-ctat genome lib [/tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.WDxxwGDlGF/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary -sample contains 37936168 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir -J /tmp/nxf.WDxxwGDlGF/EndoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.WDxxwGDlGF/EndoN_FFPE_L08_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=50000.00/min [20000], rate=54545.45/min [30000], rate=56250.00/min [40000], rate=60000.00/min [50000], rate=65217.39/min [60000], rate=67924.53/min [70000], rate=65625.00/min [80000], rate=58536.59/min [90000], rate=54545.45/min [100000], rate=51282.05/min [110000], rate=48888.89/min [120000], rate=47368.42/min [130000], rate=47272.73/min [140000], rate=47191.01/min [150000], rate=46632.12/min [160000], rate=47058.82/min [170000], rate=47441.86/min [180000], rate=47787.61/min [190000], rate=48101.27/min [200000], rate=48780.49/min [210000], rate=50000.00/min [220000], rate=51562.50/min [230000], rate=52471.48/min [240000], rate=53531.60/min [250000], rate=54744.53/min [260000], rate=54929.58/min [270000], rate=55479.45/min [280000], rate=56187.29/min [290000], rate=56862.75/min [300000], rate=57692.31/min [310000], rate=58307.21/min [320000], rate=58895.71/min [330000], rate=60000.00/min [340000], rate=60714.29/min [350000], rate=61403.51/min [360000], rate=62247.84/min [370000], rate=63610.32/min [380000], rate=64225.35/min [390000], rate=65363.13/min [400000], rate=66115.70/min [410000], rate=66307.28/min [420000], rate=66843.50/min [430000], rate=67894.74/min [440000], rate=68217.05/min [450000], rate=68877.55/min [460000], rate=69346.73/min [470000], rate=70149.25/min [480000], rate=70761.67/min [490000], rate=71359.22/min [500000], rate=72289.16/min [510000], rate=72857.14/min [520000], rate=73758.87/min [530000], rate=75000.00/min [540000], rate=76056.34/min [550000], rate=76212.47/min [560000], rate=76363.64/min [570000], rate=76681.61/min [580000], rate=76651.98/min [590000], rate=77292.58/min [600000], rate=78091.11/min [610000], rate=78540.77/min [620000], rate=79317.70/min [630000], rate=79578.95/min [640000], rate=79668.05/min [650000], rate=80082.14/min [660000], rate=80000.00/min [670000], rate=79761.90/min [680000], rate=79843.44/min [690000], rate=79922.78/min [700000], rate=80152.67/min [710000], rate=79924.95/min [720000], rate=78688.52/min [730000], rate=77659.57/min [740000], rate=76683.94/min [750000], rate=75885.33/min [760000], rate=75247.52/min [770000], rate=74757.28/min [780000], rate=74880.00/min [790000], rate=74763.41/min -building interval tree based on /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=92307.69/min [30000], rate=100000.00/min [40000], rate=96000.00/min [50000], rate=107142.86/min [60000], rate=116129.03/min [70000], rate=116666.67/min [80000], rate=126315.79/min [90000], rate=138461.54/min [100000], rate=146341.46/min [110000], rate=137500.00/min [120000], rate=135849.06/min [130000], rate=132203.39/min [140000], rate=129230.77/min [150000], rate=132352.94/min [160000], rate=133333.33/min [170000], rate=136000.00/min [180000], rate=142105.26/min [190000], rate=148051.95/min [200000], rate=148148.15/min [210000], rate=141573.03/min [220000], rate=140425.53/min [230000], rate=139393.94/min [240000], rate=137142.86/min [250000], rate=137614.68/min [260000], rate=139285.71/min [270000], rate=138461.54/min [280000], rate=140000.00/min [290000], rate=138095.24/min [300000], rate=134328.36/min [310000], rate=133812.95/min [320000], rate=129729.73/min [330000], rate=131125.83/min [340000], rate=132467.53/min [350000], rate=132911.39/min [360000], rate=134161.49/min [370000], rate=120000.00/min [380000], rate=109090.91/min [390000], rate=101739.13/min [400000], rate=96000.00/min [410000], rate=91449.81/min [420000], rate=86597.94/min [430000], rate=83225.81/min [440000], rate=80487.80/min [450000], rate=78488.37/min [460000], rate=77094.97/min [470000], rate=75806.45/min [480000], rate=75000.00/min [490000], rate=74430.38/min [500000], rate=73710.07/min [510000], rate=73381.29/min [520000], rate=73411.76/min [530000], rate=73611.11/min [540000], rate=73804.10/min [550000], rate=74157.30/min [560000], rate=74008.81/min [570000], rate=73548.39/min [580000], rate=73417.72/min [590000], rate=73291.93/min [600000], rate=73022.31/min [610000], rate=73053.89/min [620000], rate=73228.35/min [630000], rate=73398.06/min [640000], rate=73704.41/min [650000], rate=73724.01/min [660000], rate=72660.55/min [670000], rate=71785.71/min [680000], rate=71080.14/min [690000], rate=70648.46/min [700000], rate=70116.86/min [710000], rate=69721.77/min [720000], rate=69230.77/min [730000], rate=69085.17/min [740000], rate=69051.32/min [750000], rate=69124.42/min [760000], rate=69300.91/min [770000], rate=69369.37/min [780000], rate=69333.33/min [790000], rate=68497.11/min -building interval tree based on /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=70588.24/min [30000], rate=58064.52/min [40000], rate=55813.95/min [50000], rate=56603.77/min [60000], rate=58064.52/min [70000], rate=60000.00/min [80000], rate=63157.89/min [90000], rate=65853.66/min [100000], rate=62500.00/min [110000], rate=59459.46/min [120000], rate=58064.52/min [130000], rate=56521.74/min [140000], rate=56375.84/min [150000], rate=56603.77/min [160000], rate=57831.33/min [170000], rate=58285.71/min [180000], rate=59016.39/min [190000], rate=60000.00/min [200000], rate=60913.71/min [210000], rate=59433.96/min [220000], rate=58407.08/min [230000], rate=57500.00/min [240000], rate=56917.00/min [250000], rate=56818.18/min [260000], rate=56521.74/min [270000], rate=56445.99/min [280000], rate=56565.66/min [290000], rate=57236.84/min [300000], rate=58252.43/min [310000], rate=58675.08/min [320000], rate=59442.72/min [330000], rate=59281.44/min [340000], rate=58452.72/min [350000], rate=58171.75/min [360000], rate=57754.01/min [370000], rate=57662.34/min [380000], rate=57721.52/min [390000], rate=57777.78/min [400000], rate=57971.01/min [410000], rate=57882.35/min [420000], rate=58198.61/min [430000], rate=58371.04/min [440000], rate=58666.67/min [450000], rate=58951.97/min [460000], rate=59482.76/min [470000], rate=60127.93/min [480000], rate=60631.58/min [490000], rate=60369.61/min [500000], rate=60362.17/min [510000], rate=60117.88/min [520000], rate=60115.61/min [530000], rate=60341.56/min [540000], rate=60674.16/min [550000], rate=61111.11/min [560000], rate=61764.71/min [570000], rate=62408.76/min [580000], rate=62929.48/min [590000], rate=62765.96/min [600000], rate=62500.00/min [610000], rate=62564.10/min [620000], rate=62626.26/min [630000], rate=62895.17/min [640000], rate=63054.19/min [650000], rate=63311.69/min [660000], rate=64181.52/min [670000], rate=64838.71/min [680000], rate=65175.72/min [690000], rate=65506.33/min [700000], rate=65420.56/min [710000], rate=65538.46/min [720000], rate=65653.50/min [730000], rate=65667.17/min [740000], rate=65777.78/min [750000], rate=66176.47/min [760000], rate=66472.30/min [770000], rate=67053.70/min [780000], rate=67532.47/min [790000], rate=67811.16/min -building interval tree based on /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=42857.14/min [20000], rate=44444.44/min [30000], rate=45000.00/min [40000], rate=46153.85/min [50000], rate=48387.10/min [60000], rate=51428.57/min [70000], rate=53846.15/min [80000], rate=57142.86/min [90000], rate=60000.00/min [100000], rate=61855.67/min [110000], rate=62857.14/min [120000], rate=64285.71/min [130000], rate=66101.69/min [140000], rate=66666.67/min [150000], rate=64748.20/min [160000], rate=64000.00/min [170000], rate=63354.04/min [180000], rate=63905.33/min [190000], rate=64772.73/min [200000], rate=65573.77/min [210000], rate=67741.94/min [220000], rate=68750.00/min [230000], rate=71134.02/min [240000], rate=71641.79/min [250000], rate=70093.46/min [260000], rate=69333.33/min [270000], rate=70742.36/min [280000], rate=70588.24/min [290000], rate=70731.71/min [300000], rate=71146.25/min [310000], rate=72093.02/min [320000], rate=72727.27/min [330000], rate=71739.13/min [340000], rate=70103.09/min [350000], rate=70000.00/min [360000], rate=68354.43/min [370000], rate=67069.49/min [380000], rate=66086.96/min [390000], rate=65546.22/min [400000], rate=64864.86/min [410000], rate=64736.84/min [420000], rate=64450.13/min [430000], rate=64179.10/min [440000], rate=64077.67/min [450000], rate=63829.79/min [460000], rate=63448.28/min [470000], rate=62946.43/min [480000], rate=62745.10/min [490000], rate=62553.19/min [500000], rate=62761.51/min [510000], rate=63092.78/min [520000], rate=63414.63/min [530000], rate=62109.38/min [540000], rate=61016.95/min [550000], rate=60329.07/min [560000], rate=59680.28/min [570000], rate=59272.10/min [580000], rate=58983.05/min [590000], rate=58609.27/min [600000], rate=58536.59/min [610000], rate=58466.45/min [620000], rate=58307.21/min [630000], rate=58333.33/min [640000], rate=58447.49/min [650000], rate=58646.62/min [660000], rate=59016.39/min [670000], rate=59292.04/min [680000], rate=59649.12/min [690000], rate=60262.01/min [700000], rate=60606.06/min [710000], rate=60857.14/min [720000], rate=60759.49/min [730000], rate=60413.79/min [740000], rate=59919.03/min [750000], rate=59445.18/min [760000], rate=59452.41/min [770000], rate=59230.77/min [780000], rate=59016.39/min [790000], rate=58881.99/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir --filt_file /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 6000000.00 reads per min processed... 9000000.00 reads per min processed... 6000000.00 reads per min processed... 5000000.00 reads per min processed... 4500000.00 reads per min processed... 4200000.00 reads per min processed... 4000000.00 reads per min processed... 3600000.00 reads per min processed... 3529411.76 reads per min processed... 3473684.21 reads per min processed... 3272727.27 reads per min processed... 3250000.00 reads per min processed... 3230769.23 reads per min processed... 3214285.71 reads per min processed... 3200000.00 reads per min processed... 3290322.58 reads per min processed... 3375000.00 reads per min processed... 3454545.45 reads per min processed... 3529411.76 reads per min processed... 3500000.00 reads per min processed... 3473684.21 reads per min processed... 3450000.00 reads per min processed... 3512195.12 reads per min processed... 3409090.91 reads per min processed... 3391304.35 reads per min processed... 3446808.51 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.WDxxwGDlGF/EndoN_FFPE_L08_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.WDxxwGDlGF/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -58458.390367 EM: Round [1] log likelihood: -58338.710545 EM: Round [2] log likelihood: -58290.128010 EM: Round [3] log likelihood: -58266.194161 EM: Round [4] log likelihood: -58253.214656 EM: Round [5] log likelihood: -58245.810929 EM: Round [6] log likelihood: -58241.448776 EM: Round [7] log likelihood: -58238.803835 EM: Round [8] log likelihood: -58237.149147 EM: Round [9] log likelihood: -58236.077821 EM: Round [10] log likelihood: -58235.359201 EM: Round [11] log likelihood: -58234.860312 EM: Round [12] log likelihood: -58234.502734 EM: Round [13] log likelihood: -58234.238950 EM: Round [14] log likelihood: -58234.039326 EM: Round [15] log likelihood: -58233.884827 EM: Round [16] log likelihood: -58233.762878 EM: Round [17] log likelihood: -58233.664950 EM: Round [18] log likelihood: -58233.585113 EM: Round [19] log likelihood: -58233.519153 EM: Round [20] log likelihood: -58233.464014 EM: Round [21] log likelihood: -58233.417442 EM: Round [22] log likelihood: -58233.377742 EM: Round [23] log likelihood: -58233.343625 EM: Round [24] log likelihood: -58233.314093 EM: Round [25] log likelihood: -58233.288365 EM: Round [26] log likelihood: -58233.265822 EM: Round [27] log likelihood: -58233.245968 EM: Round [28] log likelihood: -58233.228401 EM: Round [29] log likelihood: -58233.212793 EM: Round [30] log likelihood: -58233.198871 EM: Round [31] log likelihood: -58233.186410 EM: Round [32] log likelihood: -58233.175221 EM: Round [33] log likelihood: -58233.165142 EM: Round [34] log likelihood: -58233.156037 EM: Round [35] log likelihood: -58233.147790 EM: Round [36] log likelihood: -58233.140300 EM: Round [37] log likelihood: -58233.133479 EM: Round [38] log likelihood: -58233.127253 EM: Round [39] log likelihood: -58233.121556 EM: Round [40] log likelihood: -58233.116330 EM: Round [41] log likelihood: -58233.111525 EM: Round [42] log likelihood: -58233.107096 EM: Round [43] log likelihood: -58233.103004 EM: Round [44] log likelihood: -58233.099214 EM: Round [45] log likelihood: -58233.095696 EM: Round [46] log likelihood: -58233.092423 EM: Round [47] log likelihood: -58233.089370 EM: Round [48] log likelihood: -58233.086516 EM: Round [49] log likelihood: -58233.083842 EM: Round [50] log likelihood: -58233.081330 EM: Round [51] log likelihood: -58233.078967 EM: Round [52] log likelihood: -58233.076737 EM: Round [53] log likelihood: -58233.074628 EM: Round [54] log likelihood: -58233.072631 EM: Round [55] log likelihood: -58233.070735 EM: Round [56] log likelihood: -58233.068931 EM: Round [57] log likelihood: -58233.067212 EM: Round [58] log likelihood: -58233.065570 EM: Round [59] log likelihood: -58233.063999 EM: Round [60] log likelihood: -58233.062494 EM: Round [61] log likelihood: -58233.061049 EM: Round [62] log likelihood: -58233.059660 EM: Round [63] log likelihood: -58233.058323 EM: Round [64] log likelihood: -58233.057033 EM: Round [65] log likelihood: -58233.055788 EM: Round [66] log likelihood: -58233.054585 EM: Round [67] log likelihood: -58233.053420 EM: Round [68] log likelihood: -58233.052291 EM: Round [69] log likelihood: -58233.051196 EM: Round [70] log likelihood: -58233.050133 EM: Round [71] log likelihood: -58233.049100 EM: Round [72] log likelihood: -58233.048096 EM: Round [73] log likelihood: -58233.047118 EM: Round [74] log likelihood: -58233.046166 EM: Round [75] log likelihood: -58233.045238 EM: Round [76] log likelihood: -58233.044333 EM: Round [77] log likelihood: -58233.043450 EM: Round [78] log likelihood: -58233.042588 EM: Round [79] log likelihood: -58233.041746 EM: Round [80] log likelihood: -58233.040923 EM: Round [81] log likelihood: -58233.040119 EM: Round [82] log likelihood: -58233.039333 EM: Round [83] log likelihood: -58233.038564 EM: Round [84] log likelihood: -58233.037812 EM: Round [85] log likelihood: -58233.037076 EM: Round [86] log likelihood: -58233.036355 EM: Round [87] log likelihood: -58233.035650 EM: Round [88] log likelihood: -58233.034959 EM: Round [89] log likelihood: -58233.034283 EM: Round [90] log likelihood: -58233.033621 EM: Round [91] log likelihood: -58233.032972 EM: Round [92] log likelihood: -58233.032337 EM: Round [93] log likelihood: -58233.031714 EM: Round [94] log likelihood: -58233.031104 EM: Round [95] log likelihood: -58233.030507 EM: Round [96] log likelihood: -58233.029921 EM: Round [97] log likelihood: -58233.029347 EM: Round [98] log likelihood: -58233.028785 EM: Round [99] log likelihood: -58233.028235 EM: Round [100] log likelihood: -58233.027695 EM: Round [101] log likelihood: -58233.027166 EM: Round [102] log likelihood: -58233.026648 EM: Round [103] log likelihood: -58233.026141 EM: Round [104] log likelihood: -58233.025644 EM: Round [105] log likelihood: -58233.025156 EM: Round [106] log likelihood: -58233.024679 EM: Round [107] log likelihood: -58233.024212 EM: Round [108] log likelihood: -58233.023754 EM: Round [109] log likelihood: -58233.023305 EM: Round [110] log likelihood: -58233.022866 EM: Round [111] log likelihood: -58233.022435 EM: Round [112] log likelihood: -58233.022014 EM: Round [113] log likelihood: -58233.021601 EM: Round [114] log likelihood: -58233.021197 EM: Round [115] log likelihood: -58233.020801 EM: Round [116] log likelihood: -58233.020413 EM: Round [117] log likelihood: -58233.020034 EM: Round [118] log likelihood: -58233.019662 EM: Round [119] log likelihood: -58233.019299 EM: Round [120] log likelihood: -58233.018943 EM: Round [121] log likelihood: -58233.018594 EM: Round [122] log likelihood: -58233.018253 EM: Round [123] log likelihood: -58233.017920 EM: Round [124] log likelihood: -58233.017593 EM: Round [125] log likelihood: -58233.017273 EM: Round [126] log likelihood: -58233.016961 EM: Round [127] log likelihood: -58233.016655 EM: Round [128] log likelihood: -58233.016355 EM: Round [129] log likelihood: -58233.016062 EM: Round [130] log likelihood: -58233.015776 EM: Round [131] log likelihood: -58233.015495 EM: Round [132] log likelihood: -58233.015221 EM: Round [133] log likelihood: -58233.014953 EM: Round [134] log likelihood: -58233.014691 EM: Round [135] log likelihood: -58233.014434 EM: Round [136] log likelihood: -58233.014184 EM: Round [137] log likelihood: -58233.013938 EM: Round [138] log likelihood: -58233.013699 EM: Round [139] log likelihood: -58233.013464 EM: Round [140] log likelihood: -58233.013235 EM: Round [141] log likelihood: -58233.013011 EM: Round [142] log likelihood: -58233.012792 EM: Round [143] log likelihood: -58233.012578 EM: Round [144] log likelihood: -58233.012368 EM: Round [145] log likelihood: -58233.012164 EM: Round [146] log likelihood: -58233.011964 EM: Round [147] log likelihood: -58233.011768 EM: Round [148] log likelihood: -58233.011577 EM: Round [149] log likelihood: -58233.011391 EM: Round [150] log likelihood: -58233.011208 EM: Round [151] log likelihood: -58233.011030 EM: Round [152] log likelihood: -58233.010856 EM: Round [153] log likelihood: -58233.010686 EM: Round [154] log likelihood: -58233.010519 EM: Round [155] log likelihood: -58233.010357 EM: Round [156] log likelihood: -58233.010198 EM: Round [157] log likelihood: -58233.010043 EM: Round [158] log likelihood: -58233.009892 EM: Round [159] log likelihood: -58233.009744 EM: Round [160] log likelihood: -58233.009599 EM: Round [161] log likelihood: -58233.009458 EM: Round [162] log likelihood: -58233.009320 EM: Round [163] log likelihood: -58233.009186 EM: Round [164] log likelihood: -58233.009054 EM: Round [165] log likelihood: -58233.008926 EM: Round [166] log likelihood: -58233.008800 EM: Round [167] log likelihood: -58233.008678 EM: Round [168] log likelihood: -58233.008558 EM: Round [169] log likelihood: -58233.008441 EM: Round [170] log likelihood: -58233.008327 EM: Round [171] log likelihood: -58233.008216 EM: Round [172] log likelihood: -58233.008107 EM: Round [173] log likelihood: -58233.008001 EM: Round [174] log likelihood: -58233.007897 EM: Round [175] log likelihood: -58233.007796 EM: Round [176] log likelihood: -58233.007697 EM: Stopping iterations at round 176 due to insufficient improvement in likelihood. EM: Starting log likelihood: -58429.992898 EM: Round [1] log likelihood: -58322.821547 EM: Round [2] log likelihood: -58280.725245 EM: Round [3] log likelihood: -58260.519805 EM: Round [4] log likelihood: -58249.731143 EM: Round [5] log likelihood: -58243.619988 EM: Round [6] log likelihood: -58240.027344 EM: Round [7] log likelihood: -58237.848351 EM: Round [8] log likelihood: -58236.482951 EM: Round [9] log likelihood: -58235.596903 EM: Round [10] log likelihood: -58235.001030 EM: Round [11] log likelihood: -58234.586239 EM: Round [12] log likelihood: -58234.288115 EM: Round [13] log likelihood: -58234.067566 EM: Round [14] log likelihood: -58233.900170 EM: Round [15] log likelihood: -58233.770215 EM: Round [16] log likelihood: -58233.667309 EM: Round [17] log likelihood: -58233.584395 EM: Round [18] log likelihood: -58233.516563 EM: Round [19] log likelihood: -58233.460321 EM: Round [20] log likelihood: -58233.413138 EM: Round [21] log likelihood: -58233.373143 EM: Round [22] log likelihood: -58233.338932 EM: Round [23] log likelihood: -58233.309433 EM: Round [24] log likelihood: -58233.283817 EM: Round [25] log likelihood: -58233.261432 EM: Round [26] log likelihood: -58233.241764 EM: Round [27] log likelihood: -58233.224395 EM: Round [28] log likelihood: -58233.208990 EM: Round [29] log likelihood: -58233.195271 EM: Round [30] log likelihood: -58233.183008 EM: Round [31] log likelihood: -58233.172010 EM: Round [32] log likelihood: -58233.162116 EM: Round [33] log likelihood: -58233.153187 EM: Round [34] log likelihood: -58233.145108 EM: Round [35] log likelihood: -58233.137777 EM: Round [36] log likelihood: -58233.131109 EM: Round [37] log likelihood: -58233.125027 EM: Round [38] log likelihood: -58233.119466 EM: Round [39] log likelihood: -58233.114369 EM: Round [40] log likelihood: -58233.109686 EM: Round [41] log likelihood: -58233.105373 EM: Round [42] log likelihood: -58233.101391 EM: Round [43] log likelihood: -58233.097706 EM: Round [44] log likelihood: -58233.094287 EM: Round [45] log likelihood: -58233.091108 EM: Round [46] log likelihood: -58233.088145 EM: Round [47] log likelihood: -58233.085376 EM: Round [48] log likelihood: -58233.082783 EM: Round [49] log likelihood: -58233.080350 EM: Round [50] log likelihood: -58233.078060 EM: Round [51] log likelihood: -58233.075900 EM: Round [52] log likelihood: -58233.073860 EM: Round [53] log likelihood: -58233.071927 EM: Round [54] log likelihood: -58233.070093 EM: Round [55] log likelihood: -58233.068348 EM: Round [56] log likelihood: -58233.066686 EM: Round [57] log likelihood: -58233.065099 EM: Round [58] log likelihood: -58233.063581 EM: Round [59] log likelihood: -58233.062127 EM: Round [60] log likelihood: -58233.060731 