Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/ddfcbb0693bc896de23657a14f3eb3/tih_rna_sample_00586_B23MVV7LT4_1.SJ.out.tab 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/4b/4aabdde5619ad56ca15175e9bdf31c/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/ddfcbb0693bc896de23657a14f3eb3/tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/8c295ff11ad8ede9fdedb3bbb32497/tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/4aabdde5619ad56ca15175e9bdf31c/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/ddfcbb0693bc896de23657a14f3eb3/tih_rna_sample_00586_B23MVV7LT4_1.Chimeric.out.junction ==> STAGING COMPLETE (7 inputs) 08:50:40 : INFO 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rate=13476923.08/min [5850000], rate=13000000.00/min [5860000], rate=13022222.22/min [5870000], rate=13044444.44/min [5880000], rate=13066666.67/min [5890000], rate=13088888.89/min [5900000], rate=13111111.11/min [5910000], rate=13133333.33/min [5920000], rate=13155555.56/min [5930000], rate=13177777.78/min [5940000], rate=13200000.00/min [5950000], rate=13222222.22/min [5960000], rate=13244444.44/min [5970000], rate=13266666.67/min [5980000], rate=13288888.89/min [5990000], rate=13311111.11/min [6000000], rate=13333333.33/min [6010000], rate=13355555.56/min [6020000], rate=12900000.00/min [6030000], rate=12921428.57/min [6040000], rate=12942857.14/min [6050000], rate=12964285.71/min [6060000], rate=12985714.29/min [6070000], rate=13007142.86/min [6080000], rate=13028571.43/min [6090000], rate=13050000.00/min [6100000], rate=13071428.57/min [6110000], rate=13092857.14/min [6120000], rate=13114285.71/min [6130000], rate=13135714.29/min [6140000], rate=13157142.86/min [6150000], rate=13178571.43/min [6160000], rate=13200000.00/min [6170000], rate=13221428.57/min [6180000], rate=12786206.90/min [6190000], rate=12806896.55/min [6200000], rate=12827586.21/min [6210000], rate=12848275.86/min [6220000], rate=12868965.52/min [6230000], rate=12889655.17/min [6240000], rate=12910344.83/min [6250000], rate=12931034.48/min [6260000], rate=12951724.14/min [6270000], rate=12972413.79/min [6280000], rate=12560000.00/min [6290000], rate=12580000.00/min [6300000], rate=12600000.00/min [6310000], rate=12620000.00/min [6320000], rate=12640000.00/min [6330000], rate=12660000.00/min [6340000], rate=12680000.00/min [6350000], rate=12700000.00/min [6360000], rate=12720000.00/min [6370000], rate=12740000.00/min [6380000], rate=12760000.00/min [6390000], rate=12780000.00/min [6400000], rate=12387096.77/min [6410000], rate=12406451.61/min [6420000], rate=12425806.45/min [6430000], rate=12445161.29/min [6440000], rate=12464516.13/min [6450000], rate=12483870.97/min [6460000], rate=12503225.81/min [6470000], rate=12522580.65/min [6480000], rate=12541935.48/min [6490000], rate=12561290.32/min [6500000], rate=12580645.16/min [6510000], rate=12600000.00/min [6520000], rate=12619354.84/min [6530000], rate=12638709.68/min [6540000], rate=12658064.52/min [6550000], rate=12677419.35/min [6560000], rate=12696774.19/min [6570000], rate=12716129.03/min [6580000], rate=12735483.87/min [6590000], rate=12754838.71/min [6600000], rate=12375000.00/min [6610000], rate=12393750.00/min [6620000], rate=12412500.00/min [6630000], rate=12431250.00/min [6640000], rate=12450000.00/min [6650000], rate=12468750.00/min [6660000], rate=12487500.00/min [6670000], rate=12506250.00/min [6680000], rate=12525000.00/min [6690000], rate=12543750.00/min [6700000], rate=12562500.00/min [6710000], rate=12581250.00/min [6720000], rate=12600000.00/min [6730000], rate=12618750.00/min [6740000], rate=12637500.00/min [6750000], rate=12656250.00/min [6760000], rate=12675000.00/min [6770000], rate=12693750.00/min [6780000], rate=12712500.00/min [6790000], rate=12731250.00/min [6800000], rate=12750000.00/min [6810000], rate=12768750.00/min [6820000], rate=12787500.00/min [6830000], rate=12806250.00/min [6840000], rate=12436363.64/min [6850000], rate=12454545.45/min [6860000], rate=12472727.27/min [6870000], rate=12490909.09/min [6880000], rate=12509090.91/min [6890000], rate=12527272.73/min [6900000], rate=12545454.55/min [6910000], rate=12563636.36/min [6920000], rate=12581818.18/min [6930000], rate=12600000.00/min [6940000], rate=12618181.82/min [6950000], rate=12636363.64/min [6960000], rate=12654545.45/min [6970000], rate=12672727.27/min [6980000], rate=12690909.09/min [6990000], rate=12709090.91/min [7000000], rate=12727272.73/min [7010000], rate=12745454.55/min [7020000], rate=12763636.36/min [7030000], rate=12781818.18/min 08:51:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00586_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00586_B23MVV7LT4_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_00586_B23MVV7LT4_1.introns: identified 6492 cancer introns 08:51:25 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00586_B23MVV7LT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00586_B23MVV7LT4_1.cancer.introns.prelim 08:51:25 : INFO : Running: touch /tmp/nxf.iGwb8oET7Y/tih_rna_sample_00586_B23MVV7LT4_1.chckpts/prelim_introns.ok 08:51:25 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00586_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00586_B23MVV7LT4_1.cancer.introns 08:51:26 : 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_00586_B23MVV7LT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00586_B23MVV7LT4_1.cancer.introns 08:51:26 : INFO : Running: touch /tmp/nxf.iGwb8oET7Y/tih_rna_sample_00586_B23MVV7LT4_1.chckpts/introns_filtered.ok 08:51:26 : INFO : -found 2375 cancer introns 08:51:26 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00586_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00586_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00586_B23MVV7LT4_1.introns.for_IGV.bed 08:51:27 : INFO : Creating the BED File. 08:51:37 : INFO : Saving Bed File as tih_rna_sample_00586_B23MVV7LT4_1.introns.for_IGV.bed 08:51:38 : INFO : Execution Time = 0.19 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00586_B23MVV7LT4_1.introns --cancer_introns tih_rna_sample_00586_B23MVV7LT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00586_B23MVV7LT4_1.introns.for_IGV.bed 08:51:38 : INFO : Running: touch /tmp/nxf.iGwb8oET7Y/tih_rna_sample_00586_B23MVV7LT4_1.chckpts/intron_igv_bed.ok 08:51:38 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00586_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00586_B23MVV7LT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam.bai 09:08:33 : INFO : Execution Time = 16.92 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00586_B23MVV7LT4_1.introns.for_IGV.bed --bam tih_rna_sample_00586_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00586_B23MVV7LT4_1 09:08:33 : INFO : Running: touch /tmp/nxf.iGwb8oET7Y/tih_rna_sample_00586_B23MVV7LT4_1.chckpts/reads_alignments_extracted.ok 09:08:33 : INFO : Running: samtools sort -o tih_rna_sample_00586_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00586_B23MVV7LT4_1.cancer_intron_reads.bam 09:08:33 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00586_B23MVV7LT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00586_B23MVV7LT4_1.cancer_intron_reads.bam 09:08:33 : INFO : Running: touch /tmp/nxf.iGwb8oET7Y/tih_rna_sample_00586_B23MVV7LT4_1.chckpts/sort_cancer_intron_reads.ok 09:08:33 : INFO : Running: samtools sort -o tih_rna_sample_00586_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00586_B23MVV7LT4_1.gene_reads.bam [bam_sort_core] merging from 74 files and 1 in-memory blocks... 09:26:45 : INFO : Execution Time = 18.19 minutes. CMD: samtools sort -o tih_rna_sample_00586_B23MVV7LT4_1.gene_reads.sorted.bam tih_rna_sample_00586_B23MVV7LT4_1.gene_reads.bam 09:26:45 : INFO : Running: touch /tmp/nxf.iGwb8oET7Y/tih_rna_sample_00586_B23MVV7LT4_1.chckpts/sort_gene_reads.ok 09:26:45 : INFO : Running: /usr/local/src/CTAT-SPLICING/bamsifter/bamsifter -c 50 -i 50 -o tih_rna_sample_00586_B23MVV7LT4_1.gene_reads.sorted.sifted.bam.tmp --keep_secondary tih_rna_sample_00586_B23MVV7LT4_1.gene_reads.sorted.bam