-ctat genome lib [/tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.KPhK3n8ICE/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary -sample contains 60743285 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir -J /tmp/nxf.KPhK3n8ICE/aih-tih-sc-598a93-R1_A23YTGFLT4_1.Chimeric.out.junction -O /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.KPhK3n8ICE/aih-tih-sc-598a93-R1_A23YTGFLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.KPhK3n8ICE/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=57142.86/min [30000], rate=62068.97/min [40000], rate=68571.43/min [50000], rate=69767.44/min [60000], rate=72000.00/min [70000], rate=76363.64/min [80000], rate=81355.93/min [90000], rate=84375.00/min [100000], rate=73170.73/min [110000], rate=65346.53/min [120000], rate=61016.95/min [130000], rate=58646.62/min [140000], rate=57534.25/min [150000], rate=54878.05/min [160000], rate=53932.58/min [170000], rate=53968.25/min [180000], rate=53731.34/min [190000], rate=53773.58/min [200000], rate=54298.64/min [210000], rate=55021.83/min [220000], rate=56170.21/min [230000], rate=57261.41/min [240000], rate=58536.59/min [250000], rate=59523.81/min [260000], rate=59770.11/min [270000], rate=60223.05/min [280000], rate=61090.91/min [290000], rate=61921.71/min [300000], rate=62717.77/min [310000], rate=63698.63/min [320000], rate=64429.53/min [330000], rate=65562.91/min [340000], rate=66666.67/min [350000], rate=68627.45/min [360000], rate=69902.91/min [370000], rate=70700.64/min [380000], rate=71473.35/min [390000], rate=72000.00/min [400000], rate=73170.73/min [410000], rate=73652.69/min [420000], rate=73900.29/min [430000], rate=74137.93/min [440000], rate=74576.27/min [450000], rate=75000.00/min [460000], rate=75824.18/min [470000], rate=77260.27/min [480000], rate=78260.87/min [490000], rate=78820.38/min [500000], rate=79365.08/min [510000], rate=79895.56/min [520000], rate=80829.02/min [530000], rate=81958.76/min [540000], rate=82025.32/min [550000], rate=81885.86/min [560000], rate=81159.42/min [570000], rate=81818.18/min [580000], rate=81882.35/min [590000], rate=82134.57/min [600000], rate=82379.86/min [610000], rate=82805.43/min [620000], rate=83035.71/min [630000], rate=82894.74/min [640000], rate=82758.62/min [650000], rate=83155.65/min [660000], rate=83018.87/min [670000], rate=82886.60/min [680000], rate=82926.83/min [690000], rate=82965.93/min [700000], rate=83168.32/min [710000], rate=83365.95/min [720000], rate=83236.99/min [730000], rate=82022.47/min [740000], rate=80874.32/min [750000], rate=79787.23/min [760000], rate=78620.69/min [770000], rate=78172.59/min [780000], rate=77870.22/min [790000], rate=77450.98/min [800000], rate=77170.42/min [810000], rate=77142.86/min -building interval tree based on /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=109090.91/min [30000], rate=78260.87/min [40000], rate=72727.27/min [50000], rate=69767.44/min [60000], rate=69230.77/min [70000], rate=70000.00/min [80000], rate=70588.24/min [90000], rate=68354.43/min [100000], rate=65217.39/min [110000], rate=62264.15/min [120000], rate=61016.95/min [130000], rate=60465.12/min [140000], rate=61313.87/min [150000], rate=62937.06/min [160000], rate=63576.16/min [170000], rate=64968.15/min [180000], rate=66666.67/min [190000], rate=65895.95/min [200000], rate=64864.86/min [210000], rate=63959.39/min [220000], rate=62857.14/min [230000], rate=61883.41/min [240000], rate=61538.46/min [250000], rate=61475.41/min [260000], rate=61904.76/min [270000], rate=63281.25/min [280000], rate=63878.33/min [290000], rate=64684.01/min [300000], rate=64056.94/min [310000], rate=63050.85/min [320000], rate=62337.66/min [330000], rate=61875.00/min [340000], rate=61631.42/min [350000], rate=61583.58/min [360000], rate=61714.29/min [370000], rate=61666.67/min [380000], rate=61788.62/min [390000], rate=62068.97/min [400000], rate=62337.66/min [410000], rate=62915.60/min [420000], rate=63636.36/min [430000], rate=64500.00/min [440000], rate=65185.19/min [450000], rate=65217.39/min [460000], rate=64788.73/min [470000], rate=64827.59/min [480000], rate=65011.29/min [490000], rate=65188.47/min [500000], rate=65217.39/min [510000], rate=65665.24/min [520000], rate=66242.04/min [530000], rate=66947.37/min [540000], rate=67782.43/min [550000], rate=68464.73/min [560000], rate=69135.80/min [570000], rate=69795.92/min [580000], rate=70445.34/min [590000], rate=71084.34/min [600000], rate=71713.15/min [610000], rate=72475.25/min [620000], rate=72798.43/min [630000], rate=72692.31/min [640000], rate=72180.45/min [650000], rate=71955.72/min [660000], rate=72000.00/min [670000], rate=72172.35/min [680000], rate=72212.39/min [690000], rate=72377.62/min [700000], rate=73043.48/min [710000], rate=73448.28/min [720000], rate=73720.14/min [730000], rate=73489.93/min [740000], rate=73509.93/min [750000], rate=73529.41/min [760000], rate=73429.95/min [770000], rate=73801.92/min [780000], rate=74050.63/min [790000], rate=74528.30/min [800000], rate=74883.00/min -building interval tree based on /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=120000.00/min [30000], rate=138461.54/min [40000], rate=126315.79/min [50000], rate=136363.64/min [60000], rate=144000.00/min [70000], rate=150000.00/min [80000], rate=165517.24/min [90000], rate=158823.53/min [100000], rate=157894.74/min [110000], rate=143478.26/min [120000], rate=146938.78/min [130000], rate=144444.44/min [140000], rate=144827.59/min [150000], rate=147540.98/min [160000], rate=150000.00/min [170000], rate=154545.45/min [180000], rate=152112.68/min [190000], rate=148051.95/min [200000], rate=144578.31/min [210000], rate=143181.82/min [220000], rate=143478.26/min [230000], rate=143750.00/min [240000], rate=145454.55/min [250000], rate=145631.07/min [260000], rate=144444.44/min [270000], rate=140869.57/min [280000], rate=140000.00/min [290000], rate=138095.24/min [300000], rate=138461.54/min [310000], rate=139849.62/min [320000], rate=139130.43/min [330000], rate=123750.00/min [340000], rate=114606.74/min [350000], rate=106060.61/min [360000], rate=98630.14/min [370000], rate=93670.89/min [380000], rate=89763.78/min [390000], rate=86346.86/min [400000], rate=83916.08/min [410000], rate=81727.57/min [420000], rate=80000.00/min [430000], rate=78658.54/min [440000], rate=77192.98/min [450000], rate=76056.34/min [460000], rate=75000.00/min [470000], rate=74406.33/min [480000], rate=74035.99/min [490000], rate=73134.33/min [500000], rate=72639.23/min [510000], rate=72000.00/min [520000], rate=71889.40/min [530000], rate=72108.84/min [540000], rate=72321.43/min [550000], rate=72687.22/min [560000], rate=72413.79/min [570000], rate=71848.74/min [580000], rate=71752.58/min [590000], rate=71659.92/min [600000], rate=71713.15/min [610000], rate=71624.27/min [620000], rate=71538.46/min [630000], rate=71726.76/min [640000], rate=71910.11/min [650000], rate=70524.41/min [660000], rate=69718.31/min [670000], rate=68953.69/min [680000], rate=68456.38/min [690000], rate=68092.11/min [700000], rate=67741.94/min [710000], rate=67405.06/min [720000], rate=67080.75/min [730000], rate=66972.48/min [740000], rate=66867.47/min [750000], rate=66864.78/min [760000], rate=66960.35/min [770000], rate=67346.94/min [780000], rate=67435.16/min [790000], rate=66854.72/min [800000], rate=66298.34/min -building interval tree based on /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=54545.45/min [20000], rate=57142.86/min [30000], rate=56250.00/min [40000], rate=57142.86/min [50000], rate=58823.53/min [60000], rate=63157.89/min [70000], rate=65625.00/min [80000], rate=68571.43/min [90000], rate=71052.63/min [100000], rate=70588.24/min [110000], rate=71739.13/min [120000], rate=74226.80/min [130000], rate=72222.22/min [140000], rate=70588.24/min [150000], rate=70866.14/min [160000], rate=71641.79/min [170000], rate=72340.43/min [180000], rate=73972.60/min [190000], rate=76000.00/min [200000], rate=74534.16/min [210000], rate=72832.37/min [220000], rate=71739.13/min [230000], rate=70769.23/min [240000], rate=70935.96/min [250000], rate=71090.05/min [260000], rate=72558.14/min [270000], rate=74311.93/min [280000], rate=75336.32/min [290000], rate=75324.68/min [300000], rate=73770.49/min [310000], rate=73809.52/min [320000], rate=72180.45/min [330000], rate=71480.14/min [340000], rate=71080.14/min [350000], rate=70469.80/min [360000], rate=70129.87/min [370000], rate=69592.48/min [380000], rate=69090.91/min [390000], rate=69230.77/min [400000], rate=68965.52/min [410000], rate=68715.08/min [420000], rate=68664.85/min [430000], rate=68435.01/min [440000], rate=68217.05/min [450000], rate=68010.08/min [460000], rate=67980.30/min [470000], rate=67788.46/min [480000], rate=67605.63/min [490000], rate=67741.94/min [500000], rate=68181.82/min [510000], rate=68609.87/min [520000], rate=68874.17/min [530000], rate=67515.92/min [540000], rate=66529.77/min [550000], rate=65868.26/min [560000], rate=64990.33/min [570000], rate=64406.78/min [580000], rate=63970.59/min [590000], rate=63783.78/min [600000], rate=63492.06/min [610000], rate=63541.67/min [620000], rate=63481.23/min [630000], rate=63105.18/min [640000], rate=63261.94/min [650000], rate=63004.85/min [660000], rate=63057.32/min [670000], rate=63307.09/min [680000], rate=63551.40/min [690000], rate=63987.64/min [700000], rate=64220.18/min [710000], rate=64741.64/min [720000], rate=65060.24/min [730000], rate=65373.13/min [740000], rate=65198.24/min [750000], rate=64748.20/min [760000], rate=64225.35/min [770000], rate=63988.92/min [780000], rate=63673.47/min [790000], rate=63368.98/min [800000], rate=63074.90/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir --filt_file /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.KPhK3n8ICE/./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... 6000000.00 reads per min processed... 4285714.29 reads per min processed... 4000000.00 reads per min processed... 3818181.82 reads per min processed... 3692307.69 reads per min processed... 3600000.00 reads per min processed... 3333333.33 reads per min processed... 3142857.14 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3085714.29 reads per min processed... 3166666.67 reads per min processed... 3157894.74 reads per min processed... 3150000.00 reads per min processed... 3142857.14 reads per min processed... 3136363.64 reads per min processed... 3130434.78 reads per min processed... 3061224.49 reads per min processed... 3058823.53 reads per min processed... 3000000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.KPhK3n8ICE/aih-tih-sc-598a93-R1_A23YTGFLT4_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.KPhK3n8ICE/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -83263.884319 EM: Round [1] log likelihood: -83162.913535 EM: Round [2] log likelihood: -83126.096788 EM: Round [3] log likelihood: -83109.436474 EM: Round [4] log likelihood: -83100.861522 EM: Round [5] log likelihood: -83096.139939 EM: Round [6] log likelihood: -83093.420829 EM: Round [7] log likelihood: -83091.790324 EM: Round [8] log likelihood: -83090.772142 EM: Round [9] log likelihood: -83090.110204 EM: Round [10] log likelihood: -83089.662940 EM: Round [11] log likelihood: -83089.349743 EM: Round [12] log likelihood: -83089.123268 EM: Round [13] log likelihood: -83088.954803 EM: Round [14] log likelihood: -83088.826370 EM: Round [15] log likelihood: -83088.726355 EM: Round [16] log likelihood: -83088.647030 EM: Round [17] log likelihood: -83088.583109 EM: Round [18] log likelihood: -83088.530883 EM: Round [19] log likelihood: -83088.487693 EM: Round [20] log likelihood: -83088.451592 EM: Round [21] log likelihood: -83088.421127 EM: Round [22] log likelihood: -83088.395200 EM: Round [23] log likelihood: -83088.372966 EM: Round [24] log likelihood: -83088.353768 EM: Round [25] log likelihood: -83088.337086 EM: Round [26] log likelihood: -83088.322509 EM: Round [27] log likelihood: -83088.309704 EM: Round [28] log likelihood: -83088.298401 EM: Round [29] log likelihood: -83088.288380 EM: Round [30] log likelihood: -83088.279458 EM: Round [31] log likelihood: -83088.271484 EM: Round [32] log likelihood: -83088.264331 EM: Round [33] log likelihood: -83088.257892 EM: Round [34] log likelihood: -83088.252077 EM: Round [35] log likelihood: -83088.246810 EM: Round [36] log likelihood: -83088.242024 EM: Round [37] log likelihood: -83088.237664 EM: Round [38] log likelihood: -83088.233680 EM: Round [39] log likelihood: -83088.230031 EM: Round [40] log likelihood: -83088.226681 EM: Round [41] log likelihood: -83088.223598 EM: Round [42] log likelihood: -83088.220754 EM: Round [43] log likelihood: -83088.218125 EM: Round [44] log likelihood: -83088.215689 EM: Round [45] log likelihood: -83088.213429 EM: Round [46] log likelihood: -83088.211327 EM: Round [47] log likelihood: -83088.209369 EM: Round [48] log likelihood: -83088.207542 EM: Round [49] log likelihood: -83088.205834 EM: Round [50] log likelihood: -83088.204235 EM: Round [51] log likelihood: -83088.202736 EM: Round [52] log likelihood: -83088.201329 EM: Round [53] log likelihood: -83088.200005 EM: Round [54] log likelihood: -83088.198760 EM: Round [55] log likelihood: -83088.197585 EM: Round [56] log likelihood: -83088.196477 EM: Round [57] log likelihood: -83088.195429 EM: Round [58] log likelihood: -83088.194438 EM: Round [59] log likelihood: -83088.193500 EM: Round [60] log likelihood: -83088.192610 EM: Round [61] log likelihood: -83088.191766 EM: Round [62] log likelihood: -83088.190964 EM: Round [63] log likelihood: -83088.190201 EM: Round [64] log likelihood: -83088.189475 EM: Round [65] log likelihood: -83088.188784 EM: Round [66] log likelihood: -83088.188125 EM: Round [67] log likelihood: -83088.187496 EM: Round [68] log likelihood: -83088.186895 EM: Round [69] log likelihood: -83088.186321 EM: Round [70] log likelihood: -83088.185772 EM: Round [71] log likelihood: -83088.185246 EM: Round [72] log likelihood: -83088.184742 EM: Round [73] log likelihood: -83088.184259 EM: Round [74] log likelihood: -83088.183796 EM: Round [75] log likelihood: -83088.183351 EM: Round [76] log likelihood: -83088.182924 EM: Round [77] log likelihood: -83088.182513 EM: Round [78] log likelihood: -83088.182118 EM: Round [79] log likelihood: -83088.181738 EM: Round [80] log likelihood: -83088.181372 EM: Round [81] log likelihood: -83088.181019 EM: Round [82] log likelihood: -83088.180679 EM: Round [83] log likelihood: -83088.180350 EM: Round [84] log likelihood: -83088.180033 EM: Round [85] log likelihood: -83088.179727 EM: Round [86] log likelihood: -83088.179432 EM: Round [87] log likelihood: -83088.179146 EM: Round [88] log likelihood: -83088.178869 EM: Round [89] log likelihood: -83088.178602 EM: Round [90] log likelihood: -83088.178343 EM: Round [91] log likelihood: -83088.178092 EM: Round [92] log likelihood: -83088.177849 EM: Round [93] log likelihood: -83088.177613 EM: Round [94] log likelihood: -83088.177385 EM: Round [95] log likelihood: -83088.177163 EM: Round [96] log likelihood: -83088.176948 EM: Round [97] log likelihood: -83088.176739 EM: Round [98] log likelihood: -83088.176536 EM: Round [99] log likelihood: -83088.176339 EM: Round [100] log likelihood: -83088.176148 EM: Round [101] log likelihood: -83088.175962 EM: Round [102] log likelihood: -83088.175781 EM: Round [103] log likelihood: -83088.175604 EM: Round [104] log likelihood: -83088.175433 EM: Round [105] log likelihood: -83088.175266 EM: Round [106] log likelihood: -83088.175104 EM: Round [107] log likelihood: -83088.174946 EM: Round [108] log likelihood: -83088.174792 EM: Round [109] log likelihood: -83088.174642 EM: Round [110] log likelihood: -83088.174496 EM: Round [111] log likelihood: -83088.174353 EM: Round [112] log likelihood: -83088.174215 EM: Round [113] log likelihood: -83088.174079 EM: Round [114] log likelihood: -83088.173947 EM: Round [115] log likelihood: -83088.173818 EM: Round [116] log likelihood: -83088.173693 EM: Round [117] log likelihood: -83088.173570 EM: Round [118] log likelihood: -83088.173450 EM: Round [119] log likelihood: -83088.173334 EM: Round [120] log likelihood: -83088.173220 EM: Round [121] log likelihood: -83088.173108 EM: Round [122] log likelihood: -83088.172999 EM: Round [123] log likelihood: -83088.172893 EM: Round [124] log likelihood: -83088.172790 EM: Round [125] log likelihood: -83088.172688 EM: Round [126] log likelihood: -83088.172589 EM: Stopping iterations at round 126 due to insufficient improvement in likelihood. EM: Starting log likelihood: -83231.668669 EM: Round [1] log likelihood: -83141.689233 EM: Round [2] log likelihood: -83109.767924 EM: Round [3] log likelihood: -83095.539374 