam
10:40:52 : INFO : Execution Time = 0.12 minutes. CMD: samtools index 659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam
10:40:52 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/659_cVw-T1-TRNA-1_A23MVY2LT4_2.gene_reads.sorted.sifted.bam.indexed.ok
10:40:52 : INFO : Running: samtools index 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam
10:40:52 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam
10:40:52 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/659_cVw-T1-TRNA-1_A23MVY2LT4_2.cancer_intron_reads.sorted.bam.indexed.ok
10:40:52 : INFO : Running: create_report 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_cVw-T1-TRNA-1_A23MVY2LT4_2.ctat-splicing.igv.html --track-config 659_cVw-T1-TRNA-1_A23MVY2LT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_cVw-T1-TRNA-1_A23MVY2LT4_2'
[W::hts_idx_load3] The index file is older than the data file: ctat_genome_lib_build_dir/refGene.sort.bed.gz.tbi
10:47:40 : INFO : Execution Time = 6.79 minutes. CMD: create_report 659_cVw-T1-TRNA-1_A23MVY2LT4_2.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_cVw-T1-TRNA-1_A23MVY2LT4_2.ctat-splicing.igv.html --track-config 659_cVw-T1-TRNA-1_A23MVY2LT4_2.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_cVw-T1-TRNA-1_A23MVY2LT4_2'
10:47:40 : INFO : Running: touch /tmp/nxf.gSBGULuPRz/659_cVw-T1-TRNA-1_A23MVY2LT4_2.chckpts/igv_create_html.ok
10:47:40 : INFO : done.