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/44/e2e49bfb5f4c3f9b981622bdc560df/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/1051b486b3fb2daaa4f58d1089fc7b/659_djb-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/2f39465ad3e48726375341986ef9c6/659_djb-T1-TRNA-1_B23MHV2LT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/2f39465ad3e48726375341986ef9c6/659_djb-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/e2e49bfb5f4c3f9b981622bdc560df/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/2f39465ad3e48726375341986ef9c6/659_djb-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction ==> STAGING COMPLETE (7 inputs) 08:38:24 : INFO : -reading 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rate=11431578.95/min [7250000], rate=11447368.42/min [7260000], rate=11463157.89/min [7270000], rate=11478947.37/min [7280000], rate=11494736.84/min [7290000], rate=11510526.32/min [7300000], rate=11526315.79/min [7310000], rate=11542105.26/min [7320000], rate=11557894.74/min [7330000], rate=11573684.21/min [7340000], rate=11589473.68/min [7350000], rate=11605263.16/min [7360000], rate=11323076.92/min [7370000], rate=11338461.54/min [7380000], rate=11353846.15/min [7390000], rate=11369230.77/min [7400000], rate=11384615.38/min [7410000], rate=11400000.00/min [7420000], rate=11415384.62/min [7430000], rate=11430769.23/min [7440000], rate=11446153.85/min [7450000], rate=11461538.46/min [7460000], rate=11476923.08/min [7470000], rate=11492307.69/min [7480000], rate=11507692.31/min [7490000], rate=11523076.92/min [7500000], rate=11538461.54/min [7510000], rate=11553846.15/min [7520000], rate=11569230.77/min [7530000], rate=11584615.38/min [7540000], rate=11600000.00/min [7550000], rate=11325000.00/min [7560000], rate=11340000.00/min [7570000], rate=11355000.00/min [7580000], rate=11370000.00/min [7590000], rate=11385000.00/min [7600000], rate=11400000.00/min [7610000], rate=11415000.00/min [7620000], rate=11430000.00/min [7630000], rate=11445000.00/min [7640000], rate=11460000.00/min [7650000], rate=11475000.00/min [7660000], rate=11490000.00/min [7670000], rate=11505000.00/min [7680000], rate=11520000.00/min [7690000], rate=11535000.00/min [7700000], rate=11550000.00/min [7710000], rate=11565000.00/min [7720000], rate=11297560.98/min [7730000], rate=11312195.12/min [7740000], rate=11326829.27/min [7750000], rate=11341463.41/min [7760000], rate=11356097.56/min [7770000], rate=11370731.71/min [7780000], rate=11385365.85/min [7790000], rate=11400000.00/min [7800000], rate=11414634.15/min [7810000], rate=11429268.29/min [7820000], rate=11443902.44/min [7830000], rate=11458536.59/min [7840000], rate=11473170.73/min [7850000], rate=11487804.88/min [7860000], rate=11502439.02/min [7870000], rate=11517073.17/min [7880000], rate=11531707.32/min [7890000], rate=11546341.46/min [7900000], rate=11560975.61/min [7910000], rate=11575609.76/min [7920000], rate=11590243.90/min [7930000], rate=11604878.05/min [7940000], rate=11342857.14/min [7950000], rate=11357142.86/min [7960000], rate=11371428.57/min [7970000], rate=11385714.29/min [7980000], rate=11400000.00/min [7990000], rate=11414285.71/min [8000000], rate=11428571.43/min [8010000], rate=11442857.14/min [8020000], rate=11457142.86/min [8030000], rate=11471428.57/min [8040000], rate=11485714.29/min [8050000], rate=11500000.00/min [8060000], rate=11514285.71/min [8070000], rate=11528571.43/min [8080000], rate=11542857.14/min 08:39:15 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_djb-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_djb-T1-TRNA-1_B23MHV2LT4_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_djb-T1-TRNA-1_B23MHV2LT4_1.introns: identified 5761 cancer introns 08:39:16 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file 659_djb-T1-TRNA-1_B23MHV2LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim 08:39:16 : INFO : Running: touch /tmp/nxf.9CUlqvljP0/659_djb-T1-TRNA-1_B23MHV2LT4_1.chckpts/prelim_introns.ok 08:39:16 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:39:17 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer.introns.prelim --min_total_reads 5 > 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer.introns 08:39:17 : INFO : Running: touch /tmp/nxf.9CUlqvljP0/659_djb-T1-TRNA-1_B23MHV2LT4_1.chckpts/introns_filtered.ok 08:39:17 : INFO : -found 2356 cancer introns 08:39:17 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_djb-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_djb-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:39:17 : INFO : Creating the BED File. 08:39:24 : INFO : Saving Bed File as 659_djb-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:39:24 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns 659_djb-T1-TRNA-1_B23MHV2LT4_1.introns --cancer_introns 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed 659_djb-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed 08:39:24 : INFO : Running: touch /tmp/nxf.9CUlqvljP0/659_djb-T1-TRNA-1_B23MHV2LT4_1.chckpts/intron_igv_bed.ok 08:39:24 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_djb-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_djb-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_djb-T1-TRNA-1_B23MHV2LT4_1 [W::hts_idx_load3] The index file is older than the data file: 659_djb-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai 09:04:21 : INFO : Execution Time = 24.94 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed 659_djb-T1-TRNA-1_B23MHV2LT4_1.introns.for_IGV.bed --bam 659_djb-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --output_prefix 659_djb-T1-TRNA-1_B23MHV2LT4_1 09:04:21 : INFO : Running: touch /tmp/nxf.9CUlqvljP0/659_djb-T1-TRNA-1_B23MHV2LT4_1.chckpts/reads_alignments_extracted.ok 09:04:21 : INFO : Running: samtools sort -o 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:04:22 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.sorted.bam 659_djb-T1-TRNA-1_B23MHV2LT4_1.cancer_intron_reads.bam 09:04:22 : INFO : Running: touch /tmp/nxf.9CUlqvljP0/659_djb-T1-TRNA-1_B23MHV2LT4_1.chckpts/sort_cancer_intron_reads.ok 09:04:22 : INFO : Running: samtools sort -o 659_djb-T1-TRNA-1_B23MHV2LT4_1.gene_reads.sorted.bam 659_djb-T1-TRNA-1_B23MHV2LT4_1.gene_reads.bam