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/1c/fbd47ca03d3954c38ebe8a47e9d9d6/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/984829ebb021881c81a4223711d2d8/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/984829ebb021881c81a4223711d2d8/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.SJ.out.tab
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/f12d139fb5465a6cc62f76ecb9ab57/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/fbd47ca03d3954c38ebe8a47e9d9d6/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/984829ebb021881c81a4223711d2d8/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (7 inputs)
09:08:13 : INFO : -reading targets list: ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-mapping reads to genes
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[10410000], rate=11566666.67/min
[10420000], rate=11577777.78/min
[10430000], rate=11588888.89/min
[10440000], rate=11389090.91/min
[10450000], rate=11400000.00/min
[10460000], rate=11410909.09/min
[10470000], rate=11421818.18/min
[10480000], rate=11432727.27/min
[10490000], rate=11443636.36/min
[10500000], rate=11454545.45/min
[10510000], rate=11465454.55/min
[10520000], rate=11476363.64/min
[10530000], rate=11487272.73/min
[10540000], rate=11498181.82/min
[10550000], rate=11509090.91/min
[10560000], rate=11520000.00/min
[10570000], rate=11530909.09/min 09:09:18 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-f71b32-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-f71b32-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-f71b32-R1_B23WHYVLT4_1.introns: identified 7980 cancer introns
09:09:19 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-f71b32-R1_B23WHYVLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer.introns.prelim
09:09:19 : INFO : Running: touch /tmp/nxf.NCQkMRVSCm/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.chckpts/prelim_introns.ok
09:09:19 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer.introns
09:09:20 : 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-f71b32-R1_B23WHYVLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer.introns
09:09:20 : INFO : Running: touch /tmp/nxf.NCQkMRVSCm/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.chckpts/introns_filtered.ok
09:09:20 : INFO : -found 3820 cancer introns
09:09:20 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-f71b32-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-f71b32-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:09:20 : INFO : Creating the BED File.
09:09:34 : INFO : Saving Bed File as aih-tih-sc-f71b32-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:09:34 : INFO : Execution Time = 0.24 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-f71b32-R1_B23WHYVLT4_1.introns --cancer_introns aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-f71b32-R1_B23WHYVLT4_1.introns.for_IGV.bed
09:09:34 : INFO : Running: touch /tmp/nxf.NCQkMRVSCm/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.chckpts/intron_igv_bed.ok
09:09:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-f71b32-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-f71b32-R1_B23WHYVLT4_1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
09:40:48 : INFO : Execution Time = 31.22 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-f71b32-R1_B23WHYVLT4_1.introns.for_IGV.bed --bam aih-tih-sc-f71b32-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-f71b32-R1_B23WHYVLT4_1
09:40:48 : INFO : Running: touch /tmp/nxf.NCQkMRVSCm/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.chckpts/reads_alignments_extracted.ok
09:40:48 : INFO : Running: samtools sort -o aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer_intron_reads.bam
09:40:49 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-f71b32-R1_B23WHYVLT4_1.cancer_intron_reads.bam
09:40:49 : INFO : Running: touch /tmp/nxf.NCQkMRVSCm/aih-tih-sc-f71b32-R1_B23WHYVLT4_1.chckpts/sort_cancer_intron_reads.ok
09:40:49 : INFO : Running: samtools sort -o aih-tih-sc-f71b32-R1_B23WHYVLT4_1.gene_reads.sorted.bam aih-tih-sc-f71b32-R1_B23WHYVLT4_1.gene_reads.bam