EM: Round [4] log likelihood: -83088.309884 EM: Round [5] log likelihood: -83084.377255 EM: Round [6] log likelihood: -83082.138878 EM: Round [7] log likelihood: -83080.811384 EM: Round [8] log likelihood: -83079.990752 EM: Round [9] log likelihood: -83079.462135 EM: Round [10] log likelihood: -83079.108054 EM: Round [11] log likelihood: -83078.862299 EM: Round [12] log likelihood: -83078.686307 EM: Round [13] log likelihood: -83078.556830 EM: Round [14] log likelihood: -83078.459362 EM: Round [15] log likelihood: -83078.384541 EM: Round [16] log likelihood: -83078.326136 EM: Round [17] log likelihood: -83078.279878 EM: Round [18] log likelihood: -83078.242773 EM: Round [19] log likelihood: -83078.212670 EM: Round [20] log likelihood: -83078.187998 EM: Round [21] log likelihood: -83078.167588 EM: Round [22] log likelihood: -83078.150559 EM: Round [23] log likelihood: -83078.136240 EM: Round [24] log likelihood: -83078.124110 EM: Round [25] log likelihood: -83078.113766 EM: Round [26] log likelihood: -83078.104887 EM: Round [27] log likelihood: -83078.097220 EM: Round [28] log likelihood: -83078.090563 EM: Round [29] log likelihood: -83078.084752 EM: Round [30] log likelihood: -83078.079654 EM: Round [31] log likelihood: -83078.075161 EM: Round [32] log likelihood: -83078.071183 EM: Round [33] log likelihood: -83078.067646 EM: Round [34] log likelihood: -83078.064489 EM: Round [35] log likelihood: -83078.061660 EM: Round [36] log likelihood: -83078.059117 EM: Round [37] log likelihood: -83078.056822 EM: Round [38] log likelihood: -83078.054745 EM: Round [39] log likelihood: -83078.052860 EM: Round [40] log likelihood: -83078.051143 EM: Round [41] log likelihood: -83078.049576 EM: Round [42] log likelihood: -83078.048142 EM: Round [43] log likelihood: -83078.046826 EM: Round [44] log likelihood: -83078.045615 EM: Round [45] log likelihood: -83078.044499 EM: Round [46] log likelihood: -83078.043468 EM: Round [47] log likelihood: -83078.042513 EM: Round [48] log likelihood: -83078.041627 EM: Round [49] log likelihood: -83078.040804 EM: Round [50] log likelihood: -83078.040037 EM: Round [51] log likelihood: -83078.039321 EM: Round [52] log likelihood: -83078.038653 EM: Round [53] log likelihood: -83078.038027 EM: Round [54] log likelihood: -83078.037439 EM: Round [55] log likelihood: -83078.036888 EM: Round [56] log likelihood: -83078.036369 EM: Round [57] log likelihood: -83078.035880 EM: Round [58] log likelihood: -83078.035419 EM: Round [59] log likelihood: -83078.034983 EM: Round [60] log likelihood: -83078.034570 EM: Round [61] log likelihood: -83078.034179 EM: Round [62] log likelihood: -83078.033808 EM: Round [63] log likelihood: -83078.033455 EM: Round [64] log likelihood: -83078.033119 EM: Round [65] log likelihood: -83078.032799 EM: Round [66] log likelihood: -83078.032494 EM: Round [67] log likelihood: -83078.032203 EM: Round [68] log likelihood: -83078.031925 EM: Round [69] log likelihood: -83078.031658 EM: Round [70] log likelihood: -83078.031403 EM: Round [71] log likelihood: -83078.031158 EM: Round [72] log likelihood: -83078.030922 EM: Round [73] log likelihood: -83078.030696 EM: Round [74] log likelihood: -83078.030478 EM: Round [75] log likelihood: -83078.030269 EM: Round [76] log likelihood: -83078.030067 EM: Round [77] log likelihood: -83078.029872 EM: Round [78] log likelihood: -83078.029684 EM: Round [79] log likelihood: -83078.029502 EM: Round [80] log likelihood: -83078.029326 EM: Round [81] log likelihood: -83078.029156 EM: Round [82] log likelihood: -83078.028991 EM: Round [83] log likelihood: -83078.028832 EM: Round [84] log likelihood: -83078.028677 EM: Round [85] log likelihood: -83078.028527 EM: Round [86] log likelihood: -83078.028381 EM: Round [87] log likelihood: -83078.028239 EM: Round [88] log likelihood: -83078.028102 EM: Round [89] log likelihood: -83078.027968 EM: Round [90] log likelihood: -83078.027838 EM: Round [91] log likelihood: -83078.027711 EM: Round [92] log likelihood: -83078.027587 EM: Round [93] log likelihood: -83078.027467 EM: Round [94] log likelihood: -83078.027350 EM: Round [95] log likelihood: -83078.027236 EM: Round [96] log likelihood: -83078.027125 EM: Round [97] log likelihood: -83078.027016 EM: Round [98] log likelihood: -83078.026910 EM: Round [99] log likelihood: -83078.026806 EM: Round [100] log likelihood: -83078.026705 EM: Round [101] log likelihood: -83078.026607 EM: Stopping iterations at round 101 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.KPhK3n8ICE/./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.