-ctat genome lib [/tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.x1KggYDsQS/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary -sample contains 49623633 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir -J /tmp/nxf.x1KggYDsQS/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.x1KggYDsQS/BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=42857.14/min [20000], rate=48000.00/min [30000], rate=47368.42/min [40000], rate=48979.59/min [50000], rate=50000.00/min [60000], rate=50704.23/min [70000], rate=53164.56/min [80000], rate=55813.95/min [90000], rate=56842.11/min [100000], rate=59405.94/min [110000], rate=61682.24/min [120000], rate=64285.71/min [130000], rate=63414.63/min [140000], rate=60869.57/min [150000], rate=59210.53/min [160000], rate=57142.86/min [170000], rate=56353.59/min [180000], rate=55958.55/min [190000], rate=56157.64/min [200000], rate=55299.54/min [210000], rate=55263.16/min [220000], rate=55696.20/min [230000], rate=56097.56/min [240000], rate=56250.00/min [250000], rate=56390.98/min [260000], rate=56934.31/min [270000], rate=57446.81/min [280000], rate=58131.49/min [290000], rate=59183.67/min [300000], rate=60000.00/min [310000], rate=60586.32/min [320000], rate=61935.48/min [330000], rate=62460.57/min [340000], rate=63157.89/min [350000], rate=64024.39/min [360000], rate=64670.66/min [370000], rate=65486.73/min [380000], rate=66086.96/min [390000], rate=66857.14/min [400000], rate=67415.73/min [410000], rate=68715.08/min [420000], rate=70000.00/min [430000], rate=71468.14/min [440000], rate=72328.77/min [450000], rate=73569.48/min [460000], rate=73796.79/min [470000], rate=74210.53/min [480000], rate=74805.19/min [490000], rate=75773.20/min [500000], rate=75949.37/min [510000], rate=76500.00/min [520000], rate=76658.48/min [530000], rate=75894.99/min [540000], rate=76959.62/min [550000], rate=77464.79/min [560000], rate=78321.68/min [570000], rate=77904.33/min [580000], rate=78026.91/min [590000], rate=78145.70/min [600000], rate=78774.62/min [610000], rate=79912.66/min [620000], rate=81045.75/min [630000], rate=81465.52/min [640000], rate=82226.98/min [650000], rate=82278.48/min [660000], rate=82672.23/min [670000], rate=83575.88/min [680000], rate=83778.23/min [690000], rate=84146.34/min [700000], rate=85192.70/min [710000], rate=85887.10/min [720000], rate=86055.78/min [730000], rate=85714.29/min [740000], rate=86549.71/min [750000], rate=87040.62/min [760000], rate=87861.27/min [770000], rate=88000.00/min [780000], rate=87969.92/min [790000], rate=87940.63/min [800000], rate=88397.79/min [810000], rate=88686.13/min [820000], rate=88808.66/min [830000], rate=89247.31/min [840000], rate=89203.54/min [850000], rate=89316.99/min [860000], rate=89583.33/min [870000], rate=89536.88/min [880000], rate=89340.10/min [890000], rate=89148.58/min [900000], rate=89256.20/min [910000], rate=89361.70/min [920000], rate=89320.39/min -building interval tree based on /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=150000.00/min [20000], rate=92307.69/min [30000], rate=128571.43/min [40000], rate=141176.47/min [50000], rate=157894.74/min [60000], rate=156521.74/min [70000], rate=144827.59/min [80000], rate=141176.47/min [90000], rate=145945.95/min [100000], rate=150000.00/min [110000], rate=143478.26/min [120000], rate=153191.49/min [130000], rate=156000.00/min [140000], rate=152727.27/min [150000], rate=142857.14/min [160000], rate=150000.00/min [170000], rate=154545.45/min [180000], rate=158823.53/min [190000], rate=156164.38/min [200000], rate=148148.15/min [210000], rate=144827.59/min [220000], rate=145054.95/min [230000], rate=145263.16/min [240000], rate=144000.00/min [250000], rate=148514.85/min [260000], rate=150000.00/min [270000], rate=148623.85/min [280000], rate=144827.59/min [290000], rate=145000.00/min [300000], rate=147540.98/min [310000], rate=151219.51/min [320000], rate=150000.00/min [330000], rate=148872.18/min [340000], rate=146762.59/min [350000], rate=145833.33/min [360000], rate=147945.21/min [370000], rate=148993.29/min [380000], rate=149019.61/min [390000], rate=149044.59/min [400000], rate=149068.32/min [410000], rate=145562.13/min [420000], rate=147368.42/min [430000], rate=149132.95/min [440000], rate=150857.14/min [450000], rate=150837.99/min [460000], rate=150000.00/min [470000], rate=146875.00/min [480000], rate=146938.78/min [490000], rate=148484.85/min [500000], rate=148514.85/min [510000], rate=149268.29/min [520000], rate=140540.54/min [530000], rate=132500.00/min [540000], rate=126562.50/min [550000], rate=121323.53/min [560000], rate=116666.67/min [570000], rate=112500.00/min [580000], rate=109090.91/min [590000], rate=106626.51/min [600000], rate=104956.27/min [610000], rate=102808.99/min [620000], rate=101086.96/min [630000], rate=99473.68/min [640000], rate=97215.19/min [650000], rate=94890.51/min [660000], rate=93176.47/min [670000], rate=92201.83/min [680000], rate=90666.67/min [690000], rate=90196.08/min [700000], rate=89743.59/min [710000], rate=89495.80/min [720000], rate=89440.99/min [730000], rate=89570.55/min [740000], rate=89156.63/min [750000], rate=88408.64/min [760000], rate=87523.99/min [770000], rate=87005.65/min [780000], rate=86666.67/min [790000], rate=86813.19/min [800000], rate=86642.60/min [810000], rate=86940.97/min [820000], rate=87079.65/min [830000], rate=87215.41/min [840000], rate=86153.85/min [850000], rate=85427.14/min [860000], rate=84451.72/min [870000], rate=84057.97/min [880000], rate=83544.30/min [890000], rate=82919.25/min [900000], rate=82317.07/min [910000], rate=81981.98/min -building interval tree based on /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=42857.14/min [20000], rate=46153.85/min [30000], rate=46153.85/min [40000], rate=46153.85/min [50000], rate=46875.00/min [60000], rate=49315.07/min [70000], rate=50602.41/min [80000], rate=50526.32/min [90000], rate=50467.29/min [100000], rate=52173.91/min [110000], rate=53225.81/min [120000], rate=55384.62/min [130000], rate=57352.94/min [140000], rate=56756.76/min [150000], rate=56962.03/min [160000], rate=57485.03/min [170000], rate=58285.71/min [180000], rate=58695.65/min [190000], rate=59685.86/min [200000], rate=60301.51/min [210000], rate=61165.05/min [220000], rate=60550.46/min [230000], rate=60000.00/min [240000], rate=59259.26/min [250000], rate=59055.12/min [260000], rate=59090.91/min [270000], rate=59558.82/min [280000], rate=60215.05/min [290000], rate=61052.63/min [300000], rate=62068.97/min [310000], rate=63050.85/min [320000], rate=64214.05/min [330000], rate=63665.59/min [340000], rate=63551.40/min [350000], rate=63444.11/min [360000], rate=63529.41/min [370000], rate=63793.10/min [380000], rate=64044.94/min [390000], rate=63934.43/min [400000], rate=64171.12/min [410000], rate=65079.37/min [420000], rate=65625.00/min [430000], rate=65984.65/min [440000], rate=66666.67/min [450000], rate=66339.07/min [460000], rate=65714.29/min [470000], rate=65277.78/min [480000], rate=64864.86/min [490000], rate=64757.71/min [500000], rate=64655.17/min [510000], rate=64421.05/min [520000], rate=64065.71/min [530000], rate=64112.90/min [540000], rate=64158.42/min [550000], rate=64327.49/min [560000], rate=64491.36/min [570000], rate=64895.64/min [580000], rate=65413.53/min [590000], rate=66044.78/min [600000], rate=66543.44/min [610000], rate=66304.35/min [620000], rate=66192.17/min [630000], rate=65968.59/min [640000], rate=66092.94/min [650000], rate=66326.53/min [660000], rate=66554.62/min [670000], rate=67111.85/min [680000], rate=67774.09/min [690000], rate=67757.77/min [700000], rate=67632.85/min [710000], rate=67511.89/min [720000], rate=67605.63/min [730000], rate=67592.59/min [740000], rate=67786.26/min [750000], rate=67873.30/min [760000], rate=68263.47/min [770000], rate=69058.30/min [780000], rate=69436.20/min [790000], rate=69808.54/min [800000], rate=70381.23/min [810000], rate=70332.85/min [820000], rate=70285.71/min [830000], rate=70538.24/min [840000], rate=70588.24/min [850000], rate=70931.85/min [860000], rate=71172.41/min [870000], rate=71214.19/min [880000], rate=71544.72/min [890000], rate=71870.79/min [900000], rate=72289.16/min [910000], rate=72703.06/min -building interval tree based on /tmp/nxf.x1KggYDsQS/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=75000.00/min [30000], rate=72000.00/min [40000], rate=77419.35/min [50000], rate=78947.37/min [60000], rate=69230.77/min [70000], rate=64615.38/min [80000], rate=63157.89/min [90000], rate=61363.64/min [100000], rate=60606.06/min [110000], rate=60550.46/min [120000], rate=60504.20/min [130000], rate=60465.12/min [140000], rate=61764.71/min [150000], rate=62500.00/min [160000], rate=64429.53/min [170000], rate=66233.77/min [180000], rate=66666.67/min [190000], rate=67455.62/min [200000], rate=68571.43/min [210000], rate=70000.00/min [220000], rate=69473.68/min [230000], rate=68656.72/min [240000], rate=68571.43/min [250000], rate=68807.34/min [260000], rate=69642.86/min [270000], rate=70742.36/min [280000], rate=71794.87/min [290000], rate=70731.71/min [300000], rate=70312.50/min [310000], rate=70188.68/min [320000], rate=71111.11/min [330000], rate=72000.00/min [340000], rate=71578.95/min [350000], rate=71672.35/min [360000], rate=72240.80/min [370000], rate=73026.32/min [380000], rate=73786.41/min [390000], rate=73125.00/min [400000], rate=73170.73/min [410000], rate=73214.29/min [420000], rate=72413.79/min [430000], rate=72268.91/min [440000], rate=71739.13/min [450000], rate=71240.11/min [460000], rate=70769.23/min [470000], rate=70324.19/min [480000], rate=69902.91/min [490000], rate=69503.55/min [500000], rate=69284.06/min [510000], rate=69230.77/min [520000], rate=69179.60/min [530000], rate=68980.48/min [540000], rate=68936.17/min [550000], rate=68893.53/min [560000], rate=68711.66/min [570000], rate=68537.07/min [580000], rate=68503.94/min [590000], rate=68871.60/min [600000], rate=69097.89/min [610000], rate=69449.72/min [620000], rate=68634.69/min [630000], rate=67985.61/min [640000], rate=67486.82/min [650000], rate=67125.65/min [660000], rate=66779.09/min [670000], rate=66556.29/min [680000], rate=66233.77/min [690000], rate=66240.00/min [700000], rate=66037.74/min [710000], rate=65944.27/min [720000], rate=66055.05/min [730000], rate=66063.35/min [740000], rate=65875.37/min [750000], rate=65693.43/min [760000], rate=65706.05/min [770000], rate=65346.53/min [780000], rate=65090.40/min [790000], rate=64931.51/min [800000], rate=65128.90/min [810000], rate=65234.90/min [820000], rate=65600.00/min [830000], rate=65960.26/min [840000], rate=66055.05/min [850000], rate=66492.83/min [860000], rate=67100.13/min [870000], rate=67268.04/min [880000], rate=67519.18/min [890000], rate=67339.22/min [900000], rate=66914.50/min [910000], rate=66504.26/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir --filt_file /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 0.00 reads per min processed... 12000000.00 reads per min processed... 9000000.00 reads per min processed... 8000000.00 reads per min processed... 7500000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 5333333.33 reads per min processed... 5400000.00 reads per min processed... 5000000.00 reads per min processed... 5076923.08 reads per min processed... 4500000.00 reads per min processed... 4333333.33 reads per min processed... 4200000.00 reads per min processed... 4090909.09 reads per min processed... 4173913.04 reads per min processed... 4080000.00 reads per min processed... 4153846.15 reads per min processed... 4071428.57 reads per min processed... 4137931.03 reads per min processed... 