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/fe/2a44b31dae12fd75e10d805ada54ab/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/8b5d53ec406ed8dc68adbd31ea2b62/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/2a44b31dae12fd75e10d805ada54ab/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/8b5d53ec406ed8dc68adbd31ea2b62/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/dbaa0e40d1b8da9e45862ca86cce30/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.PanbpDhWut/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.PanbpDhWut/./star-fusion.preliminary -sample contains 9848892 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir -J /tmp/nxf.PanbpDhWut/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.PanbpDhWut/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=54545.45/min [20000], rate=63157.89/min [30000], rate=72000.00/min [40000], rate=68571.43/min [50000], rate=66666.67/min [60000], rate=66666.67/min [70000], rate=66666.67/min [80000], rate=75000.00/min [90000], rate=83076.92/min [100000], rate=89552.24/min [110000], rate=83544.30/min [120000], rate=81818.18/min [130000], rate=78000.00/min [140000], rate=76363.64/min [150000], rate=76271.19/min [160000], rate=71111.11/min [170000], rate=72340.43/min [180000], rate=71523.18/min [190000], rate=70807.45/min [200000], rate=73619.63/min [210000], rate=76829.27/min [220000], rate=80000.00/min [230000], rate=75409.84/min [240000], rate=70588.24/min [250000], rate=70422.54/min [260000], rate=68421.05/min [270000], rate=70434.78/min [280000], rate=70886.08/min [290000], rate=70445.34/min [300000], rate=70038.91/min [310000], rate=66666.67/min [320000], rate=65753.42/min [330000], rate=65346.53/min [340000], rate=65175.72/min [350000], rate=65015.48/min [360000], rate=64670.66/min [370000], rate=64534.88/min [380000], rate=63333.33/min [390000], rate=61417.32/min [400000], rate=59850.37/min [410000], rate=59854.01/min [420000], rate=59154.93/min -building interval tree based on /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=133333.33/min [30000], rate=120000.00/min [40000], rate=114285.71/min [50000], rate=111111.11/min [60000], rate=109090.91/min [70000], rate=116666.67/min [80000], rate=123076.92/min [90000], rate=117391.30/min [100000], rate=120000.00/min [110000], rate=115789.47/min [120000], rate=114285.71/min [130000], rate=113043.48/min [140000], rate=106329.11/min [150000], rate=109756.10/min [160000], rate=106666.67/min [170000], rate=100000.00/min [180000], rate=94736.84/min [190000], rate=91935.48/min [200000], rate=93023.26/min [210000], rate=94029.85/min [220000], rate=90410.96/min [230000], rate=89032.26/min [240000], rate=90000.00/min [250000], rate=90909.09/min [260000], rate=87150.84/min [270000], rate=83505.15/min [280000], rate=84422.11/min [290000], rate=84878.05/min [300000], rate=74380.17/min [310000], rate=64137.93/min [320000], rate=58536.59/min [330000], rate=55774.65/min [340000], rate=53684.21/min [350000], rate=53299.49/min [360000], rate=53201.97/min [370000], rate=52983.29/min [380000], rate=52900.23/min [390000], rate=53061.22/min [400000], rate=53333.33/min [410000], rate=53947.37/min -building interval tree based on /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=63157.89/min [30000], rate=60000.00/min [40000], rate=61538.46/min [50000], rate=63829.79/min [60000], rate=65454.55/min [70000], rate=56756.76/min [80000], rate=49484.54/min [90000], rate=46956.52/min [100000], rate=45112.78/min [110000], rate=45517.24/min [120000], rate=41618.50/min [130000], rate=39393.94/min [140000], rate=38356.16/min [150000], rate=39647.58/min [160000], rate=40677.97/min [170000], rate=41295.55/min [180000], rate=40754.72/min [190000], rate=40140.85/min [200000], rate=39603.96/min [210000], rate=39252.34/min [220000], rate=39879.15/min [230000], rate=40588.24/min [240000], rate=40449.44/min [250000], rate=40431.27/min [260000], rate=40731.07/min [270000], rate=41221.37/min [280000], rate=40677.97/min [290000], rate=40941.18/min [300000], rate=41379.31/min [310000], rate=41986.46/min [320000], rate=42290.75/min [330000], rate=42580.65/min [340000], rate=42947.37/min [350000], rate=43478.26/min [360000], rate=44444.44/min [370000], rate=44758.06/min [380000], rate=45418.33/min [390000], rate=45792.56/min [400000], rate=46153.85/min [410000], rate=46768.06/min [420000], rate=47368.42/min -building interval tree based on /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=33333.33/min [20000], rate=32432.43/min [30000], rate=33962.26/min [40000], rate=36363.64/min [50000], rate=40540.54/min [60000], rate=38297.87/min [70000], rate=33333.33/min [80000], rate=33802.82/min [90000], rate=33333.33/min [100000], rate=34090.91/min [110000], rate=35869.57/min [120000], rate=37500.00/min [130000], rate=37864.08/min [140000], rate=37004.41/min [150000], rate=37500.00/min [160000], rate=38866.40/min [170000], rate=40316.21/min [180000], rate=39416.06/min [190000], rate=39446.37/min [200000], rate=40268.46/min [210000], rate=39375.00/min [220000], rate=39169.14/min [230000], rate=39541.55/min [240000], rate=39560.44/min [250000], rate=40106.95/min [260000], rate=40206.19/min [270000], rate=38848.92/min [280000], rate=38709.68/min [290000], rate=38410.60/min [300000], rate=38876.89/min [310000], rate=39743.59/min [320000], rate=40336.13/min [330000], rate=40325.87/min [340000], rate=39766.08/min [350000], rate=39622.64/min [360000], rate=39705.88/min [370000], rate=40144.67/min [380000], rate=40000.00/min [390000], rate=39130.43/min [400000], rate=39151.71/min [410000], rate=39486.36/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir --filt_file /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 12000000.00 reads per min processed... 6000000.00 reads per min processed... 4800000.00 reads per min processed... 4285714.29 reads per min processed... 4000000.00 reads per min processed... 3818181.82 reads per min processed... 4000000.00 reads per min processed... 4153846.15 reads per min processed... 4285714.29 reads per min processed... 4125000.00 reads per min processed... 4000000.00 reads per min processed... 4105263.16 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.PanbpDhWut/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction --tmpdir /tmp --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --max_promiscuity 10 --min_pct_dom_promiscuity 20 --min_novel_junction_support 1 --min_alt_pct_junction 10 --aggregate_novel_junction_dist 5 --min_spanning_frags_only 1 --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -23925.794678 EM: Round [1] log likelihood: -23880.609303 EM: Round [2] log likelihood: -23858.020054 EM: Round [3] log likelihood: -23845.238550 EM: Round [4] log likelihood: -23837.877637 EM: Round [5] log likelihood: -23833.618112 EM: Round [6] log likelihood: -23831.117327 EM: Round [7] log likelihood: -23829.608506 EM: Round [8] log likelihood: -23828.664374 EM: Round [9] log likelihood: -23828.049606 EM: Round [10] log likelihood: -23827.633734 EM: Round [11] log likelihood: -23827.342788 EM: Round [12] log likelihood: -23827.133431 EM: Round [13] log likelihood: -23826.979284 EM: Round [14] log likelihood: -23826.863649 EM: Round [15] log likelihood: -23826.775563 EM: Round [16] log likelihood: -23826.707587 EM: Round [17] log likelihood: -23826.654535 EM: Round [18] log likelihood: -23826.612710 EM: Round [19] log likelihood: -23826.579430 EM: Round [20] log likelihood: -23826.552716 EM: Round [21] log likelihood: -23826.531094 EM: Round [22] log likelihood: -23826.513456 EM: Round [23] log likelihood: -23826.498956 EM: Round [24] log likelihood: -23826.486949 EM: Round [25] log likelihood: -23826.476935 EM: Round [26] log likelihood: -23826.468526 EM: Round [27] log likelihood: -23826.461420 EM: Round [28] log likelihood: -23826.455377 EM: Round [29] log likelihood: -23826.450206 EM: Round [30] log likelihood: -23826.445758 EM: Round [31] log likelihood: -23826.441909 EM: Round [32] log likelihood: -23826.438562 EM: Round [33] log likelihood: -23826.435636 EM: Round [34] log likelihood: -23826.433066 EM: Round [35] log likelihood: -23826.430799 EM: Round [36] log likelihood: -23826.428790 EM: Round [37] log likelihood: -23826.427002 EM: Round [38] log likelihood: -23826.425405 EM: Round [39] log likelihood: -23826.423971 EM: Round [40] log likelihood: -23826.422680 EM: Round [41] log likelihood: -23826.421513 EM: Round [42] log likelihood: -23826.420454 EM: Round [43] log likelihood: -23826.419490 EM: Round [44] log likelihood: -23826.418610 EM: Round [45] log likelihood: -23826.417803 EM: Round [46] log likelihood: -23826.417061 EM: Round [47] log likelihood: -23826.416378 EM: Round [48] log likelihood: -23826.415746 EM: Round [49] log likelihood: -23826.415159 EM: Round [50] log likelihood: -23826.414614 EM: Round [51] log likelihood: -23826.414106 EM: Round [52] log likelihood: -23826.413632 EM: Round [53] log likelihood: -23826.413187 EM: Round [54] log likelihood: -23826.412770 EM: Round [55] log likelihood: -23826.412378 EM: Round [56] log likelihood: -23826.412008 EM: Round [57] log likelihood: -23826.411659 EM: Round [58] log likelihood: -23826.411329 EM: Round [59] log likelihood: -23826.411016 EM: Round [60] log likelihood: -23826.410719 EM: Round [61] log