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/ea/25a50b1529b18820ba5ec23f253c58/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/3d4917f45a6ef9795185c2789b33ad/tih_rna_sample_00467_B23WHTKLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/93/13be94662f02b6ae8b8d9ebe164525/tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/25a50b1529b18820ba5ec23f253c58/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/3d4917f45a6ef9795185c2789b33ad/tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/14/3d4917f45a6ef9795185c2789b33ad/tih_rna_sample_00467_B23WHTKLT4_1.SJ.out.tab ==> STAGING COMPLETE (7 inputs) 08:50:42 : INFO 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rate=12576923.08/min [10910000], rate=12588461.54/min [10920000], rate=12600000.00/min [10930000], rate=12611538.46/min [10940000], rate=12623076.92/min [10950000], rate=12634615.38/min [10960000], rate=12646153.85/min [10970000], rate=12657692.31/min [10980000], rate=12669230.77/min [10990000], rate=12680769.23/min [11000000], rate=12692307.69/min [11010000], rate=12703846.15/min [11020000], rate=12715384.62/min [11030000], rate=12726923.08/min [11040000], rate=12738461.54/min [11050000], rate=12750000.00/min [11060000], rate=12761538.46/min [11070000], rate=12773076.92/min [11080000], rate=12784615.38/min [11090000], rate=12796153.85/min [11100000], rate=12807692.31/min [11110000], rate=12819230.77/min [11120000], rate=12830769.23/min [11130000], rate=12600000.00/min [11140000], rate=12611320.75/min [11150000], rate=12622641.51/min [11160000], rate=12633962.26/min [11170000], rate=12645283.02/min [11180000], rate=12656603.77/min [11190000], rate=12667924.53/min [11200000], rate=12679245.28/min [11210000], rate=12690566.04/min [11220000], rate=12701886.79/min [11230000], rate=12713207.55/min [11240000], rate=12724528.30/min [11250000], rate=12735849.06/min [11260000], rate=12747169.81/min [11270000], rate=12758490.57/min [11280000], rate=12769811.32/min [11290000], rate=12781132.08/min [11300000], rate=12792452.83/min [11310000], rate=12803773.58/min [11320000], rate=12815094.34/min [11330000], rate=12826415.09/min [11340000], rate=12837735.85/min [11350000], rate=12849056.60/min [11360000], rate=12860377.36/min [11370000], rate=12871698.11/min [11380000], rate=12883018.87/min [11390000], rate=12655555.56/min [11400000], rate=12666666.67/min [11410000], rate=12677777.78/min [11420000], rate=12688888.89/min [11430000], rate=12700000.00/min [11440000], rate=12711111.11/min [11450000], rate=12722222.22/min [11460000], rate=12733333.33/min [11470000], rate=12744444.44/min [11480000], rate=12755555.56/min [11490000], rate=12766666.67/min [11500000], rate=12777777.78/min [11510000], rate=12788888.89/min [11520000], rate=12800000.00/min [11530000], rate=12811111.11/min [11540000], rate=12822222.22/min [11550000], rate=12833333.33/min [11560000], rate=12844444.44/min [11570000], rate=12855555.56/min [11580000], rate=12866666.67/min [11590000], rate=12877777.78/min [11600000], rate=12888888.89/min [11610000], rate=12900000.00/min [11620000], rate=12911111.11/min [11630000], rate=12922222.22/min [11640000], rate=12698181.82/min [11650000], rate=12709090.91/min [11660000], rate=12720000.00/min [11670000], rate=12730909.09/min [11680000], rate=12741818.18/min [11690000], rate=12752727.27/min [11700000], rate=12763636.36/min [11710000], rate=12774545.45/min [11720000], rate=12785454.55/min [11730000], rate=12796363.64/min [11740000], rate=12807272.73/min [11750000], rate=12818181.82/min [11760000], rate=12829090.91/min [11770000], rate=12840000.00/min [11780000], rate=12850909.09/min [11790000], rate=12861818.18/min [11800000], rate=12872727.27/min [11810000], rate=12883636.36/min [11820000], rate=12894545.45/min [11830000], rate=12905454.55/min [11840000], rate=12916363.64/min [11850000], rate=12927272.73/min [11860000], rate=12938181.82/min [11870000], rate=12949090.91/min 08:51:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00467_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00467_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_00467_B23WHTKLT4_1.introns: identified 3292 cancer introns 08:51:51 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00467_B23WHTKLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns.prelim 08:51:51 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/prelim_introns.ok 08:51:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns 08:51:52 : 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_00467_B23WHTKLT4_1.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns 08:51:52 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/introns_filtered.ok 08:51:52 : INFO : -found 2224 cancer introns 08:51:52 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00467_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed 08:51:52 : INFO : Creating the BED File. 08:52:05 : INFO : Saving Bed File as tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed 08:52:05 : INFO : Execution Time = 0.22 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00467_B23WHTKLT4_1.introns --cancer_introns tih_rna_sample_00467_B23WHTKLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed 08:52:05 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/intron_igv_bed.ok 08:52:05 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00467_B23WHTKLT4_1 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai 09:08:12 : INFO : Execution Time = 16.11 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00467_B23WHTKLT4_1.introns.for_IGV.bed --bam tih_rna_sample_00467_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00467_B23WHTKLT4_1 09:08:12 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/reads_alignments_extracted.ok 09:08:12 : INFO : Running: samtools sort -o tih_rna_sample_00467_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00467_B23WHTKLT4_1.cancer_intron_reads.bam 09:08:13 : INFO : Execution Time = 0.02 minutes. CMD: samtools sort -o tih_rna_sample_00467_B23WHTKLT4_1.cancer_intron_reads.sorted.bam tih_rna_sample_00467_B23WHTKLT4_1.cancer_intron_reads.bam 09:08:13 : INFO : Running: touch /tmp/nxf.OopZC8TrSr/tih_rna_sample_00467_B23WHTKLT4_1.chckpts/sort_cancer_intron_reads.ok 09:08:13 : INFO : Running: samtools sort -o tih_rna_sample_00467_B23WHTKLT4_1.gene_reads.sorted.bam tih_rna_sample_00467_B23WHTKLT4_1.gene_reads.bam [bam_sort_core] merging from 68 files and 1 in-memory blocks...