-ctat genome lib [/tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.laFn224CnS/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.laFn224CnS/./star-fusion.preliminary -sample contains 52859459 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir -J /tmp/nxf.laFn224CnS/aih-tih-sc-fba77b-R1_A23YTGFLT4_1.Chimeric.out.junction -O /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.laFn224CnS/aih-tih-sc-fba77b-R1_A23YTGFLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=60000.00/min [20000], rate=70588.24/min [30000], rate=72000.00/min [40000], rate=60000.00/min [50000], rate=55555.56/min [60000], rate=52941.18/min [70000], rate=52500.00/min [80000], rate=53333.33/min [90000], rate=54545.45/min [100000], rate=55045.87/min [110000], rate=55462.18/min [120000], rate=57600.00/min [130000], rate=56115.11/min [140000], rate=55629.14/min [150000], rate=55214.72/min [160000], rate=54545.45/min [170000], rate=54545.45/min [180000], rate=54545.45/min [190000], rate=54545.45/min [200000], rate=54794.52/min [210000], rate=56756.76/min [220000], rate=57142.86/min [230000], rate=57983.19/min [240000], rate=57831.33/min [250000], rate=57034.22/min [260000], rate=56521.74/min [270000], rate=56250.00/min [280000], rate=55813.95/min [290000], rate=55591.05/min [300000], rate=55045.87/min [310000], rate=54867.26/min [320000], rate=55014.33/min [330000], rate=55153.20/min [340000], rate=55737.70/min [350000], rate=56603.77/min [360000], rate=56842.11/min [370000], rate=56632.65/min [380000], rate=56575.68/min [390000], rate=56521.74/min [400000], rate=56737.59/min [410000], rate=57209.30/min [420000], rate=57798.17/min [430000], rate=58636.36/min [440000], rate=59593.68/min [450000], rate=60538.12/min [460000], rate=61469.93/min [470000], rate=62389.38/min [480000], rate=63157.89/min [490000], rate=64052.29/min [500000], rate=64794.82/min [510000], rate=65806.45/min [520000], rate=66524.52/min [530000], rate=67372.88/min [540000], rate=68067.23/min [550000], rate=68893.53/min [560000], rate=69565.22/min [570000], rate=69795.92/min [580000], rate=69461.08/min [590000], rate=69140.62/min [600000], rate=68965.52/min [610000], rate=68926.55/min [620000], rate=69144.98/min [630000], rate=69357.80/min [640000], rate=69945.36/min [650000], rate=70397.11/min [660000], rate=70840.79/min [670000], rate=70774.65/min [680000], rate=70588.24/min [690000], rate=70528.11/min [700000], rate=70469.80/min [710000], rate=70529.80/min [720000], rate=70703.76/min [730000], rate=70988.65/min [740000], rate=71612.90/min [750000], rate=72000.00/min -building interval tree based on /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=80000.00/min [30000], rate=85714.29/min [40000], rate=92307.69/min [50000], rate=81081.08/min [60000], rate=67924.53/min [70000], rate=60869.57/min [80000], rate=57831.33/min [90000], rate=55102.04/min [100000], rate=53571.43/min [110000], rate=51968.50/min [120000], rate=51063.83/min [130000], rate=51315.79/min [140000], rate=51533.74/min [150000], rate=51724.14/min [160000], rate=51891.89/min [170000], rate=52307.69/min [180000], rate=53465.35/min [190000], rate=54545.45/min [200000], rate=55555.56/min [210000], rate=56756.76/min [220000], rate=57142.86/min [230000], rate=57500.00/min [240000], rate=58064.52/min [250000], rate=59055.12/min [260000], rate=59770.11/min [270000], rate=60674.16/min [280000], rate=61538.46/min [290000], rate=62365.59/min [300000], rate=63829.79/min [310000], rate=64583.33/min [320000], rate=65753.42/min [330000], rate=66666.67/min [340000], rate=67549.67/min [350000], rate=67961.17/min [360000], rate=68571.43/min [370000], rate=68944.10/min [380000], rate=69090.91/min [390000], rate=69642.86/min [400000], rate=70588.24/min [410000], rate=70893.37/min [420000], rate=71186.44/min [430000], rate=71666.67/min [440000], rate=72131.15/min [450000], rate=72972.97/min [460000], rate=73209.55/min [470000], rate=73246.75/min [480000], rate=73657.29/min [490000], rate=73869.35/min [500000], rate=74441.69/min [510000], rate=74816.63/min [520000], rate=75362.32/min [530000], rate=75894.99/min [540000], rate=75878.22/min [550000], rate=76036.87/min [560000], rate=76018.10/min [570000], rate=76000.00/min [580000], rate=76315.79/min [590000], rate=76457.88/min [600000], rate=76595.74/min [610000], rate=76729.56/min [620000], rate=75456.39/min [630000], rate=74703.56/min [640000], rate=73988.44/min [650000], rate=73308.27/min [660000], rate=73333.33/min [670000], rate=73090.91/min [680000], rate=72857.14/min [690000], rate=72759.23/min [700000], rate=72790.29/min [710000], rate=73070.33/min [720000], rate=73344.65/min [730000], rate=72878.54/min [740000], rate=72430.67/min [750000], rate=72115.38/min [760000], rate=71924.29/min -building interval tree based on /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=75000.00/min [30000], rate=75000.00/min [40000], rate=80000.00/min [50000], rate=85714.29/min [60000], rate=92307.69/min [70000], rate=97674.42/min [80000], rate=102127.66/min [90000], rate=100000.00/min [100000], rate=93750.00/min [110000], rate=95652.17/min [120000], rate=96000.00/min [130000], rate=98734.18/min [140000], rate=102439.02/min [150000], rate=104651.16/min [160000], rate=107865.17/min [170000], rate=108510.64/min [180000], rate=108000.00/min [190000], rate=107547.17/min [200000], rate=110091.74/min [210000], rate=112500.00/min [220000], rate=112820.51/min [230000], rate=114049.59/min [240000], rate=114285.71/min [250000], rate=112781.95/min [260000], rate=113043.48/min [270000], rate=113286.71/min [280000], rate=114285.71/min [290000], rate=116000.00/min [300000], rate=114649.68/min [310000], rate=103910.61/min [320000], rate=96482.41/min [330000], rate=90410.96/min [340000], rate=85714.29/min [350000], rate=81081.08/min [360000], rate=77978.34/min [370000], rate=75000.00/min [380000], rate=72611.46/min [390000], rate=70909.09/min [400000], rate=69164.27/min [410000], rate=67768.60/min [420000], rate=66490.77/min [430000], rate=65316.46/min [440000], rate=64547.68/min [450000], rate=63981.04/min [460000], rate=63741.34/min [470000], rate=63656.88/min [480000], rate=63716.81/min [490000], rate=64052.29/min [500000], rate=64377.68/min [510000], rate=64693.45/min [520000], rate=64329.90/min [530000], rate=64372.47/min [540000], rate=64285.71/min [550000], rate=64202.33/min [560000], rate=64244.74/min [570000], rate=64406.78/min [580000], rate=64564.01/min [590000], rate=64835.16/min [600000], rate=65217.39/min [610000], rate=64664.31/min [620000], rate=64137.93/min [630000], rate=63743.68/min [640000], rate=63366.34/min [650000], rate=63106.80/min [660000], rate=62957.07/min [670000], rate=62714.51/min [680000], rate=62672.81/min [690000], rate=62727.27/min [700000], rate=62780.27/min [710000], rate=63017.75/min [720000], rate=63343.11/min [730000], rate=63021.58/min [740000], rate=62623.41/min [750000], rate=62326.87/min -building interval tree based on /tmp/nxf.laFn224CnS/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=52173.91/min [30000], rate=52941.18/min [40000], rate=54545.45/min [50000], rate=57692.31/min [60000], rate=60000.00/min [70000], rate=62686.57/min [80000], rate=66666.67/min [90000], rate=70129.87/min [100000], rate=69767.44/min [110000], rate=70967.74/min [120000], rate=72727.27/min [130000], rate=70909.09/min [140000], rate=69421.49/min [150000], rate=68181.82/min [160000], rate=68085.11/min [170000], rate=68456.38/min [180000], rate=69677.42/min [190000], rate=70370.37/min [200000], rate=68965.52/min [210000], rate=68478.26/min [220000], rate=68041.24/min [230000], rate=68316.83/min [240000], rate=69565.22/min [250000], rate=70422.54/min [260000], rate=68421.05/min [270000], rate=68354.43/min [280000], rate=67200.00/min [290000], rate=66412.21/min [300000], rate=65934.07/min [310000], rate=65263.16/min [320000], rate=64429.53/min [330000], rate=63665.59/min [340000], rate=63157.89/min [350000], rate=62500.00/min [360000], rate=62068.97/min [370000], rate=61495.84/min [380000], rate=61290.32/min [390000], rate=61256.54/min [400000], rate=61224.49/min [410000], rate=61042.18/min [420000], rate=61016.95/min [430000], rate=61428.57/min [440000], rate=61826.70/min [450000], rate=62068.97/min [460000], rate=61061.95/min [470000], rate=60645.16/min [480000], rate=60125.26/min [490000], rate=59514.17/min [500000], rate=59288.54/min [510000], rate=59073.36/min [520000], rate=58867.92/min [530000], rate=58888.89/min [540000], rate=58909.09/min [550000], rate=58823.53/min [560000], rate=58947.37/min [570000], rate=59169.55/min [580000], rate=59385.67/min [590000], rate=59898.48/min [600000], rate=60301.51/min [610000], rate=60596.03/min [620000], rate=61083.74/min [630000], rate=61463.41/min [640000], rate=61736.33/min [650000], rate=61806.66/min [660000], rate=61395.35/min [670000], rate=61094.22/min [680000], rate=60714.29/min [690000], rate=60614.93/min [700000], rate=60344.83/min [710000], rate=60169.49/min [720000], rate=60083.45/min [730000], rate=60000.00/min [740000], rate=60162.60/min [750000], rate=60321.72/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir --filt_file /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 12000000.00 reads per min processed... 6000000.00 reads per min processed... 4800000.00 reads per min processed... 4285714.29 reads per min processed... 4500000.00 reads per min processed... 4200000.00 reads per min processed... 4363636.36 reads per min processed... 4153846.15 reads per min processed... 3750000.00 reads per min processed... 3666666.67 reads per min processed... 3789473.68 reads per min processed... 3714285.71 reads per min processed... 3652173.91 reads per min processed... 3600000.00 reads per min processed... 3692307.69 reads per min processed... 3923076.92 reads per min processed... 4000000.00 reads per min processed... 3931034.48 reads per min processed... 4000000.00 reads per min processed... 3937500.00 reads per min processed... 3882352.94 reads per min processed... 3942857.14 reads per min processed... 3789473.68 reads per min processed... 3846153.85 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.laFn224CnS/aih-tih-sc-fba77b-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.laFn224CnS/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -81624.851373 EM: Round [1] log likelihood: -81550.551294 EM: Round [2] log likelihood: -81518.760833 EM: Round [3] log likelihood: -81502.107109 EM: Round [4] log likelihood: -81492.794146 EM: Round [5] log likelihood: -81487.450211 EM: Round [6] log likelihood: -81484.315972 EM: Round [7] log likelihood: -81482.428723 EM: Round [8] log likelihood: -81481.257402 EM: Round [9] log likelihood: -81480.507095 EM: Round [10] log likelihood: -81480.011582 EM: Round [11] log likelihood: -81479.675039 EM: Round [12] log likelihood: -81479.440691 EM: Round [13] log likelihood: -81479.273897 EM: Round [14] log likelihood: -81479.152889 EM: Round [15] log likelihood: -81479.063604 EM: Round [16] log likelihood: -81478.996724 EM: Round [17] log likelihood: -81478.945933 EM: Round [18] log likelihood: -81478.906866 EM: Round [19] log likelihood: -81478.876453 EM: Round [20] log likelihood: -81478.852502 EM: Round [21] log likelihood: -81478.833429 EM: Round [22] log likelihood: -81478.818074 EM: Round [23] log likelihood: -81478.805582 EM: Round [24] log likelihood: -81478.795312 EM: Round [25] log likelihood: -81478.786782 EM: Round [26] log likelihood: -81478.779628 EM: Round [27] log likelihood: -81478.773570 EM: Round [28] log likelihood: -81478.768392 EM: Round [29] log likelihood: -81478.763926 EM: Round [30] log likelihood: -81478.760041 EM: Round [31] log likelihood: -81478.756635 EM: Round [32] log likelihood: -81478.753624 EM: Round [33] log likelihood: -81478.750945 EM: Round [34] log likelihood: -81478.748543 EM: Round [35] log likelihood: -81478.746377 EM: Round [36] log likelihood: -81478.744411 EM: Round [37] log likelihood: -81478.742619 EM: Round [38] log likelihood: -81478.740975 EM: Round [39] log likelihood: -81478.739462 EM: Round [40] log likelihood: -81478.738062 EM: Round [41] log likelihood: -81478.736762 EM: Round [42] log likelihood: -81478.735552 EM: Round [43] log likelihood: -81478.734420 EM: Round [44] log likelihood: -81478.733360 EM: Round [45] log likelihood: -81478.732363 EM: Round [46] log likelihood: -81478.731424 EM: Round [47] log likelihood: -81478.730538 EM: Round [48] log likelihood: -81478.729699 EM: Round [49] log likelihood: -81478.728905 EM: Round [50] log likelihood: -81478.728151 EM: Round [51] log likelihood: -81478.727434 EM: Round [52] log likelihood: -81478.726752 EM: Round [53] log likelihood: -81478.726103 EM: Round [54] log likelihood: -81478.725483 EM: Round [55] log likelihood: -81478.724891 EM: Round [56] log likelihood: -81478.724325 EM: Round [57] log likelihood: -81478.723784 EM: Round [58] log likelihood: -81478.723266 EM: Round [59] log likelihood: -81478.722771 EM: Round [60] log likelihood: -81478.722295 EM: Round [61] log likelihood: -81478.721839 EM: Round [62] log likelihood: -81478.721402 EM: Round [63] log likelihood: -81478.720983 EM: Round [64] log likelihood: -81478.720580 EM: Round [65] log likelihood: -81478.720192 EM: Round [66] log likelihood: -81478.719820 EM: Round [67] log likelihood: -81478.719463 EM: Round [68] log likelihood: -81478.719119 EM: Round [69] log likelihood: -81478.718788 EM: Round [70] log likelihood: -81478.718470 EM: Round [71] log likelihood: -81478.718163 EM: Round [72] log likelihood: -81478.717869 EM: Round [73] log likelihood: -81478.717585 EM: Round [74] log likelihood: -81478.717311 EM: Round [75] log likelihood: -81478.717048 EM: Round [76] log likelihood: -81478.716795 EM: Round [77] log likelihood: -81478.716550 EM: Round [78] log likelihood: -81478.716315 EM: Round [79] log likelihood: -81478.716088 EM: Round [80] log likelihood: -81478.715869 EM: Round [81] log likelihood: -81478.715658 EM: Round [82] log likelihood: -81478.715455 EM: Round [83] log likelihood: -81478.715259 EM: Round [84] log likelihood: -81478.715070 EM: Round [85] log likelihood: -81478.714888 EM: Round [86] log likelihood: -81478.714712 EM: Round [87] log likelihood: -81478.714542 EM: Round [88] log likelihood: -81478.714379 EM: Round [89] log likelihood: -81478.714221 EM: Round [90] log likelihood: -81478.714068 EM: Round [91] log likelihood: -81478.713921 EM: Round [92] log likelihood: -81478.713779 EM: Round [93] log likelihood: -81478.713643 EM: Round [94] log likelihood: -81478.713510 EM: Round [95] log likelihood: -81478.713383 EM: Round [96] log likelihood: -81478.713260 EM: Round [97] log likelihood: -81478.713141 EM: Round [98] log likelihood: -81478.713026 EM: Round [99] log likelihood: -81478.712915 EM: Round [100] log likelihood: -81478.712808 EM: Round [101] log likelihood: -81478.712705 EM: Round [102] log likelihood: -81478.712605 EM: Stopping iterations at round 102 due to insufficient improvement in likelihood. EM: Starting log likelihood: -81599.261538 EM: Round [1] log likelihood: -81535.554597 EM: Round [2] log likelihood: -81509.845897 EM: Round [3] log likelihood: -81496.830430 EM: Round [4] log likelihood: -81489.661466 EM: Round [5] log likelihood: -81485.560227 EM: Round [6] log likelihood: -81483.146491 EM: Round [7] log likelihood: -81481.683688 EM: Round [8] log likelihood: -81480.768748 EM: Round [9] log likelihood: -81480.177756 EM: Round [10] log likelihood: -81479.784047 EM: Round [11] log likelihood: -81479.514245 EM: Round [12] log likelihood: -81479.324643 EM: Round [13] log likelihood: -81479.188429 EM: Round [14] log likelihood: -81479.088663 EM: Round [15] log likelihood: -81479.014340 EM: Round [16] log likelihood: -81478.958125 EM: Round [17] log likelihood: -81478.915021 EM: Round [18] log likelihood: -81478.881548 EM: Round [19] log likelihood: -81478.855247 EM: Round [20] log likelihood: -81478.834350 EM: Round [21] log likelihood: -81478.817570 EM: Round [22] log likelihood: -81478.803956 EM: Round [23] log likelihood: -81478.792802 EM: Round [24] log likelihood: -81478.783577 EM: Round [25] log likelihood: -81478.775877 EM: Round [26] log likelihood: -81478.769392 EM: Round [27] log likelihood: -81478.763884 EM: Round [28] log likelihood: -81478.759167 EM: Round [29] log likelihood: -81478.755095 EM: Round [30] log likelihood: -81478.751554 EM: Round [31] log likelihood: -81478.748453 EM: Round [32] log likelihood: -81478.745717 EM: Round [33] log likelihood: -81478.743289 EM: Round [34] log likelihood: -81478.741120 EM: Round [35] log likelihood: -81478.739173 EM: Round [36] log likelihood: -81478.737414 EM: Round [37] log likelihood: -81478.735818 EM: Round [38] log likelihood: -81478.734363 EM: Round [39] log likelihood: -81478.733031 EM: Round [40] log likelihood: -81478.731806 EM: Round [41] log likelihood: -81478.730676 EM: Round [42] log likelihood: -81478.729630 EM: Round [43] log likelihood: -81478.728658 EM: Round [44] log likelihood: -81478.727753 EM: Round [45] log likelihood: -81478.726908 EM: Round [46] log likelihood: -81478.726117 EM: Round [47] log likelihood: -81478.725375 EM: Round [48] log likelihood: -81478.724677 EM: Round [49] log likelihood: -81478.724020 EM: Round [50] log likelihood: -81478.723400 EM: Round [51] log likelihood: -81478.722815 EM: Round [52] log likelihood: -81478.722260 EM: Round [53] log likelihood: -81478.721735 EM: Round [54] log likelihood: -81478.721237 EM: Round [55] log likelihood: -81478.720764 EM: Round [56] log likelihood: -81478.720314 EM: Round [57] log likelihood: -81478.719886 EM: Round [58] log likelihood: -81478.719479 EM: Round [59] log likelihood: -81478.719090 EM: Round [60] log likelihood: -81478.718720 EM: Round [61] log likelihood: -81478.718366 EM: Round [62] log likelihood: -81478.718029 EM: Round [63] log likelihood: -81478.717706 EM: Round [64] log likelihood: -81478.717398 EM: Round [65] log likelihood: -81478.717103 EM: Round [66] log likelihood: -81478.716820 EM: Round [67] log likelihood: -81478.716550 EM: Round [68] log likelihood: -81478.716291 EM: Round [69] log likelihood: -81478.716044 EM: Round [70] log likelihood: -81478.715806 EM: Round [71] log likelihood: -81478.715578 EM: Round [72] log likelihood: -81478.715360 EM: Round [73] log likelihood: -81478.715150 EM: Round [74] log likelihood: -81478.714949 EM: Round [75] log likelihood: -81478.714757 EM: Round [76] log likelihood: -81478.714571 EM: Round [77] log likelihood: -81478.714394 EM: Round [78] log likelihood: -81478.714223 EM: Round [79] log likelihood: -81478.714059 EM: Round [80] log likelihood: -81478.713901 EM: Round [81] log likelihood: -81478.713750 EM: Round [82] log likelihood: -81478.713604 EM: Round [83] log likelihood: -81478.713464 EM: Round [84] log likelihood: -81478.713330 EM: Round [85] log likelihood: -81478.713201 EM: Round [86] log likelihood: -81478.713076 EM: Round [87] log likelihood: -81478.712957 EM: Round [88] log likelihood: -81478.712841 EM: Round [89] log likelihood: -81478.712731 EM: Round [90] log likelihood: -81478.712624 EM: Round [91] log likelihood: -81478.712521 EM: Round [92] log likelihood: -81478.712423 EM: Stopping iterations at round 92 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.laFn224CnS/./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.laFn224CnS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.laFn224CnS/./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.laFn224CnS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 52859459 > /tmp/nxf.laFn224CnS/./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.laFn224CnS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir > /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir --annotate /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.laFn224CnS/./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.laFn224CnS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir -done, see /tmp/nxf.laFn224CnS/./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.laFn224CnS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.laFn224CnS/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 552, filtered: 5806) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.laFn224CnS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.laFn224CnS/./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.laFn224CnS/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 [ENSG00000229930.1] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000224078.15] WARNING, no entry stored in dbm for [ENSG00000124097.7] WARNING, no entry stored in dbm for [ENSG00000259203.2] WARNING, no entry stored in dbm for [ENSG00000224310.1] WARNING, no entry stored in dbm for [ENSG00000264985.4] WARNING, no entry stored in dbm for [ENSG00000236229.1] WARNING, no entry stored in dbm for [ENSG00000278969.1] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000225096.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000272933.1] WARNING, no entry stored in dbm for [ENSG00000261499.2] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000279713.1] WARNING, no entry stored in dbm for [ENSG00000239791.2] WARNING, no entry stored in dbm for [ENSG00000269540.1] WARNING, no entry stored in dbm for [ENSG00000253559.1] WARNING, no entry stored in dbm for [ENSG00000282458.1] WARNING, no entry stored in dbm for [ENSG00000214892.4] WARNING, no entry stored in dbm for [ENSG00000207113.1] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000247556.6] WARNING, no entry stored in dbm for [ENSG00000261713.6] WARNING, no entry stored in dbm for [ENSG00000248791.1] WARNING, no entry stored in dbm for [ENSG00000239268.3] WARNING, no entry stored in dbm for [ENSG00000287356.1] WARNING, no entry stored in dbm for [ENSG00000224081.9] WARNING, no entry stored in dbm for [ENSG00000244265.2] WARNING, no entry