4344827.59 reads per min processed... 4400000.00 reads per min processed... 4451612.90 reads per min processed... 4500000.00 reads per min processed... 4411764.71 reads per min processed... 4457142.86 reads per min processed... 4378378.38 reads per min processed... 4421052.63 reads per min processed... 4350000.00 reads per min processed... 4390243.90 reads per min processed... 4428571.43 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.x1KggYDsQS/BreastNB_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.x1KggYDsQS/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -52996.431305 EM: Round [1] log likelihood: -52841.507743 EM: Round [2] log likelihood: -52777.336840 EM: Round [3] log likelihood: -52745.767675 EM: Round [4] log likelihood: -52728.771002 EM: Round [5] log likelihood: -52719.230889 EM: Round [6] log likelihood: -52713.722158 EM: Round [7] log likelihood: -52710.438669 EM: Round [8] log likelihood: -52708.405973 EM: Round [9] log likelihood: -52707.094497 EM: Round [10] log likelihood: -52706.212773 EM: Round [11] log likelihood: -52705.596902 EM: Round [12] log likelihood: -52705.152033 EM: Round [13] log likelihood: -52704.821402 EM: Round [14] log likelihood: -52704.569794 EM: Round [15] log likelihood: -52704.374555 EM: Round [16] log likelihood: -52704.220599 EM: Round [17] log likelihood: -52704.097555 EM: Round [18] log likelihood: -52703.998091 EM: Round [19] log likelihood: -52703.916896 EM: Round [20] log likelihood: -52703.850044 EM: Round [21] log likelihood: -52703.794580 EM: Round [22] log likelihood: -52703.748246 EM: Round [23] log likelihood: -52703.709295 EM: Round [24] log likelihood: -52703.676362 EM: Round [25] log likelihood: -52703.648366 EM: Round [26] log likelihood: -52703.624448 EM: Round [27] log likelihood: -52703.603916 EM: Round [28] log likelihood: -52703.586211 EM: Round [29] log likelihood: -52703.570880 EM: Round [30] log likelihood: -52703.557550 EM: Round [31] log likelihood: -52703.545914 EM: Round [32] log likelihood: -52703.535719 EM: Round [33] log likelihood: -52703.526754 EM: Round [34] log likelihood: -52703.518844 EM: Round [35] log likelihood: -52703.511841 EM: Round [36] log likelihood: -52703.505621 EM: Round [37] log likelihood: -52703.500079 EM: Round [38] log likelihood: -52703.495128 EM: Round [39] log likelihood: -52703.490690 EM: Round [40] log likelihood: -52703.486702 EM: Round [41] log likelihood: -52703.483108 EM: Round [42] log likelihood: -52703.479862 EM: Round [43] log likelihood: -52703.476922 EM: Round [44] log likelihood: -52703.474254 EM: Round [45] log likelihood: -52703.471826 EM: Round [46] log likelihood: -52703.469612 EM: Round [47] log likelihood: -52703.467589 EM: Round [48] log likelihood: -52703.465737 EM: Round [49] log likelihood: -52703.464038 EM: Round [50] log likelihood: -52703.462476 EM: Round [51] log likelihood: -52703.461039 EM: Round [52] log likelihood: -52703.459714 EM: Round [53] log likelihood: -52703.458489 EM: Round [54] log likelihood: -52703.457357 EM: Round [55] log likelihood: -52703.456308 EM: Round [56] log likelihood: -52703.455335 EM: Round [57] log likelihood: -52703.454431 EM: Round [58] log likelihood: -52703.453590 EM: Round [59] log likelihood: -52703.452807 EM: Round [60] log likelihood: -52703.452077 EM: Round [61] log likelihood: -52703.451396 EM: Round [62] log likelihood: -52703.450760 EM: Round [63] log likelihood: -52703.450164 EM: Round [64] log likelihood: -52703.449607 EM: Round [65] log likelihood: -52703.449086 EM: Round [66] log likelihood: -52703.448596 EM: Round [67] log likelihood: -52703.448137 EM: Round [68] log likelihood: -52703.447706 EM: Round [69] log likelihood: -52703.447300 EM: Round [70] log likelihood: -52703.446919 EM: Round [71] log likelihood: -52703.446560 EM: Round [72] log likelihood: -52703.446222 EM: Round [73] log likelihood: -52703.445903 EM: Round [74] log