-ctat genome lib [/tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.MiLITKzNY1/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary -sample contains 118711267 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir -J /tmp/nxf.MiLITKzNY1/dna_s769.Chimeric.out.junction -O /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.MiLITKzNY1/dna_s769.Chimeric.out.junction -building interval tree based on /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=40000.00/min [20000], rate=42857.14/min [30000], rate=42857.14/min [40000], rate=44444.44/min [50000], rate=46875.00/min [60000], rate=49315.07/min [70000], rate=51219.51/min [80000], rate=53333.33/min [90000], rate=53465.35/min [100000], rate=54054.05/min [110000], rate=55000.00/min [120000], rate=55384.62/min [130000], rate=56115.11/min [140000], rate=56756.76/min [150000], rate=60000.00/min [160000], rate=63157.89/min [170000], rate=64556.96/min [180000], rate=64670.66/min [190000], rate=64772.73/min [200000], rate=65217.39/min [210000], rate=64948.45/min [220000], rate=64705.88/min [230000], rate=64788.73/min [240000], rate=64573.99/min [250000], rate=64655.17/min [260000], rate=65000.00/min [270000], rate=63779.53/min [280000], rate=62453.53/min [290000], rate=61052.63/min [300000], rate=60000.00/min [310000], rate=59047.62/min [320000], rate=58358.66/min [330000], rate=57894.74/min [340000], rate=57627.12/min [350000], rate=57220.71/min [360000], rate=56992.08/min [370000], rate=56923.08/min [380000], rate=57000.00/min [390000], rate=57212.71/min [400000], rate=57553.96/min [410000], rate=57882.35/min [420000], rate=58064.52/min [430000], rate=57589.29/min [440000], rate=57142.86/min [450000], rate=56722.69/min [460000], rate=56441.72/min [470000], rate=56287.43/min [480000], rate=56140.35/min [490000], rate=56000.00/min [500000], rate=55865.92/min [510000], rate=55839.42/min [520000], rate=55913.98/min [530000], rate=55985.92/min [540000], rate=56250.00/min [550000], rate=56410.26/min [560000], rate=56470.59/min [570000], rate=56065.57/min [580000], rate=55769.23/min [590000], rate=55573.00/min [600000], rate=55130.17/min [610000], rate=54872.56/min [620000], rate=54786.45/min [630000], rate=54624.28/min [640000], rate=54623.04/min [650000], rate=54698.46/min [660000], rate=54923.72/min [670000], rate=54993.16/min -building interval tree based on /tmp/nxf.MiLITKzNY1/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=66666.67/min [30000], rate=52941.18/min [40000], rate=48000.00/min [50000], rate=47619.05/min [60000], rate=48000.00/min [70000], rate=48837.21/min [80000], rate=50000.00/min [90000], rate=50943.40/min [100000], rate=51282.05/min [110000], rate=52380.95/min [120000], rate=52941.18/min [130000], rate=53793.10/min [140000], rate=54901.96/min [150000], rate=55555.56/min [160000], rate=54237.29/min [170000], rate=53125.00/min [180000], rate=52173.91/min [190000], rate=51818.18/min [200000], rate=51502.15/min [210000], rate=51428.57/min [220000], rate=51562.50/min [230000], rate=51492.54/min [240000], rate=51612.90/min [250000], rate=51903.11/min [260000], rate=52348.99/min [270000], rate=52597.40/min [280000], rate=53164.56/min [290000], rate=53703.70/min [300000], rate=53254.44/min [310000], rate=52840.91/min [320000], rate=52459.02/min [330000], rate=52380.95/min [340000], rate=52307.69/min [350000], rate=52238.81/min [360000], rate=52300.24/min [370000], rate=52235.29/min [380000], rate=52413.79/min [390000], rate=52702.70/min [400000], rate=53215.08/min [410000], rate=53478.26/min [420000], rate=53164.56/min [430000], rate=53086.42/min [440000], rate=53012.05/min [450000], rate=53045.19/min [460000], rate=53076.92/min [470000], rate=53107.34/min [480000], rate=53136.53/min [490000], rate=53164.56/min [500000], rate=53191.49/min [510000], rate=53310.10/min [520000], rate=53516.30/min [530000], rate=53807.11/min [540000], rate=53731.34/min [550000], rate=53658.54/min [560000], rate=53503.18/min [570000], rate=53521.13/min [580000], rate=53538.46/min [590000], rate=53555.22/min [600000], rate=53571.43/min [610000], rate=53665.69/min [620000], rate=53757.23/min [630000], rate=53922.97/min [640000], rate=54084.51/min [650000], rate=54393.31/min [660000], rate=54545.45/min [670000], rate=54843.11/min -building interval tree based on /tmp/nxf.MiLITKzNY1/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=63157.89/min [30000], rate=51428.57/min [40000], rate=48979.59/min [50000], rate=49180.33/min [60000], rate=50000.00/min [70000], rate=51851.85/min [80000], rate=53333.33/min [90000], rate=54545.45/min [100000], rate=54054.05/min [110000], rate=53225.81/min [120000], rate=52554.74/min [130000], rate=52348.99/min [140000], rate=52500.00/min [150000], rate=52941.18/min [160000], rate=53932.58/min [170000], rate=55135.14/min [180000], rate=55670.10/min [190000], rate=56716.42/min [200000], rate=55555.56/min [210000], rate=55263.16/min [220000], rate=55000.00/min [230000], rate=54545.45/min [240000], rate=54545.45/min [250000], rate=54945.05/min [260000], rate=55123.67/min [270000], rate=55290.10/min [280000], rate=55813.95/min [290000], rate=56310.68/min [300000], rate=55555.56/min [310000], rate=54867.26/min [320000], rate=54237.29/min [330000], rate=53950.95/min [340000], rate=53543.31/min [350000], rate=53164.56/min [360000], rate=53071.25/min [370000], rate=52983.29/min [380000], rate=53023.26/min [390000], rate=53061.22/min [400000], rate=53215.08/min [410000], rate=53362.26/min [420000], rate=53617.02/min [430000], rate=54088.05/min [440000], rate=54320.99/min [450000], rate=54766.73/min [460000], rate=55089.82/min [470000], rate=54757.28/min [480000], rate=54237.29/min [490000], rate=53747.71/min [500000], rate=53475.94/min [510000], rate=53310.10/min [520000], rate=53061.22/min [530000], rate=53088.48/min [540000], rate=53201.97/min [550000], rate=53398.06/min [560000], rate=53418.12/min [570000], rate=52941.18/min [580000], rate=52488.69/min [590000], rate=52058.82/min [600000], rate=51724.14/min [610000], rate=51404.49/min [620000], rate=51169.19/min [630000], rate=51150.20/min [640000], rate=50928.38/min [650000], rate=50781.25/min [660000], rate=50769.23/min [670000], rate=50821.74/min -building interval tree based on /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=200000.00/min [20000], rate=133333.33/min [30000], rate=100000.00/min [40000], rate=114285.71/min [50000], rate=115384.62/min [60000], rate=78260.87/min [70000], rate=62686.57/min [80000], rate=55172.41/min [90000], rate=50943.40/min [100000], rate=47619.05/min [110000], rate=45517.24/min [120000], rate=44171.78/min [130000], rate=43093.92/min [140000], rate=42857.14/min [150000], rate=42452.83/min [160000], rate=42477.88/min [170000], rate=42677.82/min [180000], rate=42687.75/min [190000], rate=42857.14/min [200000], rate=43321.30/min [210000], rate=43298.97/min [220000], rate=43708.61/min [230000], rate=43949.04/min [240000], rate=44307.69/min [250000], rate=44642.86/min [260000], rate=45086.71/min [270000], rate=45633.80/min [280000], rate=46153.85/min [290000], rate=46648.79/min [300000], rate=46632.12/min [310000], rate=46733.67/min [320000], rate=46829.27/min [330000], rate=46919.43/min [340000], rate=47113.16/min [350000], rate=47297.30/min [360000], rate=47472.53/min [370000], rate=47741.94/min [380000], rate=48101.27/min [390000], rate=48750.00/min [400000], rate=48681.54/min [410000], rate=48330.06/min [420000], rate=48000.00/min [430000], rate=47866.42/min [440000], rate=47739.60/min [450000], rate=47619.05/min [460000], rate=47668.39/min [470000], rate=47796.61/min [480000], rate=47920.13/min [490000], rate=48117.84/min [500000], rate=48387.10/min [510000], rate=48571.43/min [520000], rate=48073.96/min [530000], rate=47819.55/min [540000], rate=47647.06/min [550000], rate=47482.01/min [560000], rate=47390.69/min [570000], rate=47302.90/min [580000], rate=47346.94/min [590000], rate=47389.56/min [600000], rate=47556.14/min [610000], rate=47718.38/min [620000], rate=47938.14/min [630000], rate=48214.29/min [640000], rate=48362.72/min [650000], rate=48567.87/min [660000], rate=48768.47/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir --filt_file /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 6000000.00 reads per min processed... 