-ctat genome lib [/tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.wRQBvkCfuH/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary -sample contains 67600638 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir -J /tmp/nxf.wRQBvkCfuH/HeadNeckN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.wRQBvkCfuH/HeadNeckN_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=54545.45/min [20000], rate=34285.71/min [30000], rate=35294.12/min [40000], rate=32876.71/min [50000], rate=33707.87/min [60000], rate=32727.27/min [70000], rate=33070.87/min [80000], rate=34782.61/min [90000], rate=36000.00/min [100000], rate=37037.04/min [110000], rate=38823.53/min [120000], rate=38918.92/min [130000], rate=37500.00/min [140000], rate=37004.41/min [150000], rate=35573.12/min [160000], rate=35424.35/min [170000], rate=35789.47/min [180000], rate=35294.12/min [190000], rate=35076.92/min [200000], rate=35502.96/min [210000], rate=35795.45/min [220000], rate=35967.30/min [230000], rate=36315.79/min [240000], rate=36828.64/min [250000], rate=37406.48/min [260000], rate=38141.81/min [270000], rate=36986.30/min [280000], rate=36051.50/min [290000], rate=34661.35/min [300000], rate=33519.55/min [310000], rate=32920.35/min [320000], rate=32487.31/min [330000], rate=32195.12/min [340000], rate=32025.12/min [350000], rate=31578.95/min [360000], rate=31532.85/min [370000], rate=31534.09/min [380000], rate=31710.71/min [390000], rate=31967.21/min [400000], rate=32214.77/min [410000], rate=32669.32/min [420000], rate=32984.29/min [430000], rate=33376.46/min [440000], rate=33716.48/min [450000], rate=34047.92/min [460000], rate=33535.84/min [470000], rate=33254.72/min [480000], rate=33141.54/min [490000], rate=33145.43/min [500000], rate=33149.17/min [510000], rate=33224.76/min [520000], rate=33262.26/min [530000], rate=33333.33/min [540000], rate=33436.53/min [550000], rate=33434.65/min [560000], rate=33300.30/min [570000], rate=33268.48/min [580000], rate=33429.39/min [590000], rate=33554.50/min [600000], rate=33519.55/min [610000], rate=33701.66/min [620000], rate=33941.61/min [630000], rate=34270.17/min [640000], rate=34563.46/min [650000], rate=34574.47/min [660000], rate=34494.77/min [670000], rate=34476.84/min [680000], rate=34343.43/min [690000], rate=34413.97/min [700000], rate=34539.47/min [710000], rate=34690.55/min [720000], rate=34838.71/min [730000], rate=35068.05/min [740000], rate=35406.70/min [750000], rate=35742.65/min [760000], rate=36104.51/min [770000], rate=36435.33/min [780000], rate=36763.55/min [790000], rate=37147.34/min [800000], rate=37354.09/min [810000], rate=37298.54/min [820000], rate=37188.21/min [830000], rate=37136.47/min [840000], rate=37031.59/min [850000], rate=36876.36/min [860000], rate=36752.14/min [870000], rate=36657.30/min [880000], rate=36743.22/min [890000], rate=36675.82/min [900000], rate=36560.60/min [910000], rate=36472.95/min [920000], rate=36604.77/min [930000], rate=36710.53/min [940000], rate=36862.75/min [950000], rate=37037.04/min [960000], rate=36994.22/min [970000], rate=36928.93/min [980000], rate=36911.49/min [990000], rate=36894.41/min [1000000], rate=36923.08/min [1010000], rate=37041.56/min [1020000], rate=37203.65/min [1030000], rate=37318.84/min [1040000], rate=37522.55/min [1050000], rate=37634.41/min [1060000], rate=37677.73/min [1070000], rate=37809.19/min -building interval tree based on /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=17647.06/min [20000], rate=19047.62/min [30000], rate=19565.22/min [40000], rate=21818.18/min [50000], rate=23076.92/min [60000], rate=23841.06/min [70000], rate=24137.93/min [80000], rate=24365.48/min [90000], rate=25000.00/min [100000], rate=25641.03/min [110000], rate=26190.48/min [120000], rate=26966.29/min [130000], rate=27177.70/min [140000], rate=27631.58/min [150000], rate=27863.78/min [160000], rate=28742.51/min [170000], rate=30088.50/min [180000], rate=31213.87/min [190000], rate=30000.00/min [200000], rate=28985.51/min [210000], rate=27753.30/min [220000], rate=26883.91/min [230000], rate=26487.52/min [240000], rate=25899.28/min [250000], rate=25862.07/min [260000], rate=25573.77/min [270000], rate=25511.81/min [280000], rate=25688.07/min [290000], rate=26126.13/min [300000], rate=26315.79/min [310000], rate=26050.42/min [320000], rate=26016.26/min [330000], rate=26294.82/min [340000], rate=26701.57/min [350000], rate=26854.22/min [360000], rate=27067.67/min [370000], rate=27509.29/min [380000], rate=27906.98/min [390000], rate=28158.84/min [400000], rate=28469.75/min [410000], rate=28771.93/min [420000], rate=29099.31/min [430000], rate=29119.64/min [440000], rate=29300.78/min [450000], rate=29508.20/min [460000], rate=29805.62/min [470000], rate=30128.21/min [480000], rate=30476.19/min [490000], rate=30593.13/min [500000], rate=30864.20/min [510000], rate=31384.62/min [520000], rate=31967.21/min [530000], rate=32515.34/min [540000], rate=32694.25/min [550000], rate=32901.30/min [560000], rate=33136.09/min [570000], rate=33431.09/min [580000], rate=33623.19/min [590000], rate=33843.21/min [600000], rate=34188.03/min [610000], rate=34463.28/min [620000], rate=34604.65/min [630000], rate=34774.61/min [640000], rate=35261.71/min [650000], rate=35779.82/min [660000], rate=36296.98/min [670000], rate=36545.45/min [680000], rate=36657.68/min [690000], rate=36931.31/min [700000], rate=37135.28/min [710000], rate=37434.09/min [720000], rate=37597.91/min [730000], rate=37823.83/min [740000], rate=37851.66/min [750000], rate=37625.42/min [760000], rate=37315.88/min [770000], rate=37500.00/min [780000], rate=37590.36/min [790000], rate=37768.92/min [800000], rate=37647.06/min [810000], rate=37791.60/min [820000], rate=38051.04/min [830000], rate=38219.49/min [840000], rate=38239.76/min [850000], rate=38288.29/min [860000], rate=38392.86/min [870000], rate=38438.88/min [880000], rate=38483.97/min [890000], rate=38583.82/min [900000], rate=38654.26/min [910000], rate=38181.82/min [920000], rate=37627.81/min [930000], rate=37374.41/min [940000], rate=37032.17/min [950000], rate=36774.19/min [960000], rate=36363.64/min [970000], rate=36149.07/min [980000], rate=35722.96/min [990000], rate=35441.53/min [1000000], rate=35294.12/min [1010000], rate=35150.81/min [1020000], rate=35152.21/min [1030000], rate=35253.85/min [1040000], rate=35135.14/min [1050000], rate=35156.25/min [1060000], rate=35274.54/min [1070000], rate=35371.90/min -building interval tree based on /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=25000.00/min [20000], rate=22641.51/min [30000], rate=21951.22/min [40000], rate=22429.91/min [50000], rate=23809.52/min [60000], rate=25000.00/min [70000], rate=25609.76/min [80000], rate=25531.91/min [90000], rate=25352.11/min [100000], rate=25751.07/min [110000], rate=26506.02/min [120000], rate=27376.43/min [130000], rate=28260.87/min [140000], rate=29577.46/min [150000], rate=30716.72/min [160000], rate=30967.74/min [170000], rate=31974.92/min [180000], rate=32826.75/min [190000], rate=32947.98/min [200000], rate=33241.00/min [210000], rate=33689.84/min [220000], rate=34464.75/min [230000], rate=34848.48/min [240000], rate=33723.65/min [250000], rate=33039.65/min [260000], rate=32980.97/min [270000], rate=32926.83/min [280000], rate=33136.09/min [290000], rate=33526.01/min [300000], rate=34026.47/min [310000], rate=34572.49/min [320000], rate=34845.74/min [330000], rate=35357.14/min [340000], rate=36106.19/min [350000], rate=36777.58/min [360000], rate=36923.08/min [370000], rate=36754.97/min [380000], rate=36421.73/min [390000], rate=36391.91/min [400000], rate=36697.25/min [410000], rate=36826.35/min [420000], rate=36950.15/min [430000], rate=37229.44/min [440000], rate=37500.00/min [450000], rate=37921.35/min [460000], rate=38227.15/min [470000], rate=38263.23/min [480000], rate=37402.60/min [490000], rate=37404.58/min [500000], rate=36719.71/min [510000], rate=36559.14/min [520000], rate=36236.93/min [530000], rate=36013.59/min [540000], rate=35960.04/min [550000], rate=36065.57/min [560000], rate=36051.50/min [570000], rate=36190.48/min [580000], rate=36439.79/min [590000], rate=36307.69/min [600000], rate=36437.25/min [610000], rate=36526.95/min [620000], rate=36614.17/min [630000], rate=36592.45/min [640000], rate=36746.41/min [650000], rate=36792.45/min [660000], rate=37009.35/min [670000], rate=36948.53/min [680000], rate=36889.69/min [690000], rate=36964.29/min [700000], rate=37037.04/min [710000], rate=37237.76/min [720000], rate=37467.48/min [730000], rate=37693.63/min [740000], rate=36633.66/min [750000], rate=36028.82/min [760000], rate=35764.71/min [770000], rate=35483.87/min [780000], rate=35240.96/min [790000], rate=34852.94/min [800000], rate=34383.95/min [810000], rate=34249.47/min [820000], rate=34024.90/min [830000], rate=33671.40/min [840000], rate=33245.38/min [850000], rate=32988.36/min [860000], rate=32803.56/min [870000], rate=32850.85/min [880000], rate=32815.41/min [890000], rate=32821.14/min [900000], rate=32786.89/min [910000], rate=32675.04/min [920000], rate=32701.42/min [930000], rate=32612.51/min [940000], rate=32413.79/min [950000], rate=32367.97/min [960000], rate=32414.18/min [970000], rate=32441.47/min [980000], rate=32540.12/min [990000], rate=32709.25/min [1000000], rate=32822.76/min [1010000], rate=32881.17/min [1020000], rate=33045.36/min [1030000], rate=33065.81/min [1040000], rate=33156.22/min [1050000], rate=33315.71/min [1060000], rate=32936.30/min -building interval tree based on /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=109090.91/min [30000], rate=94736.84/min [40000], rate=75000.00/min [50000], rate=78947.37/min [60000], rate=85714.29/min [70000], rate=85714.29/min [80000], rate=90566.04/min [90000], rate=90000.00/min [100000], rate=95238.10/min [110000], rate=90410.96/min [120000], rate=81818.18/min [130000], rate=82105.26/min [140000], rate=84000.00/min [150000], rate=81081.08/min [160000], rate=78688.52/min [170000], rate=74452.55/min [180000], rate=76595.74/min [190000], rate=77551.02/min [200000], rate=77922.08/min [210000], rate=79746.84/min [220000], rate=80981.60/min [230000], rate=81176.47/min [240000], rate=80000.00/min [250000], rate=79365.08/min [260000], rate=80000.00/min [270000], rate=80198.02/min [280000], rate=80382.78/min [290000], rate=81308.41/min [300000], rate=81447.96/min [310000], rate=71814.67/min [320000], rate=60567.82/min [330000], rate=53369.27/min [340000], rate=46575.34/min [350000], rate=41584.16/min [360000], rate=38230.09/min [370000], rate=35864.30/min [380000], rate=34131.74/min [390000], rate=32865.17/min [400000], rate=31662.27/min [410000], rate=30445.54/min [420000], rate=29964.33/min [430000], rate=29553.26/min [440000], rate=29300.78/min [450000], rate=29220.78/min [460000], rate=29113.92/min [470000], rate=29192.55/min [480000], rate=29268.29/min [490000], rate=29312.06/min [500000], rate=29382.96/min [510000], rate=29451.40/min [520000], rate=29657.79/min [530000], rate=29747.43/min [540000], rate=29889.30/min [550000], rate=30027.30/min [560000], rate=30215.83/min [570000], rate=30373.00/min [580000], rate=30393.01/min [590000], rate=30569.95/min [600000], rate=30534.35/min [610000], rate=30576.44/min [620000], rate=30794.70/min [630000], rate=30857.14/min [640000], rate=30769.23/min [650000], rate=30684.50/min [660000], rate=30793.16/min [670000], rate=30875.58/min [680000], rate=30955.99/min [690000], rate=31034.48/min [700000], rate=31111.11/min [710000], rate=31208.79/min [720000], rate=31304.35/min [730000], rate=31196.58/min [740000], rate=30876.22/min [750000], rate=30674.85/min [760000], rate=30665.77/min [770000], rate=30738.52/min [780000], rate=30769.23/min [790000], rate=30659.77/min [800000], rate=30710.17/min [810000], rate=30857.14/min [820000], rate=30982.37/min [830000], rate=31144.47/min [840000], rate=31284.92/min [850000], rate=31500.93/min [860000], rate=31637.03/min [870000], rate=31655.55/min [880000], rate=31095.41/min [890000], rate=30707.30/min [900000], rate=30577.58/min [910000], rate=30367.07/min [920000], rate=30147.46/min [930000], rate=30129.59/min [940000], rate=30080.00/min [950000], rate=30031.61/min [960000], rate=30000.00/min [970000], rate=30061.98/min [980000], rate=30076.73/min [990000], rate=30060.73/min [1000000], rate=30060.12/min [1010000], rate=30104.32/min [1020000], rate=30147.78/min [1030000], rate=30264.45/min [1040000], rate=30379.75/min [1050000], rate=30508.47/min [1060000], rate=30621.09/min [1070000], rate=30717.70/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir --filt_file /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.wRQBvkCfuH/./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... 6000000.00 reads per min processed... 4500000.00 reads per min processed... 4666666.67 reads per min processed... 4363636.36 reads per min processed... 4500000.00 reads per min processed... 4615384.62 reads per min processed... 4400000.00 reads per min processed... 4235294.12 reads per min processed... 4333333.33 reads per min processed... 4200000.00 reads per min processed... 3913043.48 reads per min processed... 3840000.00 reads per min processed... 3777777.78 reads per min processed... 3857142.86 reads per min processed... 3800000.00 reads per min processed... 3870967.74 reads per min processed... 3818181.82 reads per min processed... 3882352.94 reads per min processed... 3833333.33 reads per min processed... 4000000.00 reads per min processed... 4054054.05 reads per min processed... 4105263.16 reads per min processed... 4050000.00 reads per min processed... 4097560.98 reads per min processed... 4142857.14 reads per min processed... 4090909.09 reads per min processed... 4133333.33 reads per min processed... 4173913.04 reads per min processed... 4125000.00 reads per min processed... 4163265.31 reads per min processed... 4117647.06 reads per min processed... 4153846.15 reads per min processed... 4111111.11 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.wRQBvkCfuH/HeadNeckN_FFPE_L03_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.wRQBvkCfuH/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -53527.379761 EM: Round [1] log likelihood: -53470.209232 EM: Round [2] log likelihood: -53446.755043 EM: Round [3] log likelihood: -53434.725779 EM: Round [4] log likelihood: -53428.069296 EM: Round [5] log likelihood: -53424.270866 EM: Round [6] log likelihood: -53422.043646 EM: Round [7] log likelihood: -53420.693503 EM: Round [8] log likelihood: -53419.843801 EM: Round [9] log likelihood: -53419.288582 EM: Round [10] log likelihood: -53418.912996 EM: Round [11] log likelihood: -53418.651118 EM: Round [12] log likelihood: -53418.463787 EM: Round [13] log likelihood: -53418.326886 EM: Round [14] log likelihood: -53418.225032 EM: Round [15] log likelihood: -53418.148093 EM: Round [16] log likelihood: -53418.089197 EM: Round [17] log likelihood: -53418.043574 EM: Round [18] log likelihood: -53418.007842 EM: Round [19] log likelihood: -53417.979563 EM: Round [20] log likelihood: -53417.956955 EM: Round [21] log likelihood: -53417.938700 EM: Round [22] log likelihood: -53417.923815 EM: Round [23] log likelihood: -53417.911557 EM: Round [24] log likelihood: -53417.901364 EM: Round [25] log likelihood: -53417.892806 EM: Round [26] log likelihood: -53417.885552 EM: Round [27] log likelihood: -53417.879346 EM: Round [28] log likelihood: -53417.873989 EM: Round [29] log likelihood: -53417.869325 EM: Round [30] log likelihood: -53417.865231 EM: Round [31] log likelihood: -53417.861610 EM: Round [32] log likelihood: -53417.858384 EM: Round [33] log likelihood: -53417.855492 EM: Round [34] log likelihood: -53417.852883 EM: Round [35] log likelihood: -53417.850517 EM: Round [36] log likelihood: -53417.848361 EM: Round [37] log likelihood: -53417.846388 EM: Round [38] log likelihood: -53417.844575 EM: Round [39] log likelihood: -53417.842903 EM: Round [40] log likelihood: -53417.841358 EM: Round [41] log likelihood: -53417.839925 EM: Round [42] log likelihood: -53417.838593 EM: Round [43] log likelihood: -53417.837352 EM: Round [44] log likelihood: -53417.836195 EM: Round [45] log likelihood: -53417.835113 EM: Round [46] log likelihood: -53417.834101 EM: Round [47] log likelihood: -53417.833153 EM: Round [48] log likelihood: -53417.832263 EM: Round [49] log likelihood: -53417.831428 EM: Round [50] log likelihood: -53417.830643 EM: Round [51] log likelihood: -53417.829904 EM: Round [52] log likelihood: -53417.829209 EM: Round [53] log likelihood: -53417.828555 EM: Round [54] log likelihood: -53417.827938 EM: Round [55] log likelihood: -53417.827357 EM: Round [56] log likelihood: -53417.826808 EM: Round [57] log likelihood: -53417.826290 EM: Round [58] log likelihood: -53417.825802 EM: Round [59] log likelihood: -53417.825340 EM: Round [60] log likelihood: -53417.824904 EM: Round [61] log likelihood: -53417.824492 EM: Round [62] log likelihood: -53417.824102 EM: Round [63] log likelihood: -53417.823734 EM: Round [64] log likelihood: -53417.823385 EM: Round [65] log likelihood: -53417.823055 EM: Round [66] log likelihood: -53417.822743 EM: Round [67] log likelihood: -53417.822447 EM: Round [68] log likelihood: -53417.822167 EM: Round [69] log likelihood: -53417.821902 EM: Round [70] log likelihood: -53417.821651 EM: Round [71] log likelihood: -53417.821413 EM: Round [72] log likelihood: -53417.821187 EM: Round [73] log likelihood: -53417.820973 EM: Round [74] log likelihood: -53417.820770 EM: Round [75] log likelihood: -53417.820577 EM: Round [76] log likelihood: -53417.820395 EM: Round [77] log likelihood: -53417.820222 EM: Round [78] log likelihood: -53417.820057 EM: Round [79] log likelihood: -53417.819901 EM: Round [80] log likelihood: -53417.819753 EM: Round [81] log likelihood: -53417.819612 EM: Round [82] log likelihood: -53417.819478 EM: Round [83] log likelihood: -53417.819351 EM: Round [84] log likelihood: -53417.819231 EM: Round [85] log likelihood: -53417.819116 EM: Round [86] log likelihood: -53417.819007 EM: Round [87] log likelihood: -53417.818903 EM: Round [88] log likelihood: -53417.818805 EM: Stopping iterations at round 88 due to insufficient improvement in likelihood. EM: Starting log likelihood: -53507.045181 EM: Round [1] log likelihood: -53454.397035 EM: Round [2] log likelihood: -53433.143144 EM: Round [3] log likelihood: -53422.411537 EM: Round [4] log likelihood: -53416.576857 EM: Round [5] log likelihood: -53413.306886 EM: Round [6] log likelihood: -53411.425238 EM: Round [7] log likelihood: -53410.306977 EM: Round [8] log likelihood: -53409.617500 EM: Round [9] log likelihood: -53409.176120 EM: Round [10] log likelihood: -53408.883389 EM: Round [11] log likelihood: -53408.683023 EM: Round [12] log likelihood: -53408.542094 EM: Round [13] log likelihood: -53408.440649 EM: Round [14] log likelihood: -53408.366174 EM: Round [15] log likelihood: -53408.310558 EM: Round [16] log likelihood: -53408.268395 EM: Round [17] log likelihood: -53408.235988 EM: Round [18] log likelihood: -53408.210756 EM: Round [19] log likelihood: -53408.190866 EM: Round [20] log likelihood: -53408.174995 EM: Round [21] log likelihood: -53408.162178 EM: Round [22] log likelihood: -53408.151705 EM: Round [23] log likelihood: -53408.143045 EM: Round [24] log likelihood: -53408.135802 EM: Round [25] log likelihood: -53408.129675 EM: Round [26] log likelihood: -53408.124434 EM: Round [27] log likelihood: -53408.119906 EM: Round [28] log likelihood: -53408.115955 EM: Round [29] log likelihood: -53408.112475 EM: Round [30] log likelihood: -53408.109386 EM: Round [31] log likelihood: -53408.106621 EM: Round [32] log likelihood: -53408.104131 EM: Round [33] log likelihood: -53408.101874 EM: Round [34] log likelihood: -53408.099817 EM: Round [35] log likelihood: -53408.097934 EM: Round [36] log likelihood: -53408.096202 EM: Round [37] log likelihood: -53408.094605 EM: Round [38] log likelihood: -53408.093126 EM: Round [39] log likelihood: -53408.091754 EM: Round [40] log likelihood: -53408.090478 EM: Round [41] log likelihood: -53408.089288 EM: Round [42] log likelihood: -53408.088178 EM: Round [43] log likelihood: -53408.087140 EM: Round [44] log likelihood: -53408.086168 EM: Round [45] log likelihood: -53408.085256 EM: Round [46] log likelihood: -53408.084402 EM: Round [47] log likelihood: -53408.083599 EM: Round [48] log likelihood: -53408.082845 EM: Round [49] log likelihood: -53408.082136 EM: Round [50] log likelihood: -53408.081469 EM: Round [51] log likelihood: -53408.080841 EM: Round [52] log likelihood: -53408.080250 EM: Round [53] log likelihood: -53408.079692 EM: Round [54] log likelihood: -53408.079167 EM: Round [55] log likelihood: -53408.078672 EM: Round [56] log likelihood: -53408.078205 EM: Round [57] log likelihood: -53408.077765 EM: Round [58] log likelihood: -53408.077349 EM: Round [59] log likelihood: -53408.076956 EM: Round [60] log likelihood: -53408.076586 EM: Round [61] log likelihood: -53408.076236 EM: Round [62] log likelihood: -53408.075905 EM: Round [63] log likelihood: -53408.075592 EM: Round [64] log likelihood: -53408.075297 EM: Round [65] log likelihood: -53408.075018 EM: Round [66] log likelihood: -53408.074754 EM: Round [67] log likelihood: -53408.074504 EM: Round [68] log likelihood: -53408.074268 EM: Round [69] log likelihood: -53408.074044 EM: Round [70] log likelihood: -53408.073832 EM: Round [71] log likelihood: -53408.073632 EM: Round [72] log likelihood: -53408.073442 EM: Round [73] log likelihood: -53408.073263 EM: Round [74] log likelihood: -53408.073093 EM: Round [75] log likelihood: -53408.072932 EM: Round [76] log likelihood: -53408.072779 EM: Round [77] log likelihood: -53408.072634 EM: Round [78] log likelihood: -53408.072497 EM: Round [79] log likelihood: -53408.072367 EM: Round [80] log likelihood: -53408.072244 EM: Round [81] log likelihood: -53408.072127 EM: Round [82] log likelihood: -53408.072016 EM: Round [83] log likelihood: -53408.071911 EM: Round [84] log likelihood: -53408.071811 EM: Stopping iterations at round 84 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.wRQBvkCfuH/./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.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.wRQBvkCfuH/./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.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 67600638 > /tmp/nxf.wRQBvkCfuH/./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.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir > /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir --annotate /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.wRQBvkCfuH/./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.