EM: Round [61] log likelihood: -58233.059389 EM: Round [62] log likelihood: -58233.058097 EM: Round [63] log likelihood: -58233.056851 EM: Round [64] log likelihood: -58233.055649 EM: Round [65] log likelihood: -58233.054486 EM: Round [66] log likelihood: -58233.053361 EM: Round [67] log likelihood: -58233.052271 EM: Round [68] log likelihood: -58233.051213 EM: Round [69] log likelihood: -58233.050187 EM: Round [70] log likelihood: -58233.049189 EM: Round [71] log likelihood: -58233.048219 EM: Round [72] log likelihood: -58233.047274 EM: Round [73] log likelihood: -58233.046354 EM: Round [74] log likelihood: -58233.045457 EM: Round [75] log likelihood: -58233.044583 EM: Round [76] log likelihood: -58233.043729 EM: Round [77] log likelihood: -58233.042896 EM: Round [78] log likelihood: -58233.042082 EM: Round [79] log likelihood: -58233.041286 EM: Round [80] log likelihood: -58233.040509 EM: Round [81] log likelihood: -58233.039748 EM: Round [82] log likelihood: -58233.039004 EM: Round [83] log likelihood: -58233.038277 EM: Round [84] log likelihood: -58233.037564 EM: Round [85] log likelihood: -58233.036867 EM: Round [86] log likelihood: -58233.036184 EM: Round [87] log likelihood: -58233.035515 EM: Round [88] log likelihood: -58233.034860 EM: Round [89] log likelihood: -58233.034219 EM: Round [90] log likelihood: -58233.033590 EM: Round [91] log likelihood: -58233.032975 EM: Round [92] log likelihood: -58233.032371 EM: Round [93] log likelihood: -58233.031780 EM: Round [94] log likelihood: -58233.031201 EM: Round [95] log likelihood: -58233.030633 EM: Round [96] log likelihood: -58233.030076 EM: Round [97] log likelihood: -58233.029531 EM: Round [98] log likelihood: -58233.028997 EM: Round [99] log likelihood: -58233.028473 EM: Round [100] log likelihood: -58233.027960 EM: Round [101] log likelihood: -58233.027457 EM: Round [102] log likelihood: -58233.026964 EM: Round [103] log likelihood: -58233.026481 EM: Round [104] log likelihood: -58233.026008 EM: Round [105] log likelihood: -58233.025544 EM: Round [106] log likelihood: -58233.025090 EM: Round [107] log likelihood: -58233.024644 EM: Round [108] log likelihood: -58233.024208 EM: Round [109] log likelihood: -58233.023781 EM: Round [110] log likelihood: -58233.023362 EM: Round [111] log likelihood: -58233.022952 EM: Round [112] log likelihood: -58233.022551 EM: Round [113] log likelihood: -58233.022157 EM: Round [114] log likelihood: -58233.021772 EM: Round [115] log likelihood: -58233.021395 EM: Round [116] log likelihood: -58233.021025 EM: Round [117] log likelihood: -58233.020663 EM: Round [118] log likelihood: -58233.020309 EM: Round [119] log likelihood: -58233.019962 EM: Round [120] log likelihood: -58233.019623 EM: Round [121] log likelihood: -58233.019290 EM: Round [122] log likelihood: -58233.018965 EM: Round [123] log likelihood: -58233.018647 EM: Round [124] log likelihood: -58233.018335 EM: Round [125] log likelihood: -58233.018030 EM: Round [126] log likelihood: -58233.017732 EM: Round [127] log likelihood: -58233.017439 EM: Round [128] log likelihood: -58233.017154 EM: Round [129] log likelihood: -58233.016874 EM: Round [130] log likelihood: -58233.016600 EM: Round [131] log likelihood: -58233.016333 EM: Round [132] log likelihood: -58233.016071 EM: Round [133] log likelihood: -58233.015815 EM: Round [134] log likelihood: -58233.015564 EM: Round [135] log likelihood: -58233.015319 EM: Round [136] log likelihood: -58233.015080 EM: Round [137] log likelihood: -58233.014846 EM: Round [138] log likelihood: -58233.014616 EM: Round [139] log likelihood: -58233.014392 EM: Round [140] log likelihood: -58233.014173 EM: Round [141] log likelihood: -58233.013959 EM: Round [142] log likelihood: -58233.013750 EM: Round [143] log likelihood: -58233.013545 EM: Round [144] log likelihood: -58233.013345 EM: Round [145] log likelihood: -58233.013149 EM: Round [146] log likelihood: -58233.012958 EM: Round [147] log likelihood: -58233.012771 EM: Round [148] log likelihood: -58233.012589 EM: Round [149] log likelihood: -58233.012410 EM: Round [150] log likelihood: -58233.012236 EM: Round [151] log likelihood: -58233.012065 EM: Round [152] log likelihood: -58233.011898 EM: Round [153] log likelihood: -58233.011736 EM: Round [154] log likelihood: -58233.011577 EM: Round [155] log likelihood: -58233.011421 EM: Round [156] log likelihood: -58233.011269 EM: Round [157] log likelihood: -58233.011121 EM: Round [158] log likelihood: -58233.010976 EM: Round [159] log likelihood: -58233.010834 EM: Round [160] log likelihood: -58233.010696 EM: Round [161] log likelihood: -58233.010561 EM: Round [162] log likelihood: -58233.010429 EM: Round [163] log likelihood: -58233.010300 EM: Round [164] log likelihood: -58233.010174 EM: Round [165] log likelihood: -58233.010051 EM: Round [166] log likelihood: -58233.009931 EM: Round [167] log likelihood: -58233.009813 EM: Round [168] log likelihood: -58233.009699 EM: Round [169] log likelihood: -58233.009587 EM: Round [170] log likelihood: -58233.009478 EM: Round [171] log likelihood: -58233.009371 EM: Round [172] log likelihood: -58233.009267 EM: Round [173] log likelihood: -58233.009165 EM: Round [174] log likelihood: -58233.009065 EM: Stopping iterations at round 174 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 37936168 > /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir > /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir --annotate /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir -done, see /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.WDxxwGDlGF/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 377, filtered: 4374) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.WDxxwGDlGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.WDxxwGDlGF/./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.WDxxwGDlGF/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 [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000181577.16] 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 [ENSG00000258853.1] WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000267573.1] WARNING, no entry stored in dbm for [ENSG00000214433.4] WARNING, no entry stored in dbm for [ENSG00000225092.2] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000225840.2] WARNING, no entry stored in dbm for [ENSG00000268189.2] WARNING, no entry stored in dbm for [ENSG00000263072.8] WARNING, no entry stored in dbm for [ENSG00000286211.1] WARNING, no entry stored in dbm for [ENSG00000243771.1] WARNING, no entry stored in dbm for [ENSG00000241743.4] WARNING, no entry stored in dbm for [ENSG00000272848.2] WARNING, no entry stored in dbm for [ENSG00000211513.5] WARNING, no entry stored in dbm for [ENSG00000259393.2] WARNING, no entry stored in dbm for [ENSG00000279625.1] WARNING, no entry stored in dbm for [ENSG00000273344.1] WARNING, no entry stored in dbm for [ENSG00000247828.8] WARNING, no entry stored in dbm for [ENSG00000231721.7] WARNING, no entry stored in dbm for [ENSG00000272368.2] WARNING, no entry stored in dbm for [ENSG00000188004.11] WARNING, no entry stored in dbm for [ENSG00000286813.1] WARNING, no entry stored in dbm for [ENSG00000281207.1] WARNING, no entry stored in dbm for [ENSG00000215241.4] WARNING, no entry stored in dbm for [ENSG00000286176.2] WARNING, no entry stored in dbm for [ENSG00000214389.2] WARNING, no entry stored in dbm for [ENSG00000231022.1] WARNING, no entry stored in dbm for [ENSG00000234637.1] WARNING, no entry stored in dbm for [ENSG00000213880.3] WARNING, no entry stored in dbm for [ENSG00000213862.4] WARNING, no entry stored in dbm for [ENSG00000200296.1] WARNING, no entry stored in dbm for [ENSG00000229828.2] WARNING, no entry stored in dbm for [ENSG00000240606.3] WARNING, no entry stored in dbm for [ENSG00000275014.1] WARNING, no entry stored in dbm for [ENSG00000222974.1] WARNING, no entry stored in dbm for [ENSG00000222386.1] WARNING, no entry stored in dbm for [ENSG00000222974.1] WARNING, no entry stored in dbm for [ENSG00000201010.1] WARNING, no entry stored in dbm for [ENSG00000248223.1] WARNING, no entry stored in dbm for [ENSG00000283907.1] WARNING, no entry stored in dbm for [ENSG00000250072.6] WARNING, no entry stored in dbm for [ENSG00000224729.6] WARNING, no entry stored in dbm for [ENSG00000236778.8] WARNING, no entry stored in dbm for [ENSG00000255875.2] WARNING, no entry stored in dbm for [ENSG00000223991.1] WARNING, no entry stored in dbm for [ENSG00000236051.7] WARNING, no entry stored in dbm for [ENSG00000198886.2] WARNING, no entry stored in dbm for [ENSG00000227584.2] WARNING, no entry