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/6b/b4ff53be08c84848e21dddcdf5cfec/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/f198a43e0b3b36a809705502818a7f/659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/b4ff53be08c84848e21dddcdf5cfec/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/4472770aae09656741932a093fa6a1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/4472770aae09656741932a093fa6a1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/4472770aae09656741932a093fa6a1/659_bhK-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
09:30:21 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[7580000], rate=12291891.89/min 09:31:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bhK-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_bhK-T1-TRNA-1_B23WHTKLT4_1.introns: identified 4396 cancer introns
09:31:06 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim
09:31:06 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/prelim_introns.ok
09:31:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
09:31:06 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer.introns
09:31:06 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/introns_filtered.ok
09:31:06 : INFO : -found 2426 cancer introns
09:31:06 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
09:31:06 : INFO : Creating the BED File.
09:31:12 : INFO : Saving Bed File as 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
09:31:12 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns --cancer_introns 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed
09:31:12 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/intron_igv_bed.ok
09:31:12 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bhK-T1-TRNA-1_B23WHTKLT4_1
[W::hts_idx_load3] The index file is older than the data file: 659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
09:52:36 : INFO : Execution Time = 21.40 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed --bam 659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_bhK-T1-TRNA-1_B23WHTKLT4_1
09:52:36 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok
09:52:36 : INFO : Running: samtools sort -o 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
09:52:37 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.bam
09:52:37 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok
09:52:37 : INFO : Running: samtools sort -o 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
[bam_sort_core] merging from 100 files and 1 in-memory blocks...
10:15:10 : INFO : Execution Time = 22.56 minutes. CMD: samtools sort -o 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.bam
10:15:10 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/sort_gene_reads.ok
10:15:10 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bhK-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 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.
10:21:55 : INFO : Execution Time = 6.74 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.bam
10:21:55 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
10:21:55 : INFO : Running: samtools sort -o 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 3 files and 1 in-memory blocks...
10:22:41 : INFO : Execution Time = 0.78 minutes. CMD: samtools sort -o 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmp
10:22:41 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
10:22:41 : INFO : Running: samtools index 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
10:22:47 : INFO : Execution Time = 0.09 minutes. CMD: samtools index 659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam
10:22:47 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bhK-T1-TRNA-1_B23WHTKLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
10:22:47 : INFO : Running: samtools index 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
10:22:47 : INFO : Execution Time = 0.00 minutes. CMD: samtools index 659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam
10:22:47 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/659_bhK-T1-TRNA-1_B23WHTKLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
10:22:47 : INFO : Running: create_report 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bhK-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bhK-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bhK-T1-TRNA-1_B23WHTKLT4_1'
10:28:27 : INFO : Execution Time = 5.68 minutes. CMD: create_report 659_bhK-T1-TRNA-1_B23WHTKLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output 659_bhK-T1-TRNA-1_B23WHTKLT4_1.ctat-splicing.igv.html --track-config 659_bhK-T1-TRNA-1_B23WHTKLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: 659_bhK-T1-TRNA-1_B23WHTKLT4_1'
10:28:27 : INFO : Running: touch /tmp/nxf.KiV5Ey6ZtI/659_bhK-T1-TRNA-1_B23WHTKLT4_1.chckpts/igv_create_html.ok
10:28:27 : INFO : done.