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/77/77fc4edf04e6cc6629b3f63459e769/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/3e0f2c1075fcc3461bfa06b5cedf62/aih-tih-sc-9e2647-R1_A23YTGFLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/3e0f2c1075fcc3461bfa06b5cedf62/aih-tih-sc-9e2647-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/77fc4edf04e6cc6629b3f63459e769/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/3e0f2c1075fcc3461bfa06b5cedf62/aih-tih-sc-9e2647-R1_A23YTGFLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/635af52174aff8d04d07833580fc77/aih-tih-sc-9e2647-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai ==> STAGING COMPLETE (7 inputs) 08:54:52 : INFO 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[7840000], rate=14254545.45/min [7850000], rate=14272727.27/min [7860000], rate=14290909.09/min [7870000], rate=14309090.91/min [7880000], rate=14327272.73/min [7890000], rate=14345454.55/min [7900000], rate=14363636.36/min [7910000], rate=14381818.18/min [7920000], rate=14400000.00/min [7930000], rate=14418181.82/min [7940000], rate=14436363.64/min [7950000], rate=14454545.45/min [7960000], rate=14472727.27/min [7970000], rate=14490909.09/min [7980000], rate=14509090.91/min [7990000], rate=14527272.73/min [8000000], rate=14545454.55/min [8010000], rate=14563636.36/min [8020000], rate=14581818.18/min [8030000], rate=14600000.00/min [8040000], rate=14618181.82/min [8050000], rate=14636363.64/min [8060000], rate=14654545.45/min [8070000], rate=14241176.47/min [8080000], rate=14258823.53/min [8090000], rate=14276470.59/min [8100000], rate=14294117.65/min [8110000], rate=14311764.71/min [8120000], rate=14329411.76/min [8130000], rate=14347058.82/min [8140000], rate=14364705.88/min [8150000], rate=14382352.94/min [8160000], rate=14400000.00/min [8170000], rate=14417647.06/min [8180000], rate=14435294.12/min [8190000], rate=14452941.18/min [8200000], rate=14470588.24/min [8210000], rate=14488235.29/min [8220000], rate=14505882.35/min [8230000], rate=14523529.41/min [8240000], rate=14541176.47/min [8250000], rate=14558823.53/min [8260000], rate=14576470.59/min [8270000], rate=14594117.65/min [8280000], rate=14611764.71/min [8290000], rate=14629411.76/min [8300000], rate=14647058.82/min [8310000], rate=14664705.88/min [8320000], rate=14682352.94/min [8330000], rate=14700000.00/min [8340000], rate=14717647.06/min [8350000], rate=14735294.12/min [8360000], rate=14331428.57/min [8370000], rate=14348571.43/min [8380000], rate=14365714.29/min [8390000], rate=14382857.14/min [8400000], rate=14400000.00/min [8410000], rate=14417142.86/min [8420000], rate=14434285.71/min [8430000], rate=14451428.57/min [8440000], rate=14468571.43/min [8450000], rate=14485714.29/min [8460000], rate=14502857.14/min [8470000], rate=14520000.00/min [8480000], rate=14537142.86/min [8490000], rate=14554285.71/min [8500000], rate=14571428.57/min [8510000], rate=14588571.43/min [8520000], rate=14605714.29/min [8530000], rate=14622857.14/min [8540000], rate=14640000.00/min [8550000], rate=14657142.86/min [8560000], rate=14674285.71/min [8570000], rate=14691428.57/min [8580000], rate=14708571.43/min [8590000], rate=14725714.29/min [8600000], rate=14742857.14/min [8610000], rate=14760000.00/min 08:55:36 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-9e2647-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-9e2647-R1_A23YTGFLT4_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-9e2647-R1_A23YTGFLT4_1.introns: identified 7224 cancer introns 08:55:37 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file aih-tih-sc-9e2647-R1_A23YTGFLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer.introns.prelim 08:55:37 : INFO : Running: touch /tmp/nxf.JlZxkvHhKW/aih-tih-sc-9e2647-R1_A23YTGFLT4_1.chckpts/prelim_introns.ok 08:55:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer.introns 08:55:37 : 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-9e2647-R1_A23YTGFLT4_1.cancer.introns.prelim --min_total_reads 5 > aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer.introns 08:55:37 : INFO : Running: touch /tmp/nxf.JlZxkvHhKW/aih-tih-sc-9e2647-R1_A23YTGFLT4_1.chckpts/introns_filtered.ok 08:55:37 : INFO : -found 2926 cancer introns 08:55:37 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-9e2647-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-9e2647-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:55:38 : INFO : Creating the BED File. 08:55:44 : INFO : Saving Bed File as aih-tih-sc-9e2647-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:55:44 : INFO : Execution Time = 0.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns aih-tih-sc-9e2647-R1_A23YTGFLT4_1.introns --cancer_introns aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed aih-tih-sc-9e2647-R1_A23YTGFLT4_1.introns.for_IGV.bed 08:55:44 : INFO : Running: touch /tmp/nxf.JlZxkvHhKW/aih-tih-sc-9e2647-R1_A23YTGFLT4_1.chckpts/intron_igv_bed.ok 08:55:44 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-9e2647-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-9e2647-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-9e2647-R1_A23YTGFLT4_1 [W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-9e2647-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai 09:19:28 : INFO : Execution Time = 23.73 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed aih-tih-sc-9e2647-R1_A23YTGFLT4_1.introns.for_IGV.bed --bam aih-tih-sc-9e2647-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --output_prefix aih-tih-sc-9e2647-R1_A23YTGFLT4_1 09:19:28 : INFO : Running: touch /tmp/nxf.JlZxkvHhKW/aih-tih-sc-9e2647-R1_A23YTGFLT4_1.chckpts/reads_alignments_extracted.ok 09:19:28 : INFO : Running: samtools sort -o aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:19:29 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer_intron_reads.sorted.bam aih-tih-sc-9e2647-R1_A23YTGFLT4_1.cancer_intron_reads.bam 09:19:29 : INFO : Running: touch /tmp/nxf.JlZxkvHhKW/aih-tih-sc-9e2647-R1_A23YTGFLT4_1.chckpts/sort_cancer_intron_reads.ok 09:19:29 : INFO : Running: samtools sort -o aih-tih-sc-9e2647-R1_A23YTGFLT4_1.gene_reads.sorted.bam aih-tih-sc-9e2647-R1_A23YTGFLT4_1.gene_reads.bam