-ctat genome lib [/tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.eM4XzRXFR2/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary -sample contains 34655956 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir -J /tmp/nxf.eM4XzRXFR2/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction -O /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.eM4XzRXFR2/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=40000.00/min [20000], rate=40000.00/min [30000], rate=40909.09/min [40000], rate=42105.26/min [50000], rate=43478.26/min [60000], rate=47368.42/min [70000], rate=50000.00/min [80000], rate=47524.75/min [90000], rate=46551.72/min [100000], rate=46153.85/min [110000], rate=46478.87/min [120000], rate=47058.82/min [130000], rate=48148.15/min [140000], rate=49411.76/min [150000], rate=49180.33/min [160000], rate=49230.77/min [170000], rate=49756.10/min [180000], rate=50467.29/min [190000], rate=51121.08/min [200000], rate=51948.05/min [210000], rate=52941.18/min [220000], rate=54545.45/min [230000], rate=55200.00/min [240000], rate=56470.59/min [250000], rate=57034.22/min [260000], rate=57992.57/min [270000], rate=58909.09/min [280000], rate=59574.47/min [290000], rate=60416.67/min [300000], rate=61016.95/min [310000], rate=61589.40/min [320000], rate=62745.10/min [330000], rate=63057.32/min [340000], rate=63551.40/min [350000], rate=63829.79/min [360000], rate=64094.96/min [370000], rate=64347.83/min [380000], rate=64406.78/min [390000], rate=63934.43/min [400000], rate=64000.00/min [410000], rate=64397.91/min [420000], rate=64948.45/min [430000], rate=64987.41/min [440000], rate=64864.86/min [450000], rate=65060.24/min [460000], rate=65558.19/min -building interval tree based on /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=50000.00/min [20000], rate=54545.45/min [30000], rate=56250.00/min [40000], rate=54545.45/min [50000], rate=49180.33/min [60000], rate=46153.85/min [70000], rate=44680.85/min [80000], rate=45283.02/min [90000], rate=45378.15/min [100000], rate=45801.53/min [110000], rate=47142.86/min [120000], rate=48322.15/min [130000], rate=49367.09/min [140000], rate=50602.41/min [150000], rate=52023.12/min [160000], rate=53932.58/min [170000], rate=56666.67/min [180000], rate=58378.38/min [190000], rate=58163.27/min [200000], rate=59701.49/min [210000], rate=62068.97/min [220000], rate=63768.12/min [230000], rate=65714.29/min [240000], rate=65454.55/min [250000], rate=66079.30/min [260000], rate=67241.38/min [270000], rate=67782.43/min [280000], rate=67469.88/min [290000], rate=67181.47/min [300000], rate=67164.18/min [310000], rate=67391.30/min [320000], rate=65753.42/min [330000], rate=64495.11/min [340000], rate=63354.04/min [350000], rate=62874.25/min [360000], rate=62790.70/min [370000], rate=63793.10/min [380000], rate=63687.15/min [390000], rate=63072.78/min [400000], rate=62827.23/min [410000], rate=63239.07/min [420000], rate=62222.22/min [430000], rate=61722.49/min [440000], rate=61538.46/min [450000], rate=61643.84/min [460000], rate=62022.47/min -building interval tree based on /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=50000.00/min [20000], rate=52173.91/min [30000], rate=56250.00/min [40000], rate=60000.00/min [50000], rate=53571.43/min [60000], rate=51428.57/min [70000], rate=50602.41/min [80000], rate=50526.32/min [90000], rate=50943.40/min [100000], rate=52173.91/min [110000], rate=54098.36/min [120000], rate=55384.62/min [130000], rate=56115.11/min [140000], rate=55263.16/min [150000], rate=55555.56/min [160000], rate=56470.59/min [170000], rate=56353.59/min [180000], rate=56250.00/min [190000], rate=56435.64/min [200000], rate=57142.86/min [210000], rate=56000.00/min [220000], rate=55932.20/min [230000], rate=54980.08/min [240000], rate=54545.45/min [250000], rate=54151.62/min [260000], rate=54166.67/min [270000], rate=54000.00/min [280000], rate=54193.55/min [290000], rate=55063.29/min [300000], rate=54545.45/min [310000], rate=53757.23/min [320000], rate=53185.60/min [330000], rate=52941.18/min [340000], rate=52987.01/min [350000], rate=52896.73/min [360000], rate=53071.25/min [370000], rate=53365.38/min [380000], rate=53773.58/min [390000], rate=54166.67/min [400000], rate=54669.70/min [410000], rate=54185.02/min [420000], rate=53617.02/min [430000], rate=53195.88/min [440000], rate=52905.81/min [450000], rate=52631.58/min -building interval tree based on /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=80000.00/min [30000], rate=100000.00/min [40000], rate=100000.00/min [50000], rate=96774.19/min [60000], rate=102857.14/min [70000], rate=110526.32/min [80000], rate=100000.00/min [90000], rate=103846.15/min [100000], rate=105263.16/min [110000], rate=100000.00/min [120000], rate=102857.14/min [130000], rate=87640.45/min [140000], rate=74336.28/min [150000], rate=66176.47/min [160000], rate=61538.46/min [170000], rate=58620.69/min [180000], rate=57142.86/min [190000], rate=55882.35/min [200000], rate=55299.54/min [210000], rate=54545.45/min [220000], rate=54098.36/min [230000], rate=54117.65/min [240000], rate=54545.45/min [250000], rate=55147.06/min [260000], rate=54736.84/min [270000], rate=54915.25/min [280000], rate=54901.96/min [290000], rate=55238.10/min [300000], rate=55727.55/min [310000], rate=56193.35/min [320000], rate=55172.41/min [330000], rate=54395.60/min [340000], rate=53968.25/min [350000], rate=53571.43/min [360000], rate=53201.97/min [370000], rate=52857.14/min [380000], rate=52534.56/min [390000], rate=52232.14/min [400000], rate=51948.05/min [410000], rate=51680.67/min [420000], rate=51533.74/min [430000], rate=51292.25/min [440000], rate=51063.83/min [450000], rate=50943.40/min [460000], rate=50828.73/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir --filt_file /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 4000000.00 reads per min processed... 4500000.00 reads per min processed... 4000000.00 reads per min processed... 3750000.00 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... 4235294.12 reads per min processed... 4105263.16 reads per min processed... 4200000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.eM4XzRXFR2/1173_SFA_T1_RNA_SLD_01_A23T55JLT4_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.eM4XzRXFR2/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -21099.777560 EM: Round [1] log likelihood: -21060.168733 EM: Round [2] log likelihood: -21045.182940 EM: Round [3] log likelihood: -21038.833200 EM: Round [4] log likelihood: -21035.851140 EM: Round [5] log likelihood: -21034.338344 EM: Round [6] log likelihood: -21033.523022 EM: Round [7] log likelihood: -21033.060117 EM: Round [8] log likelihood: -21032.784509 EM: Round [9] log likelihood: -21032.613054 EM: Round [10] log likelihood: -21032.502035 EM: Round [11] log likelihood: -21032.427517 EM: Round [12] log likelihood: -21032.375873 EM: Round [13] log likelihood: -21032.339048 EM: Round [14] log likelihood: -21032.312109 EM: Round [15] log likelihood: -21032.291934 EM: Round [16] log likelihood: -21032.276489 EM: Round [17] log likelihood: -21032.264418 EM: Round [18] log likelihood: -21032.254790 EM: Round [19] log likelihood: -21032.246963 EM: Round [20] log likelihood: -21032.240481 EM: Round [21] log likelihood: -21032.235017 EM: Round [22] log likelihood: -21032.230335 EM: Round [23] log likelihood: -21032.226264 EM: Round [24] log likelihood: -21032.222675 EM: Round [25] log likelihood: -21032.219474 EM: Round [26] log likelihood: -21032.216589 EM: Round [27] log likelihood: -21032.213965 EM: Round [28] log likelihood: -21032.211562 EM: Round [29] log likelihood: -21032.209347 EM: Round [30] log likelihood: -21032.207294 EM: Round [31] log likelihood: -21032.205383 EM: Round [32] log likelihood: -21032.203599 EM: Round [33] log likelihood: -21032.201928 EM: Round [34] log likelihood: -21032.200359 EM: Round [35] log likelihood: -21032.198883 EM: Round [36] log likelihood: -21032.197492 EM: Round [37] log likelihood: -21032.196179 EM: Round [38] log likelihood: -21032.194939 EM: Round [39] log likelihood: -21032.193767 EM: Round [40] log likelihood: -21032.192658 EM: Round [41] log likelihood: -21032.191608 EM: Round [42] log likelihood: -21032.190613 EM: Round [43] log likelihood: -21032.189670 EM: Round [44] log likelihood: -21032.188776 EM: Round [45] log likelihood: -21032.187927 EM: Round [46] log likelihood: -21032.187122 EM: Round [47] log