likelihood: -23826.410437 EM: Round [62] log likelihood: -23826.410169 EM: Round [63] log likelihood: -23826.409913 EM: Round [64] log likelihood: -23826.409669 EM: Round [65] log likelihood: -23826.409437 EM: Round [66] log likelihood: -23826.409214 EM: Round [67] log likelihood: -23826.409001 EM: Round [68] log likelihood: -23826.408797 EM: Round [69] log likelihood: -23826.408602 EM: Round [70] log likelihood: -23826.408414 EM: Round [71] log likelihood: -23826.408234 EM: Round [72] log likelihood: -23826.408062 EM: Round [73] log likelihood: -23826.407895 EM: Round [74] log likelihood: -23826.407736 EM: Round [75] log likelihood: -23826.407582 EM: Round [76] log likelihood: -23826.407434 EM: Round [77] log likelihood: -23826.407292 EM: Round [78] log likelihood: -23826.407155 EM: Round [79] log likelihood: -23826.407023 EM: Round [80] log likelihood: -23826.406895 EM: Round [81] log likelihood: -23826.406773 EM: Round [82] log likelihood: -23826.406654 EM: Round [83] log likelihood: -23826.406540 EM: Round [84] log likelihood: -23826.406430 EM: Round [85] log likelihood: -23826.406323 EM: Round [86] log likelihood: -23826.406220 EM: Round [87] log likelihood: -23826.406121 EM: Stopping iterations at round 87 due to insufficient improvement in likelihood. EM: Starting log likelihood: -23905.875680 EM: Round [1] log likelihood: -23864.676478 EM: Round [2] log likelihood: -23844.569382 EM: Round [3] log likelihood: -23833.421248 EM: Round [4] log likelihood: -23827.099683 EM: Round [5] log likelihood: -23823.476133 EM: Round [6] log likelihood: -23821.359836 EM: Round [7] log likelihood: -23820.086285 EM: Round [8] log likelihood: -23819.290148 EM: Round [9] log likelihood: -23818.771776 EM: Round [10] log likelihood: -23818.420956 EM: Round [11] log likelihood: -23818.175334 EM: Round [12] log likelihood: -23817.998408 EM: Round [13] log likelihood: -23817.867963 EM: Round [14] log likelihood: -23817.769938 EM: Round [15] log likelihood: -23817.695100 EM: Round [16] log likelihood: -23817.637189 EM: Round [17] log likelihood: -23817.591843 EM: Round [18] log likelihood: -23817.555956 EM: Round [19] log likelihood: -23817.527276 EM: Round [20] log likelihood: -23817.504144 EM: Round [21] log likelihood: -23817.485325 EM: Round [22] log likelihood: -23817.469888 EM: Round [23] log likelihood: -23817.457127 EM: Round [24] log likelihood: -23817.446497 EM: Round [25] log likelihood: -23817.437580 EM: Round [26] log likelihood: -23817.430049 EM: Round [27] log likelihood: -23817.423647 EM: Round [28] log likelihood: -23817.418172 EM: Round [29] log likelihood: -23817.413463 EM: Round [30] log likelihood: -23817.409388 EM: Round [31] log likelihood: -23817.405845 EM: Round [32] log likelihood: -23817.402749 EM: Round [33] log likelihood: -23817.400029 EM: Round [34] log likelihood: -23817.397630 EM: Round [35] log likelihood: -23817.395504 EM: Round [36] log likelihood: -23817.393611 EM: Round [37] log likelihood: -23817.391920 EM: Round [38] log likelihood: -23817.390403 EM: Round [39] log likelihood: -23817.389036 EM: Round [40] log likelihood: -23817.387801 EM: Round [41] log likelihood: -23817.386680 EM: Round [42] log likelihood: -23817.385660 EM: Round [43] log likelihood: -23817.384728 EM: Round [44] log likelihood: -23817.383873 EM: Round [45] log likelihood: -23817.383088 EM: Round [46] log likelihood: -23817.382364 EM: Round [47] log likelihood: -23817.381694 EM: Round [48] log likelihood: -23817.381073 EM: Round [49] log likelihood: -23817.380495 EM: Round [50] log likelihood: -23817.379957 EM: Round [51] log likelihood: -23817.379453 EM: Round [52] log likelihood: -23817.378982 EM: Round [53] log likelihood: -23817.378539 EM: Round [54] log likelihood: -23817.378123 EM: Round [55] log likelihood: -23817.377731 EM: Round [56] log likelihood: -23817.377360 EM: Round [57] log likelihood: -23817.377010 EM: Round [58] log likelihood: -23817.376678 EM: Round [59] log likelihood: -23817.376362 EM: Round [60] log likelihood: -23817.376063 EM: Round [61] log likelihood: -23817.375778 EM: Round [62] log likelihood: -23817.375506 EM: Round [63] log likelihood: -23817.375247 EM: Round [64] log likelihood: -23817.375000 EM: Round [65] log likelihood: -23817.374764 EM: Round [66] log likelihood: -23817.374537 EM: Round [67] log likelihood: -23817.374321 EM: Round [68] log likelihood: -23817.374113 EM: Round [69] log likelihood: -23817.373914 EM: Round [70] log likelihood: -23817.373723 EM: Round [71] log likelihood: -23817.373540 EM: Round [72] log likelihood: -23817.373363 EM: Round [73] log likelihood: -23817.373194 EM: Round [74] log likelihood: -23817.373031 