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir -done, see /tmp/nxf.wRQBvkCfuH/./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.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.wRQBvkCfuH/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 408, filtered: 4225) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.wRQBvkCfuH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.wRQBvkCfuH/./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.wRQBvkCfuH/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 [ENSG00000248049.7] 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 [ENSG00000249096.7] WARNING, no entry stored in dbm for [ENSG00000242326.1] WARNING, no entry stored in dbm for [ENSG00000271776.1] WARNING, no entry stored in dbm for [ENSG00000181126.13] WARNING, no entry stored in dbm for [ENSG00000277984.1] WARNING, no entry stored in dbm for [ENSG00000251314.2] WARNING, no entry stored in dbm for [ENSG00000268163.1] WARNING, no entry stored in dbm for [ENSG00000231559.1] WARNING, no entry stored in dbm for [ENSG00000241743.4] WARNING, no entry stored in dbm for [ENSG00000241860.7] WARNING, no entry stored in dbm for [ENSG00000173811.11] WARNING, no entry stored in dbm for [ENSG00000267339.7] WARNING, no entry stored in dbm for [ENSG00000279910.1] WARNING, no entry stored in dbm for [ENSG00000248699.1] WARNING, no entry stored in dbm for [ENSG00000237588.2] WARNING, no entry stored in dbm for [ENSG00000196756.13] WARNING, no entry stored in dbm for [ENSG00000263327.6] WARNING, no entry stored in dbm for [ENSG00000275198.1] WARNING, no entry stored in dbm for [ENSG00000286796.1] WARNING, no entry stored in dbm for [ENSG00000169849.8] WARNING, no entry stored in dbm for [ENSG00000249228.1] WARNING, no entry stored in dbm for [ENSG00000271063.1] WARNING, no entry stored in dbm for [ENSG00000264350.1] WARNING, no entry stored in dbm for [ENSG00000224078.15] WARNING, no entry stored in dbm for [ENSG00000261490.1] WARNING, no entry stored in dbm for [ENSG00000285763.1] WARNING, no entry stored in dbm for [ENSG00000237087.1] WARNING, no entry stored in dbm for [ENSG00000229140.11] WARNING, no entry stored in dbm for [ENSG00000230559.1] WARNING, no entry stored in dbm for [ENSG00000231322.5] WARNING, no entry stored in dbm for [ENSG00000223202.1] WARNING, no entry stored in dbm for [ENSG00000200966.1] WARNING, no entry stored in dbm for [ENSG00000286248.1] WARNING, no entry stored in dbm for [ENSG00000270225.1] WARNING, no entry stored in dbm for [ENSG00000204959.4] WARNING, no entry stored in dbm for [ENSG00000250977.1] WARNING, no entry stored in dbm for [ENSG00000212719.13] WARNING, no entry stored in dbm for [ENSG00000250251.6] WARNING, no entry stored in dbm for [ENSG00000229569.1] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000229082.2] WARNING, no entry stored in dbm for [ENSG00000236283.5] WARNING, no entry stored in dbm for [ENSG00000203993.6] WARNING, no entry stored in dbm for [ENSG00000246889.2] WARNING, no entry stored in dbm for [ENSG00000223488.2] WARNING, no entry stored in dbm for [ENSG00000245468.4] WARNING, no entry stored in dbm for [ENSG00000223883.2] WARNING, no entry stored in dbm for [ENSG00000255171.7] WARNING, no entry stored in dbm for [ENSG00000228918.4] WARNING, no entry stored in dbm for [ENSG00000225329.3] WARNING, no entry stored in dbm for [ENSG00000267727.1] WARNING, no entry stored in dbm for [ENSG00000279569.1] WARNING, no entry stored in dbm for [ENSG00000249803.6] WARNING, no entry stored in dbm for [ENSG00000283443.1] WARNING, no entry stored in dbm for [ENSG00000223738.3] WARNING, no entry stored in dbm