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/d0/19a00aebadf03571ba2a54299ad912/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/d4e748c570fc5361d6ed1cefa6a876/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/d4e748c570fc5361d6ed1cefa6a876/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/d4e748c570fc5361d6ed1cefa6a876/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/9b48733af574286d2a86e053507593/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/19a00aebadf03571ba2a54299ad912/.command.run
==> STAGING COMPLETE (7 inputs)
08:03:44 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[5150000], rate=14714285.71/min 08:04:13 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-2f84cc-R1_B23WHYVLT4_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.
-aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns: identified 2781 cancer introns
08:04:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns.prelim
08:04:14 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok
08:04:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns
08:04:14 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns
08:04:14 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok
08:04:14 : INFO : -found 844 cancer introns
08:04:14 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed
08:04:15 : INFO : Creating the BED File.
08:04:18 : INFO : Saving Bed File as aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed
08:04:18 : INFO : Execution Time = 0.07 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed
08:04:18 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok
08:04:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-2f84cc-R1_B23WHYVLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
08:11:05 : INFO : Execution Time = 6.78 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-2f84cc-R1_B23WHYVLT4_1
08:11:05 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/reads_alignments_extracted.ok
08:11:05 : INFO : Running: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.bam
08:11:06 : INFO : Execution Time = 0.00 minutes. CMD: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.bam
08:11:06 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/sort_cancer_intron_reads.ok
08:11:06 : INFO : Running: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.bam
[bam_sort_core] merging from 28 files and 1 in-memory blocks...
08:17:56 : INFO : Execution Time = 6.83 minutes. CMD: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.bam
08:17:56 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/sort_gene_reads.ok
08:17:56 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-2f84cc-R1_B23WHYVLT4_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.
Done with chr chrX.
08:19:49 : INFO : Execution Time = 1.90 minutes. CMD: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.bam
08:19:49 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp.ok
08:19:49 : INFO : Running: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp
[bam_sort_core] merging from 1 files and 1 in-memory blocks...
08:20:15 : INFO : Execution Time = 0.43 minutes. CMD: samtools sort -o aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmp
08:20:15 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.tmpsorted.ok
08:20:15 : INFO : Running: samtools index aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam
08:20:18 : INFO : Execution Time = 0.05 minutes. CMD: samtools index aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam
08:20:18 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.gene_reads.sorted.sifted.bam.indexed.ok
08:20:19 : INFO : Running: samtools index aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam
08:20:19 : INFO : Execution Time = 0.00 minutes. CMD: samtools index aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam
08:20:19 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam.indexed.ok
08:20:19 : INFO : Running: create_report aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-2f84cc-R1_B23WHYVLT4_1'
08:24:22 : INFO : Execution Time = 4.05 minutes. CMD: create_report aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.introns.for_IGV.bed ctat_genome_lib_build_dir/ref_genome.fa --type junction --output aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.ctat-splicing.igv.html --track-config aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.igv.tracks --info-columns gene variant_name uniquely_mapped multi_mapped TCGA GTEx --title 'CTAT_Splicing: aih-tih-sc-2f84cc-R1_B23WHYVLT4_1'
08:24:22 : INFO : Running: touch /tmp/nxf.63OikFTsy7/aih-tih-sc-2f84cc-R1_B23WHYVLT4_1.chckpts/igv_create_html.ok
08:24:22 : INFO : done.