stored in dbm for [ENSG00000243273.1] WARNING, no entry stored in dbm for [ENSG00000251532.1] WARNING, no entry stored in dbm for [ENSG00000253618.1] WARNING, no entry stored in dbm for [ENSG00000250284.3] WARNING, no entry stored in dbm for [ENSG00000224897.8] WARNING, no entry stored in dbm for [ENSG00000272995.1] WARNING, no entry stored in dbm for [ENSG00000176054.6] WARNING, no entry stored in dbm for [ENSG00000232383.1] WARNING, no entry stored in dbm for [ENSG00000283095.1] WARNING, no entry stored in dbm for [ENSG00000265735.2] WARNING, no entry stored in dbm for [ENSG00000278771.1] WARNING, no entry stored in dbm for [ENSG00000206944.1] WARNING, no entry stored in dbm for [ENSG00000261233.2] WARNING, no entry stored in dbm for [ENSG00000277270.2] WARNING, no entry stored in dbm for [ENSG00000233290.3] WARNING, no entry stored in dbm for [ENSG00000256116.1] WARNING, no entry stored in dbm for [ENSG00000224870.7] WARNING, no entry stored in dbm for [ENSG00000237782.3] WARNING, no entry stored in dbm for [ENSG00000189223.15] WARNING, no entry stored in dbm for [ENSG00000241562.2] WARNING, no entry stored in dbm for [ENSG00000258592.1] WARNING, no entry stored in dbm for [ENSG00000259411.1] WARNING, no entry stored in dbm for [ENSG00000232729.8] WARNING, no entry stored in dbm for [ENSG00000245532.9] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000249464.6] WARNING, no entry stored in dbm for [ENSG00000226337.3] WARNING, no entry stored in dbm for [ENSG00000237298.10] WARNING, no entry stored in dbm for [ENSG00000226313.1] WARNING, no entry stored in dbm for [ENSG00000162840.4] WARNING, no entry stored in dbm for [ENSG00000275691.2] WARNING, no entry stored in dbm for [ENSG00000254055.2] WARNING, no entry stored in dbm for [ENSG00000205534.6] WARNING, no entry stored in dbm for [ENSG00000229619.4] WARNING, no entry stored in dbm for [ENSG00000273356.1] WARNING, no entry stored in dbm for [ENSG00000248323.7] WARNING, no entry stored in dbm for [ENSG00000229539.1] WARNING, no entry stored in dbm for [ENSG00000232164.1] WARNING, no entry stored in dbm for [ENSG00000255050.1] 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 [ENSG00000275852.1] WARNING, no entry stored in dbm for [ENSG00000224559.2] WARNING, no entry stored in dbm for [ENSG00000232471.3] WARNING, no entry stored in dbm for [ENSG00000282508.2] WARNING, no entry stored in dbm for [ENSG00000282508.2] WARNING, no entry stored in dbm for [ENSG00000224316.1] WARNING, no entry stored in dbm for [ENSG00000249669.10] WARNING, no entry stored in dbm for [ENSG00000233446.2] WARNING, no entry stored in dbm for [ENSG00000217159.2] WARNING, no entry stored in dbm for [ENSG00000233930.4] WARNING, no entry stored in dbm for [ENSG00000286948.1] WARNING, no entry stored in dbm for [ENSG00000186082.9] WARNING, no entry stored in dbm for [ENSG00000230426.4] WARNING, no entry stored in dbm for [ENSG00000278212.2] WARNING, no entry stored in dbm for [ENSG00000270903.1] WARNING, no entry stored in dbm for [ENSG00000281344.1] WARNING, no entry stored in dbm for [ENSG00000281344.1] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000241549.8] WARNING, no entry stored in dbm for [ENSG00000183666.17] WARNING, no entry stored in dbm for [ENSG00000231013.2] WARNING, no entry stored in dbm for [ENSG00000250427.1] WARNING, no entry stored in dbm for [ENSG00000196295.12] WARNING, no entry stored in dbm for [ENSG00000257252.6] WARNING, no entry stored in dbm for [ENSG00000236991.6] WARNING, no entry stored in dbm for [ENSG00000248539.1] WARNING, no entry stored in dbm for [ENSG00000287597.1] WARNING, no entry stored