for [ENSG00000259722.2] WARNING, no entry stored in dbm for [ENSG00000234705.2] WARNING, no entry stored in dbm for [ENSG00000248890.2] WARNING, no entry stored in dbm for [ENSG00000197847.12] WARNING, no entry stored in dbm for [ENSG00000238105.7] WARNING, no entry stored in dbm for [ENSG00000239821.3] WARNING, no entry stored in dbm for [ENSG00000280441.3] WARNING, no entry stored in dbm for [ENSG00000237975.7] WARNING, no entry stored in dbm for [ENSG00000256737.1] WARNING, no entry stored in dbm for [ENSG00000232036.2] WARNING, no entry stored in dbm for [ENSG00000254791.1] WARNING, no entry stored in dbm for [ENSG00000215374.6] WARNING, no entry stored in dbm for [ENSG00000279141.3] WARNING, no entry stored in dbm for [ENSG00000245532.9] WARNING, no entry stored in dbm for [ENSG00000258084.6] WARNING, no entry stored in dbm for [ENSG00000242756.2] WARNING, no entry stored in dbm for [ENSG00000260542.1] WARNING, no entry stored in dbm for [ENSG00000231890.8] WARNING, no entry stored in dbm for [ENSG00000239345.2] WARNING, no entry stored in dbm for [ENSG00000242193.11] WARNING, no entry stored in dbm for [ENSG00000267559.5] WARNING, no entry stored in dbm for [ENSG00000286755.1] WARNING, no entry stored in dbm for [ENSG00000283541.1] WARNING, no entry stored in dbm for [ENSG00000273073.1] WARNING, no entry stored in dbm for [ENSG00000254873.1] WARNING, no entry stored in dbm for [ENSG00000219188.1] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000259706.1] WARNING, no entry stored in dbm for [ENSG00000225624.1] WARNING, no entry stored in dbm for [ENSG00000241654.1] WARNING, no entry stored in dbm for [ENSG00000228340.6] WARNING, no entry stored in dbm for [ENSG00000282961.1] WARNING, no entry stored in dbm for [ENSG00000256035.1] WARNING, no entry stored in dbm for [ENSG00000230551.4] WARNING, no entry stored in dbm for [ENSG00000285388.1] WARNING, no entry stored in dbm for [ENSG00000229124.7] 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 [ENSG00000287485.1] WARNING, no entry stored in dbm for [ENSG00000277047.5] WARNING, no entry stored in dbm for [ENSG00000284738.1] WARNING, no entry stored in dbm for [ENSG00000254473.1] WARNING, no entry stored in dbm for [ENSG00000287991.1] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000207955.5] WARNING, no entry stored in dbm for [ENSG00000275139.1] WARNING, no entry stored in dbm for [ENSG00000286774.1] WARNING, no entry stored in dbm for [ENSG00000278182.1] WARNING, no entry stored in dbm for [ENSG00000261499.2] WARNING, no entry stored in dbm for [ENSG00000255185.6] WARNING, no entry stored in dbm for [ENSG00000285755.2] WARNING, no entry stored in dbm for [ENSG00000254111.3] WARNING, no entry stored in dbm for [ENSG00000275374.1] WARNING, no entry stored in dbm for [ENSG00000248973.3] WARNING, no entry stored in dbm for [ENSG00000276337.1] WARNING, no entry stored in dbm for [ENSG00000170409.7] WARNING, no entry stored in dbm for [ENSG00000265936.1] WARNING, no entry stored in dbm for [ENSG00000214259.3] WARNING, no entry stored in dbm for [ENSG00000218175.2] WARNING, no entry stored in dbm for [ENSG00000188850.9] WARNING, no entry stored in dbm for [ENSG00000251199.6] WARNING, no entry stored in dbm for [ENSG00000275016.5] WARNING, no entry stored in dbm for [ENSG00000226266.6] WARNING, no entry stored in dbm for [ENSG00000261117.1] WARNING, no entry stored in dbm for [ENSG00000279865.1] WARNING, no entry stored in dbm for [ENSG00000250182.3] WARNING, no entry stored in dbm for [ENSG00000200434.1] WARNING, no entry stored in dbm for [ENSG00000271394.1] WARNING, no entry stored in dbm for [ENSG00000200794.1] * STAR-Fusion complete. See output: /tmp/nxf.wRQBvkCfuH/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)