likelihood: -21032.186358 EM: Round [48] log likelihood: -21032.185633 EM: Round [49] log likelihood: -21032.184944 EM: Round [50] log likelihood: -21032.184289 EM: Round [51] log likelihood: -21032.183667 EM: Round [52] log likelihood: -21032.183076 EM: Round [53] log likelihood: -21032.182515 EM: Round [54] log likelihood: -21032.181981 EM: Round [55] log likelihood: -21032.181473 EM: Round [56] log likelihood: -21032.180991 EM: Round [57] log likelihood: -21032.180532 EM: Round [58] log likelihood: -21032.180095 EM: Round [59] log likelihood: -21032.179680 EM: Round [60] log likelihood: -21032.179285 EM: Round [61] log likelihood: -21032.178909 EM: Round [62] log likelihood: -21032.178551 EM: Round [63] log likelihood: -21032.178211 EM: Round [64] log likelihood: -21032.177886 EM: Round [65] log likelihood: -21032.177578 EM: Round [66] log likelihood: -21032.177284 EM: Round [67] log likelihood: -21032.177004 EM: Round [68] log likelihood: -21032.176738 EM: Round [69] log likelihood: -21032.176484 EM: Round [70] log likelihood: -21032.176243 EM: Round [71] log likelihood: -21032.176013 EM: Round [72] log likelihood: -21032.175793 EM: Round [73] log likelihood: -21032.175584 EM: Round [74] log likelihood: -21032.175385 EM: Round [75] log likelihood: -21032.175195 EM: Round [76] log likelihood: -21032.175014 EM: Round [77] log likelihood: -21032.174842 EM: Round [78] log likelihood: -21032.174678 EM: Round [79] log likelihood: -21032.174521 EM: Round [80] log likelihood: -21032.174371 EM: Round [81] log likelihood: -21032.174229 EM: Round [82] log likelihood: -21032.174093 EM: Round [83] log likelihood: -21032.173963 EM: Round [84] log likelihood: -21032.173839 EM: Round [85] log likelihood: -21032.173721 EM: Round [86] log likelihood: -21032.173608 EM: Round [87] log likelihood: -21032.173501 EM: Round [88] log likelihood: -21032.173398 EM: Round [89] log likelihood: -21032.173300 EM: Stopping iterations at round 89 due to insufficient improvement in likelihood. EM: Starting log likelihood: -21082.865723 EM: Round [1] log likelihood: -21045.781875 EM: Round [2] log likelihood: -21033.065359 EM: Round [3] log likelihood: -21028.026610 EM: Round [4] log likelihood: -21025.782134 EM: Round [5] log likelihood: -21024.697098 EM: Round [6] log likelihood: -21024.137771 EM: Round [7] log likelihood: -21023.832672 EM: Round [8] log likelihood: -21023.657137 EM: Round [9] log likelihood: -21023.550836 EM: Round [10] log likelihood: -21023.483239 EM: Round [11] log likelihood: -21023.438245 EM: Round [12] log likelihood: -21023.407018 EM: Round [13] log likelihood: -21023.384510 EM: Round [14] log likelihood: -21023.367729 EM: Round [15] log likelihood: -21023.354831 EM: Round [16] log likelihood: -21023.344645 EM: Round [17] log likelihood: -21023.336398 EM: Round [18] log likelihood: -21023.329573 EM: Round [19] log likelihood: -21023.323809 EM: Round [20] log likelihood: -21023.318853 EM: Round [21] log likelihood: -21023.314526 EM: Round [22] log likelihood: -21023.310696 EM: Round [23] log likelihood: -21023.307264 EM: Round [24] log likelihood: -21023.304160 EM: Round [25] log likelihood: -21023.301327 EM: Round [26] log likelihood: -21023.298724 EM: Round [27] log likelihood: -21023.296319 EM: Round [28] log likelihood: -21023.294085 EM: Round [29] log likelihood: -21023.292003 EM: Round [30] log likelihood: -21023.290056 EM: Round [31] log likelihood: -21023.288230 EM: Round [32] log likelihood: -21023.286515 EM: Round [33] log likelihood: -21023.284899 EM: Round [34] log likelihood: -21023.283377 EM: Round [35] log likelihood: -21023.281939 EM: Round [36] log likelihood: -21023.280581 EM: Round [37] log likelihood: -21023.279297 EM: Round [38] log likelihood: -21023.278081 EM: Round [39] log likelihood: -21023.276930 EM: Round [40] log likelihood: -21023.275840 EM: Round [41] log likelihood: -21023.274806 EM: Round [42] log likelihood: -21023.273826 EM: Round [43] log likelihood: -21023.272896 EM: Round [44] log likelihood: -21023.272013 EM: Round [45] log likelihood: -21023.271176 EM: Round [46] log likelihood: -21023.270380 EM: Round [47] log likelihood: -21023.269625 EM: Round [48] log likelihood: -21023.268908 EM: Round [49] log likelihood: -21023.268226 EM: Round [50] log likelihood: -21023.267578 EM: Round [51] log likelihood: -21023.266963 EM: Round [52] log likelihood: -21023.266377 EM: Round [53] log likelihood: -21023.265821 EM: Round [54] log likelihood: -21023.265292 EM: Round [55] log likelihood: -21023.264789 EM: Round [56] log likelihood: -21023.264310 EM: Round [57] log likelihood: -21023.263855 EM: Round [58] log likelihood: -21023.263422 EM: Round [59] log likelihood: -21023.263010 EM: Round [60] log likelihood: -21023.262617 EM: Round [61] log likelihood: -21023.262244 EM: Round [62] log likelihood: -21023.261889 EM: Round [63] log likelihood: -21023.261551 EM: Round [64] log likelihood: -21023.261229 EM: Round [65] log likelihood: -21023.260922 EM: Round [66] log likelihood: -21023.260630 EM: Round [67] log likelihood: -21023.260352 EM: Round [68] log likelihood: -21023.260087 EM: Round [69] log likelihood: -21023.259835 EM: Round [70] log likelihood: -21023.259595 EM: Round [71] log likelihood: -21023.259366 EM: Round [72] log likelihood: -21023.259148 EM: Round [73] log likelihood: -21023.258940 EM: Round [74] log likelihood: -21023.258742 EM: Round [75] log likelihood: -21023.258553 EM: Round [76] log likelihood: -21023.258373 EM: Round [77] log likelihood: -21023.258201 EM: Round [78] log likelihood: -21023.258037 EM: Round [79] log likelihood: -21023.257881 EM: Round [80] log likelihood: -21023.257733 EM: Round [81] log likelihood: -21023.257591 EM: Round [82] log likelihood: -21023.257455 EM: Round [83] log likelihood: -21023.257326 EM: Round [84] log likelihood: -21023.257203 EM: Round [85] log likelihood: -21023.257085 EM: Round [86] log likelihood: -21023.256973 EM: Round [87] log likelihood: -21023.256866 EM: Round [88] log likelihood: -21023.256763 EM: Round [89] log likelihood: -21023.256665 EM: Stopping iterations at round 89 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.eM4XzRXFR2/./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.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.eM4XzRXFR2/./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.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 34655956 > /tmp/nxf.eM4XzRXFR2/./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.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir > /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir --annotate /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.eM4XzRXFR2/./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.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir -done, see /tmp/nxf.eM4XzRXFR2/./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.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.eM4XzRXFR2/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 340, filtered: 2108) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.eM4XzRXFR2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.eM4XzRXFR2/./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.eM4XzRXFR2/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000253784.1] WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000175061.18] WARNING, no entry stored in dbm for [ENSG00000229140.11] WARNING, no entry stored in dbm for [ENSG00000215483.11] WARNING, no entry stored in dbm for [ENSG00000227638.2] WARNING, no entry stored in dbm for [ENSG00000276375.1] WARNING, no entry stored in dbm for [ENSG00000240225.10] WARNING, no entry stored in dbm for [ENSG00000232386.9] 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 [ENSG00000127589.4] WARNING, no entry stored in dbm for [ENSG00000199568.1] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000181984.11] WARNING, no entry stored in dbm for [ENSG00000258038.6] WARNING, no entry stored in dbm for [ENSG00000281896.1] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000266904.6] WARNING, no entry stored in dbm for [ENSG00000211459.2] 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 [ENSG00000248980.1] WARNING, no entry stored in dbm for [ENSG00000238062.6] WARNING, no entry stored in dbm for [ENSG00000247498.10] WARNING, no entry stored in dbm for [ENSG00000226083.5] WARNING, no entry stored in dbm for [ENSG00000285045.1] WARNING, no entry stored