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/eb/d0a68d20cc829a14f294a545421c80/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/ed8ab40cc666e7cde180b9436ec767/tih_rna_sample_00090_B23WHTKLT4_2.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/ed8ab40cc666e7cde180b9436ec767/tih_rna_sample_00090_B23WHTKLT4_2.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/69fc5d9f08da4d2d3c9d2f69c88918/tih_rna_sample_00090_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/ed8ab40cc666e7cde180b9436ec767/tih_rna_sample_00090_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/eb/d0a68d20cc829a14f294a545421c80/.command.run ==> STAGING COMPLETE (7 inputs) 08:38:54 : INFO 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rate=22820000.00/min [11420000], rate=22840000.00/min [11430000], rate=22860000.00/min [11440000], rate=22880000.00/min [11450000], rate=22900000.00/min [11460000], rate=22920000.00/min [11470000], rate=22940000.00/min [11480000], rate=22960000.00/min [11490000], rate=22980000.00/min [11500000], rate=23000000.00/min [11510000], rate=23020000.00/min [11520000], rate=23040000.00/min [11530000], rate=23060000.00/min [11540000], rate=23080000.00/min [11550000], rate=23100000.00/min [11560000], rate=23120000.00/min [11570000], rate=23140000.00/min [11580000], rate=23160000.00/min [11590000], rate=23180000.00/min [11600000], rate=23200000.00/min [11610000], rate=23220000.00/min [11620000], rate=23240000.00/min [11630000], rate=23260000.00/min [11640000], rate=23280000.00/min [11650000], rate=23300000.00/min [11660000], rate=23320000.00/min [11670000], rate=22587096.77/min [11680000], rate=22606451.61/min [11690000], rate=22625806.45/min [11700000], rate=22645161.29/min [11710000], rate=22664516.13/min [11720000], rate=22683870.97/min [11730000], rate=22703225.81/min [11740000], rate=22722580.65/min [11750000], rate=22741935.48/min [11760000], rate=22761290.32/min [11770000], rate=22780645.16/min [11780000], rate=22800000.00/min [11790000], rate=22819354.84/min [11800000], rate=22838709.68/min [11810000], rate=22858064.52/min [11820000], rate=22877419.35/min [11830000], rate=22896774.19/min [11840000], rate=22916129.03/min [11850000], rate=22935483.87/min [11860000], rate=22954838.71/min [11870000], rate=22974193.55/min [11880000], rate=22993548.39/min [11890000], rate=23012903.23/min [11900000], rate=23032258.06/min [11910000], rate=23051612.90/min [11920000], rate=23070967.74/min [11930000], rate=23090322.58/min [11940000], rate=23109677.42/min [11950000], rate=23129032.26/min [11960000], rate=23148387.10/min [11970000], rate=23167741.94/min [11980000], rate=23187096.77/min [11990000], rate=23206451.61/min [12000000], rate=23225806.45/min [12010000], rate=23245161.29/min [12020000], rate=23264516.13/min [12030000], rate=23283870.97/min [12040000], rate=23303225.81/min [12050000], rate=23322580.65/min [12060000], rate=23341935.48/min [12070000], rate=23361290.32/min [12080000], rate=23380645.16/min [12090000], rate=23400000.00/min [12100000], rate=23419354.84/min [12110000], rate=22706250.00/min [12120000], rate=22725000.00/min [12130000], rate=22743750.00/min [12140000], rate=22762500.00/min [12150000], rate=22781250.00/min [12160000], rate=22800000.00/min [12170000], rate=22818750.00/min [12180000], rate=22837500.00/min [12190000], rate=22856250.00/min [12200000], rate=22875000.00/min [12210000], rate=22893750.00/min [12220000], rate=22912500.00/min [12230000], rate=22931250.00/min [12240000], rate=22950000.00/min [12250000], rate=22968750.00/min [12260000], rate=22987500.00/min [12270000], rate=23006250.00/min [12280000], rate=23025000.00/min [12290000], rate=23043750.00/min [12300000], rate=23062500.00/min [12310000], rate=23081250.00/min [12320000], rate=23100000.00/min [12330000], rate=23118750.00/min [12340000], rate=23137500.00/min [12350000], rate=23156250.00/min [12360000], rate=23175000.00/min [12370000], rate=23193750.00/min [12380000], rate=23212500.00/min [12390000], rate=23231250.00/min [12400000], rate=23250000.00/min [12410000], rate=23268750.00/min [12420000], rate=23287500.00/min [12430000], rate=23306250.00/min [12440000], rate=23325000.00/min [12450000], rate=23343750.00/min [12460000], rate=23362500.00/min [12470000], rate=23381250.00/min [12480000], rate=23400000.00/min [12490000], rate=23418750.00/min [12500000], rate=23437500.00/min [12510000], rate=23456250.00/min [12520000], rate=23475000.00/min [12530000], rate=23493750.00/min [12540000], rate=22800000.00/min [12550000], rate=22818181.82/min 08:39:34 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00090_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00090_B23WHTKLT4_2.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_00090_B23WHTKLT4_2.introns: identified 4079 cancer introns 08:39:35 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file tih_rna_sample_00090_B23WHTKLT4_2.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns.prelim 08:39:35 : INFO : Running: touch /tmp/nxf.DwdXUpU3ZC/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/prelim_introns.ok 08:39:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns 08:39:35 : 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_00090_B23WHTKLT4_2.cancer.introns.prelim --min_total_reads 5 > tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns 08:39:35 : INFO : Running: touch /tmp/nxf.DwdXUpU3ZC/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/introns_filtered.ok 08:39:35 : INFO : -found 2574 cancer introns 08:39:35 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00090_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed 08:39:36 : INFO : Creating the BED File. 08:39:41 : INFO : Saving Bed File as tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed 08:39:41 : INFO : Execution Time = 0.10 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns tih_rna_sample_00090_B23WHTKLT4_2.introns --cancer_introns tih_rna_sample_00090_B23WHTKLT4_2.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed 08:39:41 : INFO : Running: touch /tmp/nxf.DwdXUpU3ZC/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/intron_igv_bed.ok 08:39:41 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00090_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00090_B23WHTKLT4_2 [W::hts_idx_load3] The index file is older than the data file: tih_rna_sample_00090_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam.bai 08:54:25 : INFO : Execution Time = 14.74 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed tih_rna_sample_00090_B23WHTKLT4_2.introns.for_IGV.bed --bam tih_rna_sample_00090_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --output_prefix tih_rna_sample_00090_B23WHTKLT4_2 08:54:25 : INFO : Running: touch /tmp/nxf.DwdXUpU3ZC/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/reads_alignments_extracted.ok 08:54:25 : INFO : Running: samtools sort -o tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.bam 08:54:26 : INFO : Execution Time = 0.01 minutes. CMD: samtools sort -o tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.sorted.bam tih_rna_sample_00090_B23WHTKLT4_2.cancer_intron_reads.bam 08:54:26 : INFO : Running: touch /tmp/nxf.DwdXUpU3ZC/tih_rna_sample_00090_B23WHTKLT4_2.chckpts/sort_cancer_intron_reads.ok 08:54:26 : INFO : Running: samtools sort -o tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.sorted.bam tih_rna_sample_00090_B23WHTKLT4_2.gene_reads.bam