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.KPhK3n8ICE/./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.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 60743285 > /tmp/nxf.KPhK3n8ICE/./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.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir > /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir --annotate /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.KPhK3n8ICE/./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.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir -done, see /tmp/nxf.KPhK3n8ICE/./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.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.KPhK3n8ICE/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 699, filtered: 5443) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.KPhK3n8ICE/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.KPhK3n8ICE/./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.KPhK3n8ICE/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000278975.1] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000225292.2] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000262801.6] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000231826.6] WARNING, no entry stored in dbm for [ENSG00000228323.2] WARNING, no entry stored in dbm for [ENSG00000275708.1] 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 [ENSG00000270139.1] WARNING, no entry stored in dbm for [ENSG00000229526.2] WARNING, no entry stored in dbm for [ENSG00000251557.2] WARNING, no entry stored in dbm for [ENSG00000225465.10] WARNING, no entry stored in dbm for [ENSG00000259461.1] WARNING, no entry stored in dbm for [ENSG00000214826.5] WARNING, no entry stored in dbm for [ENSG00000189149.12] WARNING, no entry stored in dbm for [ENSG00000203865.11] WARNING, no entry stored in dbm for [ENSG00000215158.9] WARNING, no entry stored in dbm for [ENSG00000226472.8] WARNING, no entry stored in dbm for [ENSG00000237004.4] WARNING, no entry stored in dbm for [ENSG00000196796.5] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000213916.2] WARNING, no entry stored in dbm for [ENSG00000263527.1] WARNING, no entry stored in dbm for [ENSG00000235903.9] WARNING, no entry stored in dbm for [ENSG00000272848.2] WARNING, no entry stored in dbm for [ENSG00000187172.15] WARNING, no entry stored in dbm for [ENSG00000235499.1] WARNING, no entry stored in dbm for [ENSG00000204684.4] WARNING, no entry stored in dbm for [ENSG00000227508.6] WARNING, no entry stored in dbm for [ENSG00000270641.1] WARNING, no entry stored in dbm for [ENSG00000251443.2] WARNING, no entry stored in dbm for [ENSG00000277304.1] WARNING, no entry stored in dbm for [ENSG00000203645.2] WARNING, no entry stored in dbm for [ENSG00000241357.1] WARNING, no entry stored in dbm for [ENSG00000234911.2] WARNING, no entry stored in dbm for [ENSG00000264112.1] WARNING, no entry stored in dbm for [ENSG00000249635.1] WARNING, no entry stored in dbm for [ENSG00000177410.13] WARNING, no entry stored in dbm for [ENSG00000236292.1] WARNING, no entry stored in dbm for [ENSG00000106610.15] WARNING, no entry stored in dbm for [ENSG00000182796.14] WARNING, no entry stored in dbm for [ENSG00000239332.6] WARNING, no entry stored in dbm for [ENSG00000248121.8] WARNING, no entry stored in dbm for [ENSG00000273609.1] WARNING, no entry stored in dbm for [ENSG00000217653.1] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000287411.1] WARNING, no entry stored in dbm for [ENSG00000227681.5] WARNING, no entry stored in dbm for [ENSG00000249096.7] WARNING, no entry stored in dbm for [ENSG00000229235.1] WARNING, no entry stored in dbm for [ENSG00000223508.5] WARNING, no entry stored in dbm for [ENSG00000261641.2] WARNING, no entry