likelihood: -52703.445603 EM: Round [75] log likelihood: -52703.445320 EM: Round [76] log likelihood: -52703.445052 EM: Round [77] log likelihood: -52703.444799 EM: Round [78] log likelihood: -52703.444560 EM: Round [79] log likelihood: -52703.444335 EM: Round [80] log likelihood: -52703.444121 EM: Round [81] log likelihood: -52703.443919 EM: Round [82] log likelihood: -52703.443727 EM: Round [83] log likelihood: -52703.443546 EM: Round [84] log likelihood: -52703.443374 EM: Round [85] log likelihood: -52703.443212 EM: Round [86] log likelihood: -52703.443057 EM: Round [87] log likelihood: -52703.442911 EM: Round [88] log likelihood: -52703.442772 EM: Round [89] log likelihood: -52703.442640 EM: Round [90] log likelihood: -52703.442514 EM: Round [91] log likelihood: -52703.442395 EM: Round [92] log likelihood: -52703.442282 EM: Round [93] log likelihood: -52703.442175 EM: Round [94] log likelihood: -52703.442073 EM: Round [95] log likelihood: -52703.441976 EM: Stopping iterations at round 95 due to insufficient improvement in likelihood. EM: Starting log likelihood: -52951.855113 EM: Round [1] log likelihood: -52816.771758 EM: Round [2] log likelihood: -52763.183690 EM: Round [3] log likelihood: -52737.258272 EM: Round [4] log likelihood: -52723.440416 EM: Round [5] log likelihood: -52715.749141 EM: Round [6] log likelihood: -52711.347843 EM: Round [7] log likelihood: -52708.752358 EM: Round [8] log likelihood: -52707.165295 EM: Round [9] log likelihood: -52706.154823 EM: Round [10] log likelihood: -52705.484296 EM: Round [11] log likelihood: -52705.021448 EM: Round [12] log likelihood: -52704.690370 EM: Round [13] log likelihood: -52704.446123 EM: Round [14] log likelihood: -52704.261186 EM: Round [15] log likelihood: -52704.118103 EM: Round [16] log likelihood: -52704.005417 EM: Round [17] log likelihood: -52703.915356 EM: Round [18] log likelihood: -52703.842491 EM: Round [19] log likelihood: -52703.782926 EM: Round [20] log likelihood: -52703.733800 EM: Round [21] log likelihood: -52703.692970 EM: Round [22] log likelihood: -52703.658805 EM: Round [23] log likelihood: -52703.630044 EM: Round [24] log likelihood: -52703.605699 EM: Round [25] log likelihood: -52703.584989 EM: Round [26] log likelihood: -52703.567292 EM: Round [27] log likelihood: -52703.552105 EM: Round [28] log likelihood: -52703.539020 EM: Round [29] log likelihood: -52703.527707 EM: Round [30] log likelihood: -52703.517891 EM: Round [31] log likelihood: -52703.509346 EM: Round [32] log likelihood: -52703.501886 EM: Round [33] log likelihood: -52703.495353 EM: Round [34] log likelihood: -52703.489618 EM: Round [35] log likelihood: -52703.484569 EM: Round [36] log likelihood: -52703.480113 EM: Round [37] log likelihood: -52703.476172 EM: Round [38] log likelihood: -52703.472678 EM: Round [39] log likelihood: -52703.469574 EM: Round [40] log likelihood: -52703.466811 EM: Round [41] log likelihood: -52703.464345 EM: Round [42] log likelihood: -52703.462142 EM: Round [43] log likelihood: -52703.460170 EM: Round [44] log likelihood: -52703.458401 EM: Round [45] log likelihood: -52703.456811 EM: Round [46] log likelihood: -52703.455381 EM: Round [47] log likelihood: -52703.454091 EM: Round [48] log likelihood: -52703.452927 EM: Round [49] log likelihood: -52703.451875 EM: Round [50] log likelihood: -52703.450923 EM: Round [51] log likelihood: -52703.450059 EM: Round [52] log likelihood: -52703.449275 EM: Round [53] log likelihood: -52703.448562 EM: Round [54] log likelihood: -52703.447913 EM: Round [55] log likelihood: -52703.447322 EM: Round [56] log likelihood: -52703.446782 EM: Round [57] log likelihood: -52703.446289 EM: Round [58] log likelihood: -52703.445838 EM: Round [59] log likelihood: -52703.445425 EM: Round [60] log likelihood: -52703.445047 EM: Round [61] log likelihood: -52703.444699 EM: Round [62] log likelihood: -52703.444379 EM: Round [63] log likelihood: -52703.444085 EM: Round [64] log likelihood: -52703.443814 EM: Round [65] log likelihood: -52703.443565 EM: Round [66] log likelihood: -52703.443334 EM: Round [67] log likelihood: -52703.443121 EM: Round [68] log likelihood: -52703.442924 EM: Round [69] log likelihood: -52703.442742 EM: Round [70] log likelihood: -52703.442573 EM: Round [71] log likelihood: -52703.442416 EM: Round [72] log likelihood: -52703.442270 EM: Round [73] log likelihood: -52703.442135 EM: Round [74] log likelihood: -52703.442009 EM: Round [75] log likelihood: -52703.441892 EM: Round [76] log likelihood: -52703.441782 EM: Round [77] log likelihood: -52703.441680 EM: Round [78] log likelihood: -52703.441584 EM: Stopping iterations at round 78 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.x1KggYDsQS/./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.x1KggYDsQS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.x1KggYDsQS/./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.x1KggYDsQS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 49623633 > /tmp/nxf.x1KggYDsQS/./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.x1KggYDsQS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir > /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir --annotate /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.x1KggYDsQS/./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.x1KggYDsQS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir -done, see /tmp/nxf.x1KggYDsQS/./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.x1KggYDsQS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.x1KggYDsQS/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 278, filtered: 3166) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.x1KggYDsQS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.x1KggYDsQS/./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.x1KggYDsQS/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000240498.9] WARNING, no entry stored in dbm for [ENSG00000181126.13] WARNING, no entry stored in dbm for [ENSG00000255108.1] WARNING, no entry stored in dbm for [ENSG00000251143.1] WARNING, no entry stored in dbm for [ENSG00000205959.4] WARNING, no entry stored in dbm for [ENSG00000251314.2] WARNING, no entry stored in dbm for [ENSG00000205853.12] WARNING, no entry stored in dbm for [ENSG00000212939.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000212939.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000228655.7] WARNING, no entry stored in dbm for [ENSG00000281896.1] WARNING, no entry stored in dbm for [ENSG00000265788.2] WARNING, no entry stored in dbm for [ENSG00000235217.6] WARNING, no entry stored in dbm for [ENSG00000227598.1] WARNING, no entry stored in dbm for [ENSG00000283426.1] WARNING, no entry stored in dbm for [ENSG00000239809.1] WARNING, no entry stored in dbm for [ENSG00000270830.1] WARNING, no entry stored in dbm for [ENSG00000257074.3] WARNING, no entry stored in dbm for [ENSG00000241030.1] WARNING, no entry stored in dbm for [ENSG00000206585.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000270722.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000273768.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000277918.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000206737.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000206888.1] WARNING, no entry stored in dbm for [ENSG00000264940.5] WARNING, no entry stored in dbm for [ENSG00000206975.1] WARNING, no entry stored in dbm for [ENSG00000264940.5] WARNING, no entry stored in dbm for [ENSG00000207389.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000207513.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000206588.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000206596.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000207005.