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/b4/90e35a84110b1491b35308fbbf0050/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/8a7d33286577814638e7e5cd03b512/FFPE_V4_0002_RNA_0001_A23T55JLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/8a7d33286577814638e7e5cd03b512/FFPE_V4_0002_RNA_0001_A23T55JLT4_1.SJ.out.tab Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/8a7d33286577814638e7e5cd03b512/FFPE_V4_0002_RNA_0001_A23T55JLT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/90e35a84110b1491b35308fbbf0050/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/79271e97b1eaf9b226ab03289fcf44/FFPE_V4_0002_RNA_0001_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai ==> STAGING COMPLETE (7 inputs) 08:56:55 : 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rate=18583333.33/min [11160000], rate=18600000.00/min [11170000], rate=18616666.67/min [11180000], rate=18633333.33/min [11190000], rate=18650000.00/min [11200000], rate=18666666.67/min [11210000], rate=18683333.33/min [11220000], rate=18700000.00/min [11230000], rate=18716666.67/min [11240000], rate=18733333.33/min [11250000], rate=18750000.00/min [11260000], rate=18766666.67/min [11270000], rate=18783333.33/min [11280000], rate=18800000.00/min [11290000], rate=18816666.67/min [11300000], rate=18833333.33/min [11310000], rate=18850000.00/min [11320000], rate=18866666.67/min [11330000], rate=18883333.33/min [11340000], rate=18900000.00/min [11350000], rate=18916666.67/min [11360000], rate=18933333.33/min [11370000], rate=18950000.00/min [11380000], rate=18966666.67/min [11390000], rate=18983333.33/min [11400000], rate=18486486.49/min [11410000], rate=18502702.70/min [11420000], rate=18518918.92/min [11430000], rate=18535135.14/min [11440000], rate=18551351.35/min [11450000], rate=18567567.57/min [11460000], rate=18583783.78/min [11470000], rate=18600000.00/min [11480000], rate=18616216.22/min [11490000], rate=18632432.43/min [11500000], rate=18648648.65/min [11510000], rate=18664864.86/min [11520000], rate=18681081.08/min [11530000], rate=18697297.30/min [11540000], rate=18713513.51/min [11550000], rate=18729729.73/min [11560000], rate=18745945.95/min [11570000], rate=18762162.16/min [11580000], rate=18778378.38/min [11590000], rate=18794594.59/min [11600000], rate=18810810.81/min [11610000], rate=18827027.03/min [11620000], rate=18843243.24/min [11630000], rate=18859459.46/min [11640000], rate=18875675.68/min [11650000], rate=18891891.89/min [11660000], rate=18908108.11/min [11670000], rate=18924324.32/min [11680000], rate=18940540.54/min [11690000], rate=18956756.76/min [11700000], rate=18972972.97/min [11710000], rate=18989189.19/min [11720000], rate=19005405.41/min [11730000], rate=19021621.62/min [11740000], rate=19037837.84/min [11750000], rate=19054054.05/min [11760000], rate=19070270.27/min [11770000], rate=19086486.49/min [11780000], rate=18600000.00/min [11790000], rate=18615789.47/min [11800000], rate=18631578.95/min [11810000], rate=18647368.42/min [11820000], rate=18663157.89/min [11830000], rate=18678947.37/min [11840000], rate=18694736.84/min [11850000], rate=18710526.32/min [11860000], rate=18726315.79/min [11870000], rate=18742105.26/min [11880000], rate=18757894.74/min [11890000], rate=18773684.21/min [11900000], rate=18789473.68/min [11910000], rate=18805263.16/min [11920000], rate=18821052.63/min [11930000], rate=18836842.11/min [11940000], rate=18852631.58/min [11950000], rate=18868421.05/min [11960000], rate=18884210.53/min [11970000], rate=18900000.00/min [11980000], rate=18915789.47/min [11990000], rate=18931578.95/min [12000000], rate=18947368.42/min [12010000], rate=18963157.89/min [12020000], rate=18978947.37/min [12030000], rate=18994736.84/min [12040000], rate=19010526.32/min [12050000], rate=19026315.79/min [12060000], rate=19042105.26/min [12070000], rate=19057894.74/min [12080000], rate=19073684.21/min [12090000], rate=18600000.00/min [12100000], rate=18615384.62/min [12110000], rate=18630769.23/min [12120000], rate=18646153.85/min [12130000], rate=18661538.46/min [12140000], rate=18676923.08/min [12150000], rate=18692307.69/min [12160000], rate=18707692.31/min [12170000], rate=18723076.92/min [12180000], rate=18738461.54/min 08:57:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0002_RNA_0001_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0002_RNA_0001_A23T55JLT4_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. -FFPE_V4_0002_RNA_0001_A23T55JLT4_1.introns: identified 6343 cancer introns 08:57:43 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/annotate_cancer_introns.pl --introns_file FFPE_V4_0002_RNA_0001_A23T55JLT4_1.introns --ctat_genome_lib ctat_genome_lib_build_dir --intron_col 0 > FFPE_V4_0002_RNA_0001_A23T55JLT4_1.cancer.introns.prelim 08:57:43 : INFO : Running: touch /tmp/nxf.pDr6TgcWJU/FFPE_V4_0002_RNA_0001_A23T55JLT4_1.chckpts/prelim_introns.ok 08:57:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0002_RNA_0001_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0002_RNA_0001_A23T55JLT4_1.cancer.introns 08:57:43 : INFO : Execution Time = 0.01 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/filter_by_min_total_reads.py --cancer_intron_candidates FFPE_V4_0002_RNA_0001_A23T55JLT4_1.cancer.introns.prelim --min_total_reads 5 > FFPE_V4_0002_RNA_0001_A23T55JLT4_1.cancer.introns 08:57:43 : INFO : Running: touch /tmp/nxf.pDr6TgcWJU/FFPE_V4_0002_RNA_0001_A23T55JLT4_1.chckpts/introns_filtered.ok 08:57:43 : INFO : -found 3203 cancer introns 08:57:43 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0002_RNA_0001_A23T55JLT4_1.introns --cancer_introns FFPE_V4_0002_RNA_0001_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0002_RNA_0001_A23T55JLT4_1.introns.for_IGV.bed 08:57:44 : INFO : Creating the BED File. 08:57:51 : INFO : Saving Bed File as FFPE_V4_0002_RNA_0001_A23T55JLT4_1.introns.for_IGV.bed 08:57:51 : INFO : Execution Time = 0.12 minutes. CMD: /usr/local/src/CTAT-SPLICING/util/make_igv_splice_bed.py --all_introns FFPE_V4_0002_RNA_0001_A23T55JLT4_1.introns --cancer_introns FFPE_V4_0002_RNA_0001_A23T55JLT4_1.cancer.introns --genome_lib_dir ctat_genome_lib_build_dir --output_bed FFPE_V4_0002_RNA_0001_A23T55JLT4_1.introns.for_IGV.bed 08:57:51 : INFO : Running: touch /tmp/nxf.pDr6TgcWJU/FFPE_V4_0002_RNA_0001_A23T55JLT4_1.chckpts/intron_igv_bed.ok 08:57:51 : INFO : Running: /usr/local/src/CTAT-SPLICING/util/igv_read_alignment_extractor.py --igv_introns_bed FFPE_V4_0002_RNA_0001_A23T55JLT4_1.introns.for_IGV.bed --bam FFPE_V4_0002_RNA_0001_A23T55JLT4_1.Aligned.sortedByCoord.out.bam --output_prefix FFPE_V4_0002_RNA_0001_A23T55JLT4_1 [W::hts_idx_load3] The index file is older than the data file: FFPE_V4_0002_RNA_0001_A23T55JLT4_1.Aligned.sortedByCoord.out.bam.bai