in dbm for [ENSG00000231793.5] WARNING, no entry stored in dbm for [ENSG00000235123.5] WARNING, no entry stored in dbm for [ENSG00000266733.7] WARNING, no entry stored in dbm for [ENSG00000241743.4] WARNING, no entry stored in dbm for [ENSG00000233025.1] WARNING, no entry stored in dbm for [ENSG00000223959.8] WARNING, no entry stored in dbm for [ENSG00000251623.2] WARNING, no entry stored in dbm for [ENSG00000232229.6] WARNING, no entry stored in dbm for [ENSG00000244161.1] WARNING, no entry stored in dbm for [ENSG00000259217.2] WARNING, no entry stored in dbm for [ENSG00000251842.1] WARNING, no entry stored in dbm for [ENSG00000201852.1] WARNING, no entry stored in dbm for [ENSG00000184224.3] WARNING, no entry stored in dbm for [ENSG00000283662.1] WARNING, no entry stored in dbm for [ENSG00000283326.1] WARNING, no entry stored in dbm for [ENSG00000278428.1] WARNING, no entry stored in dbm for [ENSG00000205634.7] WARNING, no entry stored in dbm for [ENSG00000231028.9] WARNING, no entry stored in dbm for [ENSG00000244723.3] WARNING, no entry stored in dbm for [ENSG00000206066.3] WARNING, no entry stored in dbm for [ENSG00000255108.1] WARNING, no entry stored in dbm for [ENSG00000279147.1] WARNING, no entry stored in dbm for [ENSG00000232512.6] WARNING, no entry stored in dbm for [ENSG00000200131.1] WARNING, no entry stored in dbm for [ENSG00000226476.6] WARNING, no entry stored in dbm for [ENSG00000226476.6] WARNING, no entry stored in dbm for [ENSG00000226476.6] WARNING, no entry stored in dbm for [ENSG00000228044.3] WARNING, no entry stored in dbm for [ENSG00000232576.2] WARNING, no entry stored in dbm for [ENSG00000235020.5] WARNING, no entry stored in dbm for [ENSG00000279609.1] WARNING, no entry stored in dbm for [ENSG00000236777.1] WARNING, no entry stored in dbm for [ENSG00000279032.1] WARNING, no entry stored in dbm for [ENSG00000228274.4] WARNING, no entry stored in dbm for [ENSG00000272734.1] WARNING, no entry stored in dbm for [ENSG00000245532.9] WARNING, no entry stored in dbm for [ENSG00000264112.1] WARNING, no entry stored in dbm for [ENSG00000230576.1] WARNING, no entry stored in dbm for [ENSG00000277125.1] WARNING, no entry stored in dbm for [ENSG00000215158.9] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000280828.1] WARNING, no entry stored in dbm for [ENSG00000286279.1] WARNING, no entry stored in dbm for [ENSG00000251314.2] WARNING, no entry stored in dbm for [ENSG00000282375.1] WARNING, no entry stored in dbm for [ENSG00000287431.1] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000285569.2] WARNING, no entry stored in dbm for [ENSG00000259848.9] WARNING, no entry stored in dbm for [ENSG00000235027.1] WARNING, no entry stored in dbm for [ENSG00000229212.8] WARNING, no entry stored in dbm for [ENSG00000287677.2] WARNING, no entry stored in dbm for [ENSG00000215263.2] WARNING, no entry stored in dbm for [ENSG00000240674.1] WARNING, no entry stored in dbm for [ENSG00000259603.1] WARNING, no entry stored in dbm for [ENSG00000258017.2] WARNING, no entry stored in dbm for [ENSG00000282051.1] WARNING, no entry stored in dbm for [ENSG00000268120.1] WARNING, no entry stored in dbm for [ENSG00000287859.1] WARNING, no entry stored in dbm for [ENSG00000244161.1] WARNING, no entry stored in dbm for [ENSG00000286125.1] WARNING, no entry stored in dbm for [ENSG00000274712.2] WARNING, no entry stored in dbm for [ENSG00000274712.2] WARNING, no entry stored in dbm for [ENSG00000264067.1] WARNING, no entry stored in dbm for [ENSG00000214970.8] * STAR-Fusion complete. See output: /tmp/nxf.laFn224CnS/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)