EM: Round [75] log likelihood: -23817.372874 EM: Round [76] log likelihood: -23817.372723 EM: Round [77] log likelihood: -23817.372578 EM: Round [78] log likelihood: -23817.372437 EM: Round [79] log likelihood: -23817.372302 EM: Round [80] log likelihood: -23817.372172 EM: Round [81] log likelihood: -23817.372047 EM: Round [82] log likelihood: -23817.371926 EM: Round [83] log likelihood: -23817.371809 EM: Round [84] log likelihood: -23817.371696 EM: Round [85] log likelihood: -23817.371587 EM: Round [86] log likelihood: -23817.371482 EM: Round [87] log likelihood: -23817.371381 EM: Round [88] log likelihood: -23817.371283 EM: Stopping iterations at round 88 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered * Running CMD: /usr/local/src/STAR-Fusion/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 9848892 > /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM * Running CMD: /usr/local/src/STAR-Fusion/util/append_breakpoint_junction_info.pl /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir > /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir --annotate /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot * Running CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir -done, see /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass * Running CMD: /usr/local/src/STAR-Fusion/util/filter_likely_RT_artifacts.pl --fusions /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 192, filtered: 1976) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.PanbpDhWut/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass.minFFPM.0.00001.pass star-fusion.fusion_predictions.tsv * Running CMD: /usr/local/src/STAR-Fusion/util/column_exclusions.pl star-fusion.fusion_predictions.tsv JunctionReads,SpanningFrags > star-fusion.fusion_predictions.abridged.tsv * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions star-fusion.fusion_predictions.abridged.tsv --genome_lib_dir /tmp/nxf.PanbpDhWut/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000203688.6] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000239899.3] WARNING, no entry stored in dbm for [ENSG00000241175.3] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000287356.1] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000265758.1] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000260464.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000270641.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000228862.4] WARNING, no entry stored in dbm for [ENSG00000251504.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000227195.11] WARNING, no entry stored in dbm for [ENSG00000266962.2] WARNING, no entry stored in dbm for [ENSG00000272269.1] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000133519.12] WARNING, no entry stored in dbm for [ENSG00000281903.2] WARNING, no entry stored in dbm for [ENSG00000237339.5] WARNING, no entry stored in dbm for [ENSG00000223823.1] WARNING, no entry stored in dbm for [ENSG00000281912.1] WARNING, no entry stored in dbm for [ENSG00000235703.6] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000273619.1] WARNING, no entry stored in dbm for [ENSG00000225465.10] WARNING, no entry stored in dbm for [ENSG00000261505.1] WARNING, no entry stored in dbm for [ENSG00000287242.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000226950.8] WARNING, no entry stored in dbm for [ENSG00000214347.8] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000236064.2] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000168405.17] WARNING, no entry stored in dbm for [ENSG00000271434.3] WARNING, no entry stored in dbm for [ENSG00000226312.7] WARNING, no entry stored in dbm for [ENSG00000241743.4] WARNING, no entry stored in dbm for [ENSG00000271270.7] WARNING, no entry stored in dbm for [ENSG00000227486.2] WARNING, no entry stored in dbm for [ENSG00000249690.1] WARNING, no entry stored in dbm for [ENSG00000274993.1] WARNING, no entry stored in dbm for [ENSG00000272970.3] WARNING, no entry stored in dbm for [ENSG00000230773.9] WARNING, no entry stored in dbm for [ENSG00000288549.1] WARNING, no entry stored in dbm for [ENSG00000288549.1] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [ENSG00000232386.9] WARNING, no entry stored in dbm for [ENSG00000248978.2] WARNING, no entry stored in dbm for [ENSG00000234222.6] WARNING, no entry stored in dbm for [ENSG00000233491.8] WARNING, no entry stored in dbm for [ENSG00000260573.4] WARNING, no entry stored in dbm for [ENSG00000278959.1] WARNING, no entry stored in dbm for [IGL.g@-ext] * STAR-Fusion complete. See output: /tmp/nxf.PanbpDhWut/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)