-ctat genome lib [/tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.56jxr4OFHH/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary -sample contains 30694500 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir -J /tmp/nxf.56jxr4OFHH/ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.56jxr4OFHH/ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=54545.45/min [30000], rate=47368.42/min [40000], rate=45283.02/min [50000], rate=44776.12/min [60000], rate=45000.00/min [70000], rate=46153.85/min [80000], rate=47524.75/min [90000], rate=47787.61/min [100000], rate=48780.49/min [110000], rate=50381.68/min [120000], rate=50704.23/min [130000], rate=51655.63/min [140000], rate=52500.00/min [150000], rate=53892.22/min [160000], rate=55813.95/min [170000], rate=57627.12/min [180000], rate=59016.39/min [190000], rate=60638.30/min [200000], rate=61855.67/min [210000], rate=62376.24/min [220000], rate=63157.89/min [230000], rate=64186.05/min [240000], rate=65158.37/min [250000], rate=66079.30/min [260000], rate=67241.38/min [270000], rate=68644.07/min [280000], rate=69709.54/min [290000], rate=70731.71/min [300000], rate=71713.15/min [310000], rate=72656.25/min [320000], rate=73846.15/min [330000], rate=75572.52/min [340000], rate=76981.13/min [350000], rate=77205.88/min [360000], rate=78832.12/min [370000], rate=79285.71/min [380000], rate=79720.28/min [390000], rate=80136.99/min [400000], rate=81355.93/min [410000], rate=82000.00/min [420000], rate=82352.94/min [430000], rate=82958.20/min [440000], rate=83544.30/min [450000], rate=84639.50/min [460000], rate=85714.29/min [470000], rate=85714.29/min [480000], rate=86746.99/min [490000], rate=86725.66/min [500000], rate=86956.52/min [510000], rate=87679.08/min [520000], rate=87887.32/min [530000], rate=89325.84/min [540000], rate=90250.70/min [550000], rate=90659.34/min [560000], rate=90566.04/min [570000], rate=91200.00/min [580000], rate=91578.95/min [590000], rate=91472.87/min [600000], rate=91603.05/min [610000], rate=92191.44/min [620000], rate=92537.31/min [630000], rate=92195.12/min [640000], rate=90780.14/min [650000], rate=89861.75/min [660000], rate=88988.76/min [670000], rate=87772.93/min [680000], rate=87366.17/min [690000], rate=86792.45/min [700000], rate=86242.30/min [710000], rate=86234.82/min [720000], rate=86055.78/min [730000], rate=85882.35/min [740000], rate=86213.59/min [750000], rate=86206.90/min [760000], rate=85714.29/min -building interval tree based on /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=60000.00/min [20000], rate=63157.89/min [30000], rate=66666.67/min [40000], rate=68571.43/min [50000], rate=73170.73/min [60000], rate=76595.74/min [70000], rate=73684.21/min [80000], rate=69565.22/min [90000], rate=66666.67/min [100000], rate=65217.39/min [110000], rate=66666.67/min [120000], rate=66666.67/min [130000], rate=67241.38/min [140000], rate=68292.68/min [150000], rate=69767.44/min [160000], rate=71111.11/min [170000], rate=73381.29/min [180000], rate=72000.00/min [190000], rate=70807.45/min [200000], rate=69767.44/min [210000], rate=69613.26/min [220000], rate=69841.27/min [230000], rate=69696.97/min [240000], rate=69565.22/min [250000], rate=69767.44/min [260000], rate=70909.09/min [270000], rate=72645.74/min [280000], rate=73043.48/min [290000], rate=73417.72/min [300000], rate=73770.49/min [310000], rate=71814.67/min [320000], rate=70848.71/min [330000], rate=70462.63/min [340000], rate=70103.09/min [350000], rate=70234.11/min [360000], rate=69902.91/min [370000], rate=69811.32/min [380000], rate=69512.20/min [390000], rate=69436.20/min [400000], rate=69767.44/min [410000], rate=69886.36/min [420000], rate=70391.06/min [430000], rate=70879.12/min [440000], rate=71739.13/min [450000], rate=72386.06/min [460000], rate=72631.58/min [470000], rate=72680.41/min [480000], rate=72544.08/min [490000], rate=72413.79/min [500000], rate=72463.77/min [510000], rate=72684.09/min [520000], rate=73411.76/min [530000], rate=73953.49/min [540000], rate=73636.36/min [550000], rate=73170.73/min [560000], rate=72885.03/min [570000], rate=72611.46/min [580000], rate=72803.35/min [590000], rate=72839.51/min [600000], rate=73022.31/min [610000], rate=74089.07/min [620000], rate=75000.00/min [630000], rate=75298.80/min [640000], rate=75739.64/min [650000], rate=75728.16/min [660000], rate=75572.52/min [670000], rate=75422.14/min [680000], rate=75415.90/min [690000], rate=75685.56/min [700000], rate=75949.37/min [710000], rate=76344.09/min [720000], rate=76595.74/min [730000], rate=77385.16/min [740000], rate=77894.74/min [750000], rate=78125.00/min [760000], rate=78485.37/min -building interval tree based on /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=109090.91/min [30000], rate=112500.00/min [40000], rate=114285.71/min [50000], rate=130434.78/min [60000], rate=128571.43/min [70000], rate=144827.59/min [80000], rate=145454.55/min [90000], rate=142105.26/min [100000], rate=146341.46/min [110000], rate=140425.53/min [120000], rate=141176.47/min [130000], rate=141818.18/min [140000], rate=144827.59/min [150000], rate=152542.37/min [160000], rate=147692.31/min [170000], rate=150000.00/min [180000], rate=147945.21/min [190000], rate=148051.95/min [200000], rate=146341.46/min [210000], rate=148235.29/min [220000], rate=148314.61/min [230000], rate=146808.51/min [240000], rate=146938.78/min [250000], rate=144230.77/min [260000], rate=144444.44/min [270000], rate=143362.83/min [280000], rate=144827.59/min [290000], rate=141463.41/min [300000], rate=129496.40/min [310000], rate=119230.77/min [320000], rate=109714.29/min [330000], rate=103125.00/min [340000], rate=98076.92/min [350000], rate=93333.33/min [360000], rate=89256.20/min [370000], rate=87058.82/min [380000], rate=85074.63/min [390000], rate=83870.97/min [400000], rate=82474.23/min [410000], rate=82274.25/min [420000], rate=81818.18/min [430000], rate=81132.08/min [440000], rate=81230.77/min [450000], rate=81325.30/min [460000], rate=81656.80/min [470000], rate=81739.13/min [480000], rate=80898.88/min [490000], rate=80547.95/min [500000], rate=80428.95/min [510000], rate=80526.32/min [520000], rate=81038.96/min [530000], rate=81329.92/min [540000], rate=81407.04/min [550000], rate=81683.17/min [560000], rate=82352.94/min [570000], rate=81428.57/min [580000], rate=80555.56/min [590000], rate=79550.56/min [600000], rate=78947.37/min [610000], rate=78709.68/min [620000], rate=77987.42/min [630000], rate=77618.07/min [640000], rate=77263.58/min [650000], rate=77227.72/min [660000], rate=77343.75/min [670000], rate=77456.65/min [680000], rate=77419.35/min [690000], rate=77673.55/min [700000], rate=77348.07/min [710000], rate=76481.15/min [720000], rate=76056.34/min [730000], rate=75647.67/min [740000], rate=75254.24/min [750000], rate=75000.00/min -building interval tree based on /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=80000.00/min [30000], rate=85714.29/min [40000], rate=88888.89/min [50000], rate=93750.00/min [60000], rate=90000.00/min [70000], rate=89361.70/min [80000], rate=90566.04/min [90000], rate=90000.00/min [100000], rate=84507.04/min [110000], rate=82500.00/min [120000], rate=81818.18/min [130000], rate=82105.26/min [140000], rate=83168.32/min [150000], rate=84112.15/min [160000], rate=84955.75/min [170000], rate=82926.83/min [180000], rate=81203.01/min [190000], rate=83823.53/min [200000], rate=85714.29/min [210000], rate=85714.29/min [220000], rate=84615.38/min [230000], rate=85185.19/min [240000], rate=85207.10/min [250000], rate=86206.90/min [260000], rate=84324.32/min [270000], rate=82653.06/min [280000], rate=82758.62/min [290000], rate=80930.23/min [300000], rate=79295.15/min [310000], rate=78151.26/min [320000], rate=77108.43/min [330000], rate=76447.88/min [340000], rate=75836.43/min [350000], rate=75268.82/min [360000], rate=75261.32/min [370000], rate=75510.20/min [380000], rate=75247.52/min [390000], rate=75241.16/min [400000], rate=75471.70/min [410000], rate=75692.31/min [420000], rate=76363.64/min [430000], rate=77245.51/min [440000], rate=76967.93/min [450000], rate=75842.70/min [460000], rate=75204.36/min [470000], rate=74406.33/min [480000], rate=73657.29/min [490000], rate=72952.85/min [500000], rate=72639.23/min [510000], rate=72511.85/min [520000], rate=72389.79/min [530000], rate=72108.84/min [540000], rate=71523.18/min [550000], rate=71274.30/min [560000], rate=71489.36/min [570000], rate=71698.11/min [580000], rate=72199.17/min [590000], rate=72244.90/min [600000], rate=73170.73/min [610000], rate=73790.32/min [620000], rate=74103.59/min [630000], rate=74556.21/min [640000], rate=74131.27/min [650000], rate=73446.33/min [660000], rate=72794.12/min [670000], rate=72563.18/min [680000], rate=72084.81/min [690000], rate=71750.43/min [700000], rate=71428.57/min [710000], rate=71118.53/min [720000], rate=71169.69/min [730000], rate=71219.51/min [740000], rate=71382.64/min [750000], rate=71884.98/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir --filt_file /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.56jxr4OFHH/./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... 9000000.00 reads per min processed... 8000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 5400000.00 reads per min processed... 5000000.00 reads per min processed... 5076923.08 reads per min processed... 5142857.14 reads per min processed... 4875000.00 reads per min processed... 4941176.47 reads per min processed... 5000000.00 reads per min processed... 5052631.58 reads per min processed... 5100000.00 reads per min processed... 5142857.14 reads per min processed... 5181818.18 reads per min processed... 5217391.30 reads per min processed... 5040000.00 reads per min processed... 5076923.08 reads per min processed... 5111111.11 reads per min processed... 4965517.24 reads per min processed... 5000000.00 reads per min processed... 5032258.06 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.56jxr4OFHH/ColoN_FFPE_L02_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.56jxr4OFHH/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -44967.404931 EM: Round [1] log likelihood: -44826.249782 EM: Round [2] log likelihood: -44768.775124 EM: Round [3] log likelihood: -44740.176890 EM: Round [4] log likelihood: -44724.699340 EM: Round [5] log likelihood: -44715.965464 EM: Round [6] log likelihood: -44710.869115 EM: Round [7] log likelihood: -44707.790871 EM: Round [8] log likelihood: -44705.864663 EM: Round [9] log likelihood: -44704.617396 EM: Round [10] log likelihood: -44703.783613 EM: Round [11] log likelihood: -44703.209721 EM: Round [12] log likelihood: -44702.804041 EM: Round [13] log likelihood: -44702.510209 EM: Round [14] log likelihood: -44702.292614 EM: Round [15] log likelihood: -44702.128187 EM: Round [16] log likelihood: -44702.001630 EM: Round [17] log likelihood: -44701.902579 EM: Round [18] log likelihood: -44701.823870 EM: Round [19] log likelihood: -44701.760455 EM: Round [20] log likelihood: -44701.708716 EM: Round [21] log likelihood: -44701.666015 EM: Round [22] log likelihood: -44701.630399 EM: Round [23] log likelihood: -44701.600402 EM: Round [24] log likelihood: -44701.574907 EM: Round [25] log likelihood: -44701.553053 EM: Round [26] log likelihood: -44701.534171 EM: Round [27] log likelihood: -44701.517731 EM: Round [28] log likelihood: -44701.503315 EM: Round [29] log likelihood: -44701.490586 EM: Round [30] log likelihood: -44701.479271 EM: Round [31] log likelihood: -44701.469150 EM: Round [32] log likelihood: -44701.460042 EM: Round [33] log likelihood: -44701.451797 EM: Round [34] log likelihood: -44701.444293 EM: Round [35] log likelihood: -44701.437427 EM: Round [36] log likelihood: -44701.431114 EM: Round [37] log likelihood: -44701.425282 EM: Round [38] log likelihood: -44701.419871 EM: Round [39] log likelihood: -44701.414831 EM: Round [40] log likelihood: -44701.410117 EM: Round [41] log likelihood: -44701.405694 EM: Round [42] log likelihood: -44701.401531 EM: Round [43] log likelihood: -44701.397600 EM: Round [44] log likelihood: -44701.393879 EM: Round [45] log likelihood: -44701.390349 EM: Round [46] log likelihood: -44701.386992 EM: Round [47] log likelihood: -44701.383793 EM: Round [48] log likelihood: -44701.380740 EM: Round [49] log likelihood: -44701.377822 EM: Round [50] log likelihood: -44701.375028 EM: Round [51] log likelihood: -44701.372350 EM: Round [52] log likelihood: -44701.369780 EM: Round [53] log likelihood: -44701.367312 EM: Round [54] log likelihood: -44701.364939 EM: Round [55] log likelihood: -44701.362655 EM: Round [56] log likelihood: -44701.360457 EM: Round [57] log likelihood: -44701.358339 EM: Round [58] log likelihood: -44701.356297 EM: Round [59] log likelihood: -44701.354328 EM: Round [60] log likelihood: -44701.352428 EM: Round [61] log likelihood: -44701.350594 EM: Round [62] log likelihood: -44701.348823 EM: Round [63] log likelihood: -44701.347113 EM: Round [64] log likelihood: -44701.345461 EM: Round [65] log likelihood: -44701.343865 EM: Round [66] log likelihood: -44701.342321 EM: Round [67] log likelihood: -44701.340830 EM: Round [68] log likelihood: -44701.339387 EM: Round [69] log likelihood: -44701.337992 EM: Round [70] log likelihood: -44701.336643 EM: Round [71] log likelihood: -44701.335338 EM: Round [72] log likelihood: -44701.334075 EM: Round [73] log likelihood: -44701.332853 EM: Round [74] log likelihood: -44701.331671 EM: Round [75] log likelihood: -44701.330527 EM: Round [76] log likelihood: -44701.329419 EM: Round [77] log likelihood: -44701.328347 EM: Round [78] log likelihood: -44701.327309 EM: Round [79] log likelihood: -44701.326305 EM: Round [80] log likelihood: -44701.325332 EM: Round [81] log likelihood: -44701.324390 EM: Round [82] log likelihood: -44701.323477 EM: Round [83] log likelihood: -44701.322594 EM: Round [84] log likelihood: -44701.321738 EM: Round [85] log likelihood: -44701.320909 EM: Round [86] log likelihood: -44701.320106 EM: Round [87] log likelihood: -44701.319328 EM: Round [88] log likelihood: -44701.318574 EM: Round [89] log likelihood: -44701.317844 EM: Round [90] log likelihood: -44701.317136 EM: Round [91] log likelihood: -44701.316450 EM: Round [92] log likelihood: -44701.315785 EM: Round [93] log likelihood: -44701.315140 EM: Round [94] log likelihood: -44701.314516 EM: Round [95] log likelihood: -44701.313910 EM: Round [96] log likelihood: -44701.313322 EM: Round [97] log likelihood: -44701.312753 EM: Round [98] log likelihood: -44701.312201 EM: Round [99] log likelihood: -44701.311665 EM: Round [100] log likelihood: -44701.311145 EM: Round [101] log likelihood: -44701.310641 EM: Round [102] log likelihood: -44701.310152 EM: Round [103] log likelihood: -44701.309678 EM: Round [104] log likelihood: -44701.309218 EM: Round [105] log likelihood: -44701.308771 EM: Round [106] log likelihood: -44701.308338 EM: Round [107] log likelihood: -44701.307917 EM: Round [108] log likelihood: -44701.307508 EM: Round [109] log likelihood: -44701.307112 EM: Round [110] log likelihood: -44701.306727 EM: Round [111] log likelihood: -44701.306353 EM: Round [112] log likelihood: -44701.305990 EM: Round [113] log likelihood: -44701.305638 EM: Round [114] log likelihood: -44701.305295 EM: Round [115] log likelihood: -44701.304962 EM: Round [116] log likelihood: -44701.304639 EM: Round [117] log likelihood: -44701.304325 EM: Round [118] log likelihood: -44701.304020 EM: Round [119] log likelihood: -44701.303724 EM: Round [120] log likelihood: -44701.303436 EM: Round [121] log likelihood: -44701.303156 EM: Round [122] log likelihood: -44701.302884 EM: Round [123] log likelihood: -44701.302619 EM: Round [124] log likelihood: -44701.302362 EM: Round [125] log likelihood: -44701.302112 EM: Round [126] log likelihood: -44701.301868 EM: Round [127] log likelihood: -44701.301632 EM: Round [128] log likelihood: -44701.301402 EM: Round [129] log likelihood: -44701.301178 EM: Round [130] log likelihood: -44701.300960 EM: Round [131] log likelihood: -44701.300748 EM: Round [132] log likelihood: -44701.300542 EM: Round [133] log likelihood: -44701.300341 EM: Round [134] log likelihood: -44701.300146 EM: Round [135] log likelihood: -44701.299956 EM: Round [136] log likelihood: -44701.299771 EM: Round [137] log likelihood: -44701.299591 EM: Round [138] log likelihood: -44701.299416 EM: Round [139] log likelihood: -44701.299245 EM: Round [140] log likelihood: -44701.299079 EM: Round [141] log likelihood: -44701.298918 EM: Round [142] log likelihood: -44701.298760 EM: Round [143] log likelihood: -44701.298606 EM: Round [144] log likelihood: -44701.298457 EM: Round [145] log likelihood: -44701.298311 EM: Round [146] log likelihood: -44701.298170 EM: Round [147] log likelihood: -44701.298031 EM: Round [148] log likelihood: -44701.297897 EM: Round [149] log likelihood: -44701.297765 EM: Round [150] log likelihood: -44701.297637 EM: Round [151] log likelihood: -44701.297513 EM: Round [152] log likelihood: -44701.297391 EM: Round [153] log likelihood: -44701.297273 EM: Round [154] log likelihood: -44701.297157 EM: Round [155] log likelihood: -44701.297045 EM: Round [156] log likelihood: -44701.296935 EM: Round [157] log likelihood: -44701.296828 EM: Round [158] log likelihood: -44701.296723 EM: Round [159] log likelihood: -44701.296622 EM: Round [160] log likelihood: -44701.296522 EM: Stopping iterations at round 160 due to insufficient improvement in likelihood. EM: Starting log likelihood: -44927.931917 EM: Round [1] log likelihood: -44804.785007 EM: Round [2] log likelihood: -44756.408030 EM: Round [3] log likelihood: -44732.773174 EM: Round [4] log likelihood: -44720.144920 EM: Round [5] log likelihood: -44713.081896 EM: Round [6] log likelihood: -44708.984019 EM: Round [7] log likelihood: -44706.517778 EM: Round [8] log likelihood: -44704.978264 EM: Round [9] log likelihood: -44703.983181 EM: Round [10] log likelihood: -44703.318910 EM: Round [11] log likelihood: -44702.862149 EM: Round [12] log likelihood: -44702.539427 EM: Round [13] log likelihood: -44702.305640 EM: Round [14] log likelihood: -44702.132343 EM: Round [15] log likelihood: -44702.001143 EM: Round [16] log likelihood: -44701.899873 EM: Round [17] log likelihood: -44701.820311 EM: Round [18] log likelihood: -44701.756786 EM: Round [19] log likelihood: -44701.705316 EM: Round [20] log likelihood: -44701.663051 EM: Round [21] log likelihood: -44701.627918 EM: Round [22] log likelihood: -44701.598385 EM: Round [23] log likelihood: -44701.573304 EM: Round [24] log likelihood: -44701.551801 EM: Round [25] log likelihood: -44701.533203 EM: Round [26] log likelihood: -44701.516985 EM: Round [27] log likelihood: -44701.502734 EM: Round [28] log likelihood: -44701.490120 EM: Round [29] log likelihood: -44701.478879 EM: Round [30] log likelihood: -44701.468798 EM: Round [31] log likelihood: -44701.459701 EM: Round [32] log likelihood: -44701.451446 EM: Round [33] log likelihood: -44701.443913 EM: Round [34] log likelihood: -44701.437006 EM: Round [35] log likelihood: -44701.430641 EM: Round [36] log likelihood: -44701.424751 EM: Round [37] log likelihood: -44701.419277 EM: Round [38] log likelihood: -44701.414170 EM: Round [39] log likelihood: -44701.409388 EM: Round [40] log likelihood: -44701.404898 EM: Round [41] log likelihood: -44701.400667 EM: Round [42] log likelihood: -44701.396671 EM: Round [43] log likelihood: -44701.392887 EM: Round [44] log likelihood: -44701.389295 EM: Round [45] log likelihood: -44701.385880 EM: Round [46] log likelihood: -44701.382625 EM: Round [47] log likelihood: -44701.379520 EM: Round [48] log likelihood: -44701.376552 EM: Round [49] log likelihood: -44701.373711 EM: Round [50] log likelihood: -44701.370989 EM: Round [51] log likelihood: -44701.368379 EM: Round [52] log likelihood: -44701.365872 EM: Round [53] log likelihood: -44701.363464 EM: Round [54] log likelihood: -44701.361148 EM: Round [55] log likelihood: -44701.358920 EM: Round [56] log likelihood: -44701.356774 EM: Round [57] log likelihood: -44701.354708 EM: Round [58] log likelihood: -44701.352716 EM: Round [59] log likelihood: -44701.350796 EM: Round [60] log likelihood: -44701.348943 EM: Round [61] log likelihood: -44701.347156 EM: Round [62] log likelihood: -44701.345432 EM: Round [63] log likelihood: -44701.343767 EM: Round [64] log likelihood: -44701.342159 EM: Round [65] log likelihood: -44701.340607 EM: Round [66] log likelihood: -44701.339107 EM: Round [67] log likelihood: -44701.337658 EM: Round [68] log likelihood: -44701.336258 EM: Round [69] log likelihood: -44701.334905 EM: Round [70] log likelihood: -44701.333598 EM: Round [71] log likelihood: -44701.332334 EM: Round [72] log likelihood: -44701.331112 EM: Round [73] log likelihood: -44701.329931 EM: Round [74] log likelihood: -44701.328789 EM: Round [75] log likelihood: -44701.327684 EM: Round [76] log likelihood: -44701.326616 EM: Round [77] log likelihood: -44701.325583 EM: Round [78] log likelihood: -44701.324584 EM: Round [79] log likelihood: -44701.323617 EM: Round [80] log likelihood: -44701.322682 EM: Round [81] log likelihood: -44701.321778 EM: Round [82] log likelihood: -44701.320903 EM: Round [83] log likelihood: -44701.320056 EM: Round [84] log likelihood: -44701.319237 EM: Round [85] log likelihood: -44701.318444 EM: Round [86] log likelihood: -44701.317677 EM: Round [87] log likelihood: -44701.316935 EM: Round [88] log likelihood: -44701.316216 EM: Round [89] log likelihood: -44701.315520 EM: Round [90] log likelihood: -44701.314847 EM: Round [91] log likelihood: -44701.314195 EM: Round [92] log likelihood: -44701.313564 EM: Round [93] log likelihood: -44701.312953 EM: Round [94] log likelihood: -44701.312361 EM: Round [95] log likelihood: -44701.311788 EM: Round [96] log likelihood: -44701.311233 EM: Round [97] log likelihood: -44701.310696 EM: Round [98] log likelihood: -44701.310175 EM: Round [99] log likelihood: -44701.309671 EM: Round [100] log likelihood: -44701.309182 EM: Round [101] log likelihood: -44701.308709 EM: Round [102] log likelihood: -44701.308250 EM: Round [103] log likelihood: -44701.307806 EM: Round [104] log likelihood: -44701.307375 EM: Round [105] log likelihood: -44701.306958 EM: Round [106] log likelihood: -44701.306553 EM: Round [107] log likelihood: -44701.306161 EM: Round [108] log likelihood: -44701.305781 EM: Round [109] log likelihood: -44701.305412 EM: Round [110] log likelihood: -44701.305055 EM: Round [111] log likelihood: -44701.304708 EM: Round [112] log likelihood: -44701.304372 EM: Round [113] log likelihood: -44701.304046 EM: Round [114] log likelihood: -44701.303730 EM: Round [115] log likelihood: -44701.303423 EM: Round [116] log likelihood: -44701.303126 EM: Round [117] log likelihood: -44701.302837 EM: Round [118] log likelihood: -44701.302557 EM: Round [119] log likelihood: -44701.302285 EM: Round [120] log likelihood: -44701.302021 EM: Round [121] log likelihood: -44701.301765 EM: Round [122] log likelihood: -44701.301516 EM: Round [123] log likelihood: -44701.301275 EM: Round [124] log likelihood: -44701.301041 EM: Round [125] log likelihood: -44701.300813 EM: Round [126] log likelihood: -44701.300592 EM: Round [127] log likelihood: -44701.300378 EM: Round [128] log likelihood: -44701.300169 EM: Round [129] log likelihood: -44701.299967 EM: Round [130] log likelihood: -44701.299770 EM: Round [131] log likelihood: -44701.299579 EM: Round [132] log likelihood: -44701.299393 EM: Round [133] log likelihood: -44701.299213 EM: Round [134] log likelihood: -44701.299037 EM: Round [135] log likelihood: -44701.298867 EM: Round [136] log likelihood: -44701.298701 EM: Round [137] log likelihood: -44701.298540 EM: Round [138] log likelihood: -44701.298384 EM: Round [139] log likelihood: -44701.298232 EM: Round [140] log likelihood: -44701.298084 EM: Round [141] log likelihood: -44701.297940 EM: Round [142] log likelihood: -44701.297800 EM: Round [143] log likelihood: -44701.297663 EM: Round [144] log likelihood: -44701.297531 EM: Round [145] log likelihood: -44701.297402 EM: Round [146] log likelihood: -44701.297277 EM: Round [147] log likelihood: -44701.297155 EM: Round [148] log likelihood: -44701.297036 EM: Round [149] log likelihood: -44701.296920 EM: Round [150] log likelihood: -44701.296808 EM: Round [151] log likelihood: -44701.296698 EM: Round [152] log likelihood: -44701.296592 EM: Round [153] log likelihood: -44701.296488 EM: Round [154] log likelihood: -44701.296387 EM: Round [155] log likelihood: -44701.296288 EM: Stopping iterations at round 155 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 30694500 > /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir > /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir --annotate /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir -done, see /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 200, filtered: 2935) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000181577.16] WARNING, no entry stored in dbm for [ENSG00000247809.9] WARNING, no entry stored in dbm for [ENSG00000230202.1] WARNING, no entry stored in dbm for [ENSG00000181126.13] WARNING, no entry stored in dbm for [ENSG00000258537.5] WARNING, no entry stored in dbm for [ENSG00000250802.7] WARNING, no entry stored in dbm for [ENSG00000255319.5] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000285367.1] WARNING, no entry stored in dbm for [ENSG00000240549.2] WARNING, no entry stored in dbm for [ENSG00000258313.1] WARNING, no entry stored in dbm for [ENSG00000272447.1] WARNING, no entry stored in dbm for [ENSG00000267433.1] WARNING, no entry stored in dbm for [ENSG00000185986.12] WARNING, no entry stored in dbm for [ENSG00000214135.8] WARNING, no entry stored in dbm for [ENSG00000246889.2] WARNING, no entry stored in dbm for [ENSG00000270111.3] WARNING, no entry stored in dbm for [ENSG00000196183.5] WARNING, no entry stored in dbm for [ENSG00000202441.2] WARNING, no entry stored in dbm for [ENSG00000202124.1] WARNING, no entry stored in dbm for [ENSG00000202441.2] WARNING, no entry stored in dbm for [ENSG00000238711.1] WARNING, no entry stored in dbm for [ENSG00000202441.2] WARNING, no entry stored in dbm for [ENSG00000201377.1] WARNING, no entry stored in dbm for [ENSG00000202441.2] WARNING, no entry stored in dbm for [ENSG00000199400.1] WARNING, no entry stored in dbm for [ENSG00000202441.2] WARNING, no entry stored in dbm for [ENSG00000267482.1] WARNING, no entry stored in dbm for [ENSG00000207357.1] WARNING, no entry stored in dbm for [ENSG00000263934.5] WARNING, no entry stored in dbm for [ENSG00000278525.1] WARNING, no entry stored in dbm for [ENSG00000263740.2] WARNING, no entry stored in dbm for [ENSG00000278525.1] WARNING, no entry stored in dbm for [ENSG00000244642.3] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000200794.1] WARNING, no entry stored in dbm for [ENSG00000269900.3] WARNING, no entry stored in dbm for [ENSG00000127957.18] WARNING, no entry stored in dbm for [ENSG00000271538.6] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000232610.1] WARNING, no entry stored in dbm for [ENSG00000261610.1] WARNING, no entry stored in dbm for [ENSG00000228666.1] WARNING, no entry stored in dbm for [ENSG00000280927.1] WARNING, no entry stored in dbm for [ENSG00000257137.7] WARNING, no entry stored in dbm for [ENSG00000226581.2] WARNING, no entry stored in dbm for [ENSG00000261863.1] WARNING, no entry stored in dbm for [ENSG00000283103.3] WARNING, no entry stored in dbm for [ENSG00000270926.1] 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 [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000240477.1] WARNING, no entry stored in dbm for [ENSG00000232022.7] WARNING, no entry stored in dbm for [ENSG00000270482.1] WARNING, no entry stored in dbm for [ENSG00000267328.1] WARNING, no entry stored in dbm for [ENSG00000173077.16] WARNING, no entry stored in dbm for [ENSG00000255136.3] WARNING, no entry stored in dbm for [ENSG00000242186.2] WARNING, no entry stored in dbm for [ENSG00000266522.1] WARNING, no entry stored in dbm for [ENSG00000254590.1] WARNING, no entry stored in dbm for [ENSG00000196312.15] WARNING, no entry stored in dbm for [ENSG00000272106.1] WARNING, no entry stored in dbm for [ENSG00000235582.2] WARNING, no entry stored in dbm for [ENSG00000280285.1] WARNING, no entry stored in dbm for [ENSG00000279406.1] WARNING, no entry stored in dbm for [ENSG00000279738.1] WARNING, no entry stored in dbm for [ENSG00000271519.1] WARNING, no entry stored in dbm for [ENSG00000232855.7] WARNING, no entry stored in dbm for [ENSG00000229930.1] WARNING, no entry stored in dbm for [ENSG00000284675.1] WARNING, no entry stored in dbm for [ENSG00000282057.1] WARNING, no entry stored in dbm for [ENSG00000283849.1] WARNING, no entry stored in dbm for [ENSG00000239268.3] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000224016.2] WARNING, no entry stored in dbm for [ENSG00000264151.6] WARNING, no entry stored in dbm for [ENSG00000264151.6] WARNING, no entry stored in dbm for [ENSG00000264151.6] WARNING, no entry stored in dbm for [ENSG00000257337.7] WARNING, no entry stored in dbm for [ENSG00000185641.6] WARNING, no entry stored in dbm for [ENSG00000235725.1] WARNING, no entry stored in dbm for [ENSG00000284052.1] WARNING, no entry stored in dbm for [ENSG00000271163.1] WARNING, no entry stored in dbm for [ENSG00000271394.1] WARNING, no entry stored in dbm for [ENSG00000200794.1] * STAR-Fusion complete. See output: /tmp/nxf.56jxr4OFHH/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)