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000206652.1] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000240606.3] WARNING, no entry stored in dbm for [ENSG00000266828.2] WARNING, no entry stored in dbm for [ENSG00000200312.1] WARNING, no entry stored in dbm for [ENSG00000222969.1] WARNING, no entry stored in dbm for [ENSG00000127957.18] WARNING, no entry stored in dbm for [ENSG00000237000.1] WARNING, no entry stored in dbm for [ENSG00000285681.2] WARNING, no entry stored in dbm for [ENSG00000239636.1] WARNING, no entry stored in dbm for [ENSG00000273643.1] WARNING, no entry stored in dbm for [ENSG00000237468.2] 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 [ENSG00000273986.1] WARNING, no entry stored in dbm for [ENSG00000224699.9] WARNING, no entry stored in dbm for [ENSG00000249878.1] WARNING, no entry stored in dbm for [ENSG00000265413.1] WARNING, no entry stored in dbm for [ENSG00000233098.9] WARNING, no entry stored in dbm for [ENSG00000288663.1] WARNING, no entry stored in dbm for [ENSG00000224110.3] WARNING, no entry stored in dbm for [ENSG00000232527.8] WARNING, no entry stored in dbm for [ENSG00000272779.1] WARNING, no entry stored in dbm for [ENSG00000204241.8] WARNING, no entry stored in dbm for [ENSG00000230415.1] WARNING, no entry stored in dbm for [ENSG00000280734.3] WARNING, no entry stored in dbm for [ENSG00000235687.9] WARNING, no entry stored in dbm for [ENSG00000237750.2] WARNING, no entry stored in dbm for [ENSG00000244040.7] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000245067.7] WARNING, no entry stored in dbm for [ENSG00000226239.2] WARNING, no entry stored in dbm for [ENSG00000243478.9] WARNING, no entry stored in dbm for [ENSG00000281383.1] WARNING, no entry stored in dbm for [ENSG00000280800.1] WARNING, no entry stored in dbm for [ENSG00000281181.1] WARNING, no entry stored in dbm for [ENSG00000280614.1] WARNING, no entry stored in dbm for [ENSG00000229321.2] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000234709.2] 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 [ENSG00000228604.3] WARNING, no entry stored in dbm for [ENSG00000235687.9] WARNING, no entry stored in dbm for [ENSG00000280013.1] WARNING, no entry stored in dbm for [ENSG00000080947.15] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000267280.5] WARNING, no entry stored in dbm for [ENSG00000168405.17] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000238013.1] WARNING, no entry stored in dbm for [ENSG00000239899.3] WARNING, no entry stored in dbm for [ENSG00000242158.3] WARNING, no entry stored in dbm for [ENSG00000229807.12] WARNING, no entry stored in dbm for [ENSG00000231649.3] WARNING, no entry stored in dbm for [ENSG00000224905.7] WARNING, no entry stored in dbm for [ENSG00000215559.8] WARNING, no entry stored in dbm for [ENSG00000274502.1] WARNING, no entry stored in dbm for [ENSG00000215559.8] WARNING, no entry stored in dbm for [ENSG00000272574.1] WARNING, no entry stored in dbm for [ENSG00000218426.5] WARNING, no entry stored in dbm for [ENSG00000236667.1] WARNING, no entry stored in dbm for [ENSG00000272668.2] WARNING, no entry stored in dbm for [ENSG00000287991.1] WARNING, no entry stored in dbm for [ENSG00000271989.1] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000283345.1] WARNING, no entry stored in dbm for [ENSG00000215302.8] WARNING, no entry stored in dbm for [ENSG00000261441.1] WARNING, no entry stored in dbm for [ENSG00000251244.2] WARNING, no entry stored in dbm for [ENSG00000286935.1] WARNING, no entry stored in dbm for [ENSG00000259511.3] WARNING, no entry stored in dbm for [ENSG00000242299.1] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [ENSG00000268509.2] WARNING, no entry stored in dbm for [ENSG00000254485.5] WARNING, no entry stored in dbm for [ENSG00000232386.9] * STAR-Fusion complete. See output: /tmp/nxf.x1KggYDsQS/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)