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/c1/3e34abccd85a52eb9095a499b1e1fa/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/f3cd8145eac896f42d606440633efa/tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/f3cd8145eac896f42d606440633efa/tih_rna_sample_00146_B23WHTKLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/cfbc4ab5b2a73c739a299563ce9dcb/tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/3e34abccd85a52eb9095a499b1e1fa/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2d/f3cd8145eac896f42d606440633efa/tih_rna_sample_00146_B23WHTKLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (7 inputs) 08:50:35 : INFO 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rate=10660465.12/min [7650000], rate=10674418.60/min [7660000], rate=10688372.09/min [7670000], rate=10702325.58/min [7680000], rate=10716279.07/min [7690000], rate=10730232.56/min [7700000], rate=10500000.00/min [7710000], rate=10513636.36/min [7720000], rate=10527272.73/min [7730000], rate=10540909.09/min [7740000], rate=10554545.45/min [7750000], rate=10568181.82/min [7760000], rate=10581818.18/min [7770000], rate=10595454.55/min [7780000], rate=10609090.91/min [7790000], rate=10622727.27/min [7800000], rate=10636363.64/min [7810000], rate=10650000.00/min [7820000], rate=10663636.36/min [7830000], rate=10677272.73/min [7840000], rate=10690909.09/min [7850000], rate=10704545.45/min [7860000], rate=10718181.82/min [7870000], rate=10731818.18/min [7880000], rate=10506666.67/min [7890000], rate=10520000.00/min [7900000], rate=10533333.33/min [7910000], rate=10546666.67/min [7920000], rate=10560000.00/min [7930000], rate=10573333.33/min [7940000], rate=10586666.67/min [7950000], rate=10600000.00/min [7960000], rate=10613333.33/min [7970000], rate=10626666.67/min [7980000], rate=10640000.00/min [7990000], rate=10653333.33/min [8000000], rate=10666666.67/min [8010000], rate=10680000.00/min [8020000], rate=10693333.33/min [8030000], rate=10706666.67/min [8040000], rate=10720000.00/min [8050000], rate=10733333.33/min [8060000], rate=10746666.67/min [8070000], rate=10760000.00/min [8080000], rate=10773333.33/min [8090000], rate=10786666.67/min [8100000], rate=10800000.00/min [8110000], rate=10813333.33/min [8120000], rate=10826666.67/min [8130000], rate=10604347.83/min [8140000], rate=10617391.30/min [8150000], rate=10630434.78/min [8160000], rate=10643478.26/min [8170000], rate=10656521.74/min [8180000], rate=10669565.22/min [8190000], rate=10682608.70/min [8200000], rate=10695652.17/min [8210000], rate=10708695.65/min [8220000], rate=10721739.13/min [8230000], rate=10734782.61/min [8240000], rate=10747826.09/min [8250000], rate=10760869.57/min [8260000], rate=10773913.04/min [8270000], rate=10786956.52/min [8280000], rate=10800000.00/min [8290000], rate=10813043.48/min [8300000], rate=10826086.96/min [8310000], rate=10839130.43/min [8320000], rate=10852173.91/min [8330000], rate=10865217.39/min [8340000], rate=10878260.87/min [8350000], rate=10891304.35/min [8360000], rate=10904347.83/min [8370000], rate=10685106.38/min [8380000], rate=10697872.34/min [8390000], rate=10710638.30/min [8400000], rate=10723404.26/min [8410000], rate=10736170.21/min [8420000], rate=10748936.17/min [8430000], rate=10761702.13/min [8440000], rate=10774468.09/min [8450000], rate=10787234.04/min [8460000], rate=10800000.00/min [8470000], rate=10812765.96/min [8480000], rate=10825531.91/min [8490000], rate=10838297.87/min [8500000], rate=10851063.83/min [8510000], rate=10863829.79/min [8520000], rate=10876595.74/min 08:51:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00146_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00146_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. -tih_rna_sample_00146_B23WHTKLT4_1.introns: identified 6528 cancer introns 08:51:35 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00146_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns.prelim 08:51:35 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/prelim_introns.ok 08:51:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns 08:51:35 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns 08:51:35 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/introns_filtered.ok 08:51:35 : INFO : -found 3336 cancer introns 08:51:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00146_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed 08:51:36 : INFO : Creating the BED File. 08:51:53 : INFO : Saving Bed File as tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed 08:51:54 : INFO : Execution Time = 0.30 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00146_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00146_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed 08:51:54 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/intron_igv_bed.ok 08:51:54 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00146_B23WHTKLT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai 09:18:43 : INFO : Execution Time = 26.82 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00146_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00146_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00146_B23WHTKLT4_1 09:18:43 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok 09:18:43 : INFO : Running: samtools sort -o tih_rna_sample_00146_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00146_B23WHTKLT4_1.cancer_intron_reads.bam 09:18:44 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o tih_rna_sample_00146_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00146_B23WHTKLT4_1.cancer_intron_reads.bam 09:18:44 : INFO : Running: touch /tmp/nxf.hcAwnpJQDw/tih_rna_sample_00146_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok 09:18:44 : INFO : Running: samtools sort -o tih_rna_sample_00146_B23WHTKLT4_1.gene_reads.sorted.bam tih_rna_sample_00146_B23WHTKLT4_1.gene_reads.bam