stored in dbm for [ENSG00000239586.1] WARNING, no entry stored in dbm for [ENSG00000254541.1] WARNING, no entry stored in dbm for [ENSG00000278913.1] WARNING, no entry stored in dbm for [ENSG00000275449.1] WARNING, no entry stored in dbm for [ENSG00000234769.7] WARNING, no entry stored in dbm for [ENSG00000284419.1] WARNING, no entry stored in dbm for [ENSG00000267472.1] WARNING, no entry stored in dbm for [ENSG00000259134.7] WARNING, no entry stored in dbm for [ENSG00000251372.6] WARNING, no entry stored in dbm for [ENSG00000227128.5] WARNING, no entry stored in dbm for [ENSG00000243438.1] WARNING, no entry stored in dbm for [ENSG00000201113.1] WARNING, no entry stored in dbm for [ENSG00000200814.1] WARNING, no entry stored in dbm for [ENSG00000207029.1] WARNING, no entry stored in dbm for [ENSG00000200153.1] WARNING, no entry stored in dbm for [ENSG00000273768.1] WARNING, no entry stored in dbm for [ENSG00000206737.1] WARNING, no entry stored in dbm for [ENSG00000207389.1] WARNING, no entry stored in dbm for [ENSG00000207513.1] WARNING, no entry stored in dbm for [ENSG00000206588.1] WARNING, no entry stored in dbm for [ENSG00000206596.1] WARNING, no entry stored in dbm for [ENSG00000207005.1] WARNING, no entry stored in dbm for [ENSG00000206652.1] WARNING, no entry stored in dbm for [ENSG00000258232.2] WARNING, no entry stored in dbm for [ENSG00000231160.10] WARNING, no entry stored in dbm for [ENSG00000241286.2] WARNING, no entry stored in dbm for [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000240875.6] WARNING, no entry stored in dbm for [ENSG00000231419.6] WARNING, no entry stored in dbm for [ENSG00000281344.1] WARNING, no entry stored in dbm for [ENSG00000229212.8] WARNING, no entry stored in dbm for [ENSG00000239533.6] WARNING, no entry stored in dbm for [ENSG00000284209.2] WARNING, no entry stored in dbm for [ENSG00000244265.2] WARNING, no entry stored in dbm for [ENSG00000224032.7] WARNING, no entry stored in dbm for [ENSG00000259762.1] WARNING, no entry stored in dbm for [ENSG00000263883.1] WARNING, no entry stored in dbm for [ENSG00000230447.2] WARNING, no entry stored in dbm for [ENSG00000233937.7] WARNING, no entry stored in dbm for [ENSG00000187172.15] WARNING, no entry stored in dbm for [ENSG00000233937.7] WARNING, no entry stored in dbm for [ENSG00000248103.1] WARNING, no entry stored in dbm for [ENSG00000260913.1] WARNING, no entry stored in dbm for [ENSG00000203993.6] WARNING, no entry stored in dbm for [ENSG00000255248.9] WARNING, no entry stored in dbm for [ENSG00000237357.2] WARNING, no entry stored in dbm for [ENSG00000259663.2] WARNING, no entry stored in dbm for [ENSG00000243069.8] WARNING, no entry stored in dbm for [ENSG00000275598.1] WARNING, no entry stored in dbm for [ENSG00000270780.1] WARNING, no entry stored in dbm for [ENSG00000234589.4] WARNING, no entry stored in dbm for [ENSG00000232121.1] WARNING, no entry stored in dbm for [ENSG00000287029.1] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000235119.1] WARNING, no entry stored in dbm for [ENSG00000266680.1] WARNING, no entry stored in dbm for [ENSG00000288543.1] WARNING, no entry stored in dbm for [ENSG00000229700.1] WARNING, no entry stored in dbm for [ENSG00000243744.2] WARNING, no entry stored in dbm for [ENSG00000215057.4] WARNING, no entry stored in dbm for [ENSG00000261499.2] WARNING, no entry stored in dbm for [ENSG00000263826.1] WARNING, no entry stored in dbm for [ENSG00000261167.1] WARNING, no entry stored in dbm for [ENSG00000242474.3] WARNING, no entry stored in dbm for [ENSG00000256625.1] WARNING, no entry stored in dbm for [ENSG00000185485.14] WARNING, no entry stored in dbm for [ENSG00000280828.1] WARNING, no entry stored in dbm for [ENSG00000283050.2] WARNING, no entry stored in dbm for [ENSG00000253361.3] WARNING, no entry stored in dbm for [ENSG00000244604.1] WARNING, no entry stored in dbm for [ENSG00000248515.2] WARNING, no entry stored in dbm for [ENSG00000231721.7] WARNING, no entry stored in dbm for [ENSG00000268120.1] WARNING, no entry stored in dbm for [ENSG00000228327.3] WARNING, no entry stored in dbm for [ENSG00000248560.1] WARNING, no entry stored in dbm for [ENSG00000278915.1] * STAR-Fusion complete. See output: /tmp/nxf.WDxxwGDlGF/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)