stored in dbm for [ENSG00000254610.3] WARNING, no entry stored in dbm for [ENSG00000252650.1] WARNING, no entry stored in dbm for [ENSG00000231093.1] WARNING, no entry stored in dbm for [ENSG00000203993.6] WARNING, no entry stored in dbm for [ENSG00000218018.3] WARNING, no entry stored in dbm for [ENSG00000196796.5] WARNING, no entry stored in dbm for [ENSG00000234156.3] WARNING, no entry stored in dbm for [ENSG00000228204.2] WARNING, no entry stored in dbm for [ENSG00000248466.1] WARNING, no entry stored in dbm for [ENSG00000233401.1] WARNING, no entry stored in dbm for [ENSG00000239556.4] WARNING, no entry stored in dbm for [ENSG00000239556.4] WARNING, no entry stored in dbm for [ENSG00000269350.1] WARNING, no entry stored in dbm for [ENSG00000176728.10] WARNING, no entry stored in dbm for [ENSG00000227827.3] WARNING, no entry stored in dbm for [ENSG00000279682.1] WARNING, no entry stored in dbm for [ENSG00000243753.5] WARNING, no entry stored in dbm for [ENSG00000227621.1] WARNING, no entry stored in dbm for [ENSG00000200554.1] WARNING, no entry stored in dbm for [ENSG00000258488.2] WARNING, no entry stored in dbm for [ENSG00000266379.6] WARNING, no entry stored in dbm for [ENSG00000235927.4] WARNING, no entry stored in dbm for [ENSG00000258036.2] WARNING, no entry stored in dbm for [ENSG00000235531.11] WARNING, no entry stored in dbm for [ENSG00000228526.7] WARNING, no entry stored in dbm for [ENSG00000270069.1] WARNING, no entry stored in dbm for [ENSG00000249669.10] WARNING, no entry stored in dbm for [ENSG00000181355.21] WARNING, no entry stored in dbm for [ENSG00000277561.5] WARNING, no entry stored in dbm for [ENSG00000248323.7] WARNING, no entry stored in dbm for [ENSG00000231312.7] WARNING, no entry stored in dbm for [ENSG00000275716.1] WARNING, no entry stored in dbm for [ENSG00000226822.3] WARNING, no entry stored in dbm for [ENSG00000241288.8] WARNING, no entry stored in dbm for [ENSG00000261008.7] WARNING, no entry stored in dbm for [ENSG00000229891.2] WARNING, no entry stored in dbm for [ENSG00000236511.2] WARNING, no entry stored in dbm for [ENSG00000242512.9] WARNING, no entry stored in dbm for [ENSG00000228794.10] WARNING, no entry stored in dbm for [ENSG00000237667.7] WARNING, no entry stored in dbm for [ENSG00000182648.13] WARNING, no entry stored in dbm for [ENSG00000282508.2] WARNING, no entry stored in dbm for [ENSG00000250334.6] WARNING, no entry stored in dbm for [ENSG00000229240.9] WARNING, no entry stored in dbm for [ENSG00000260388.2] WARNING, no entry stored in dbm for [ENSG00000179219.5] WARNING, no entry stored in dbm for [ENSG00000245849.8] WARNING, no entry stored in dbm for [ENSG00000226869.6] WARNING, no entry stored in dbm for [ENSG00000226235.1] WARNING, no entry stored in dbm for [ENSG00000231870.4] WARNING, no entry stored in dbm for [ENSG00000225264.3] WARNING, no entry stored in dbm for [ENSG00000236567.2] WARNING, no entry stored in dbm for [ENSG00000285534.1] WARNING, no entry stored in dbm for [ENSG00000231607.13] WARNING, no entry stored in dbm for [ENSG00000244627.5] WARNING, no entry stored in dbm for [ENSG00000253552.8] WARNING, no entry stored in dbm for [ENSG00000251297.1] WARNING, no entry stored in dbm for [ENSG00000270255.1] WARNING, no entry stored in dbm for [ENSG00000258886.2] WARNING, no entry stored in dbm for [ENSG00000276550.4] WARNING, no entry stored in dbm for [ENSG00000234177.5] WARNING, no entry stored in dbm for [ENSG00000244306.11] WARNING, no entry stored in dbm for [ENSG00000231721.7] WARNING, no entry stored in dbm for [ENSG00000283001.2] WARNING, no entry stored in dbm for [ENSG00000229358.3] WARNING, no entry stored in dbm for [ENSG00000227769.7] WARNING, no entry stored in dbm for [ENSG00000177822.8] WARNING, no entry stored in dbm for [ENSG00000263862.2] WARNING, no entry stored in dbm for [ENSG00000234983.1] WARNING, no entry stored in dbm for [ENSG00000255052.5] WARNING, no entry stored in dbm for [ENSG00000254016.3] WARNING, no entry stored in dbm for [ENSG00000231528.3] WARNING, no entry stored in dbm for [ENSG00000227954.7] WARNING, no entry stored in dbm for [ENSG00000260528.5] WARNING, no entry stored in dbm for [ENSG00000234709.2] WARNING, no entry stored in dbm for [ENSG00000274378.1] WARNING, no entry stored in dbm for [ENSG00000213130.3] WARNING, no entry stored in dbm for [ENSG00000227117.6] WARNING, no entry stored in dbm for [ENSG00000278771.1] WARNING, no entry stored in dbm for [ENSG00000232907.8] WARNING, no entry stored in dbm for [ENSG00000288011.1] WARNING, no entry stored in dbm for [ENSG00000219404.2] WARNING, no entry stored in dbm for [ENSG00000286458.1] WARNING, no entry stored in dbm for [ENSG00000287923.1] WARNING, no entry stored in dbm for [ENSG00000284740.1] WARNING, no entry stored in dbm for [ENSG00000280445.1] WARNING, no entry stored in dbm for [ENSG00000251204.1] WARNING, no entry stored in dbm for [ENSG00000226312.7] WARNING, no entry stored in dbm for [ENSG00000288091.1] WARNING, no entry stored in dbm for [ENSG00000229989.4] WARNING, no entry stored in dbm for [ENSG00000223773.7] WARNING, no entry stored in dbm for [ENSG00000283041.1] WARNING, no entry stored in dbm for [ENSG00000196796.5] WARNING, no entry stored in dbm for [ENSG00000258584.2] WARNING, no entry stored in dbm for [ENSG00000225670.4] WARNING, no entry stored in dbm for [ENSG00000280341.1] WARNING, no entry stored in dbm for [ENSG00000204177.10] WARNING, no entry stored in dbm for [ENSG00000255355.1] WARNING, no entry stored in dbm for [ENSG00000253144.1] WARNING, no entry stored in dbm for [ENSG00000235486.1] WARNING, no entry stored in dbm for [ENSG00000235085.3] WARNING, no entry stored in dbm for [ENSG00000284612.1] WARNING, no entry stored in dbm for [ENSG00000235494.2] WARNING, no entry stored in dbm for [ENSG00000286109.1] WARNING, no entry stored in dbm for [ENSG00000225032.5] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000274261.2] WARNING, no entry stored in dbm for [ENSG00000287562.1] WARNING, no entry stored in dbm for [ENSG00000270209.1] WARNING, no entry stored in dbm for [ENSG00000176515.1] WARNING, no entry stored in dbm for [ENSG00000226310.1] WARNING, no entry stored in dbm for [ENSG00000225689.2] WARNING, no entry stored in dbm for [ENSG00000230869.1] WARNING, no entry stored in dbm for [ENSG00000272140.2] WARNING, no entry stored in dbm for [ENSG00000280029.4] WARNING, no entry stored in dbm for [ENSG00000280029.4] WARNING, no entry stored in dbm for [ENSG00000283453.2] WARNING, no entry stored in dbm for [ENSG00000261499.2] WARNING, no entry stored in dbm for [ENSG00000282572.2] WARNING, no entry stored in dbm for [ENSG00000247679.3] WARNING, no entry stored in dbm for [ENSG00000254701.3] WARNING, no entry stored in dbm for [ENSG00000261719.1] WARNING, no entry stored in dbm for [ENSG00000243655.2] WARNING, no entry stored in dbm for [ENSG00000284675.1] WARNING, no entry stored in dbm for [ENSG00000224409.1] WARNING, no entry stored in dbm for [ENSG00000248376.2] WARNING, no entry stored in dbm for [ENSG00000261444.1] WARNING, no entry stored in dbm for [ENSG00000277458.1] WARNING, no entry stored in dbm for [ENSG00000286895.1] WARNING, no entry stored in dbm for [ENSG00000259200.2] WARNING, no entry stored in dbm for [ENSG00000283674.3] WARNING, no entry stored in dbm for [ENSG00000259555.1] WARNING, no entry stored in dbm for [ENSG00000280331.1] WARNING, no entry stored in dbm for [ENSG00000251131.2] WARNING, no entry stored in dbm for [ENSG00000259429.5] WARNING, no entry stored in dbm for [ENSG00000214883.4] WARNING, no entry stored in dbm for [ENSG00000273674.5] WARNING, no entry stored in dbm for [ENSG00000284711.1] WARNING, no entry stored in dbm for [ENSG00000230073.1] WARNING, no entry stored in dbm for [ENSG00000214331.8] WARNING, no entry stored in dbm for [ENSG00000257403.2] WARNING, no entry stored in dbm for [ENSG00000271699.5] WARNING, no entry stored in dbm for [ENSG00000267191.2] WARNING, no entry stored in dbm for [ENSG00000266869.2] WARNING, no entry stored in dbm for [ENSG00000283538.3] WARNING, no entry stored in dbm for [ENSG00000268565.1] WARNING, no entry stored in dbm for [ENSG00000278920.1] WARNING, no entry stored in dbm for [ENSG00000253966.1] * STAR-Fusion complete. See output: /tmp/nxf.KPhK3n8ICE/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)