in dbm for [ENSG00000245958.6] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000287411.1] WARNING, no entry stored in dbm for [ENSG00000242058.2] WARNING, no entry stored in dbm for [ENSG00000241625.3] WARNING, no entry stored in dbm for [ENSG00000278771.1] WARNING, no entry stored in dbm for [ENSG00000241625.3] WARNING, no entry stored in dbm for [ENSG00000276168.1] WARNING, no entry stored in dbm for [ENSG00000241625.3] WARNING, no entry stored in dbm for [ENSG00000282885.2] WARNING, no entry stored in dbm for [ENSG00000237298.10] WARNING, no entry stored in dbm for [ENSG00000205578.6] WARNING, no entry stored in dbm for [ENSG00000206763.1] WARNING, no entry stored in dbm for [ENSG00000244257.5] WARNING, no entry stored in dbm for [ENSG00000274602.5] WARNING, no entry stored in dbm for [ENSG00000215604.3] WARNING, no entry stored in dbm for [ENSG00000236051.7] WARNING, no entry stored in dbm for [ENSG00000236172.7] WARNING, no entry stored in dbm for [ENSG00000267519.6] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000249669.10] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000254101.7] WARNING, no entry stored in dbm for [ENSG00000254101.7] WARNING, no entry stored in dbm for [ENSG00000229694.7] WARNING, no entry stored in dbm for [ENSG00000285964.1] WARNING, no entry stored in dbm for [ENSG00000259673.6] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000260276.2] WARNING, no entry stored in dbm for [ENSG00000225465.10] WARNING, no entry stored in dbm for [ENSG00000270255.1] WARNING, no entry stored in dbm for [ENSG00000245322.7] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000183666.17] WARNING, no entry stored in dbm for [ENSG00000183666.17] WARNING, no entry stored in dbm for [ENSG00000230368.2] WARNING, no entry stored in dbm for [ENSG00000228742.11] WARNING, no entry stored in dbm for [ENSG00000179523.5] WARNING, no entry stored in dbm for [ENSG00000186704.9] WARNING, no entry stored in dbm for [ENSG00000250091.3] WARNING, no entry stored in dbm for [ENSG00000230869.1] WARNING, no entry stored in dbm for [ENSG00000261751.1] WARNING, no entry stored in dbm for [ENSG00000100058.12] 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 [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000283805.1] WARNING, no entry stored in dbm for [ENSG00000215146.5] WARNING, no entry stored in dbm for [ENSG00000204177.10] WARNING, no entry stored in dbm for [ENSG00000236794.5] WARNING, no entry stored in dbm for [ENSG00000280441.3] WARNING, no entry stored in dbm for [ENSG00000236794.5] WARNING, no entry stored in dbm for [ENSG00000280441.3] WARNING, no entry stored in dbm for [ENSG00000251066.1] WARNING, no entry stored in dbm for [ENSG00000256591.5] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000163016.10] WARNING, no entry stored in dbm for [ENSG00000227619.3] WARNING, no entry stored in dbm for [ENSG00000275953.1] WARNING, no entry stored in dbm for [ENSG00000233290.3] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000287708.1] WARNING, no entry stored in dbm for [ENSG00000231113.2] WARNING, no entry stored in dbm for [ENSG00000230912.1] WARNING, no entry stored in dbm for [ENSG00000230869.1] WARNING, no entry stored in dbm for [ENSG00000237238.3] WARNING, no entry stored in dbm for [ENSG00000248449.2] WARNING, no entry stored in dbm for [ENSG00000218227.3] WARNING, no entry stored in dbm for [ENSG00000239315.4] WARNING, no entry stored in dbm for [ENSG00000214999.3] WARNING, no entry stored in dbm for [ENSG00000288075.1] WARNING, no entry stored in dbm for [ENSG00000180764.13] WARNING, no entry stored in dbm for [ENSG00000249741.2] WARNING, no entry stored in dbm for [ENSG00000231747.1] WARNING, no entry stored in dbm for [ENSG00000228375.1] WARNING, no entry stored in dbm for [ENSG00000272140.2] WARNING, no entry stored in dbm for [ENSG00000242338.6] WARNING, no entry stored in dbm for [ENSG00000285106.2] WARNING, no entry stored in dbm for [ENSG00000224152.1] WARNING, no entry stored in dbm for [ENSG00000277283.1] WARNING, no entry stored in dbm for [ENSG00000215483.11] * STAR-Fusion complete. See output: /tmp/nxf.eM4XzRXFR2/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)