4500000.00 reads per min processed... 4800000.00 reads per min processed... 5000000.00 reads per min processed... 4500000.00 reads per min processed... 4666666.67 reads per min processed... 4800000.00 reads per min processed... 4500000.00 reads per min processed... 4615384.62 reads per min processed... 4400000.00 reads per min processed... 4500000.00 reads per min processed... 4588235.29 reads per min processed... 4666666.67 reads per min processed... 4736842.11 reads per min processed... 4571428.57 reads per min processed... 4636363.64 reads per min processed... 4695652.17 reads per min processed... 4560000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.MiLITKzNY1/dna_s769.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.MiLITKzNY1/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -167812.974637 EM: Round [1] log likelihood: -167707.624153 EM: Round [2] log likelihood: -167673.628140 EM: Round [3] log likelihood: -167658.772093 EM: Round [4] log likelihood: -167651.005698 EM: Round [5] log likelihood: -167646.507331 EM: Round [6] log likelihood: -167643.738398 EM: Round [7] log likelihood: -167641.963804 EM: Round [8] log likelihood: -167640.790784 EM: Round [9] log likelihood: -167639.994783 EM: Round [10] log likelihood: -167639.441828 EM: Round [11] log likelihood: -167639.049479 EM: Round [12] log likelihood: -167638.765678 EM: Round [13] log likelihood: -167638.556782 EM: Round [14] log likelihood: -167638.400571 EM: Round [15] log likelihood: -167638.282076 EM: Round [16] log likelihood: -167638.191016 EM: Round [17] log likelihood: -167638.120210 EM: Round [18] log likelihood: -167638.064558 EM: Round [19] log likelihood: -167638.020386 EM: Round [20] log likelihood: -167637.985006 EM: Round [21] log likelihood: -167637.956432 EM: Round [22] log likelihood: -167637.933176 EM: Round [23] log likelihood: -167637.914110 EM: Round [24] log likelihood: -167637.898373 EM: Round [25] log likelihood: -167637.885302 EM: Round [26] log likelihood: -167637.874378 EM: Round [27] log likelihood: -167637.865196 EM: Round [28] log likelihood: -167637.857436 EM: Round [29] log likelihood: -167637.850842 EM: Round [30] log likelihood: -167637.845211 EM: Round [31] log likelihood: -167637.840378 EM: Round [32] log likelihood: -167637.836210 EM: Round [33] log likelihood: -167637.832598 EM: Round [34] log likelihood: -167637.829455 EM: Round [35] log likelihood: -167637.826707 EM: Round [36] log likelihood: -167637.824293 EM: Round [37] log likelihood: -167637.822166 EM: Round [38] log likelihood: -167637.820281 EM: Round [39] log likelihood: -167637.818607 EM: Round [40] log likelihood: -167637.817112 EM: Round [41] log likelihood: -167637.815773 EM: Round [42] log likelihood: -167637.814569 EM: Round [43] log likelihood: -167637.813483 EM: Round [44] log likelihood: -167637.812500 EM: Round [45] log likelihood: -167637.811607 EM: Round [46] log likelihood: -167637.810793 EM: Round [47] log likelihood: -167637.810049 EM: Round [48] log likelihood: -167637.809367 EM: Round [49] log likelihood: -167637.808740 EM: Round [50] log likelihood: -167637.808162 EM: Round [51] log likelihood: -167637.807629 EM: Round [52] log likelihood: -167637.807134 EM: Round [53] log likelihood: -167637.806675 EM: Round [54] log likelihood: -167637.806247 EM: Round [55] log likelihood: -167637.805849 EM: Round [56] log likelihood: -167637.805477 EM: Round [57] log likelihood: -167637.805128 EM: Round [58] log likelihood: -167637.804801 EM: Round [59] log likelihood: -167637.804494 EM: Round [60] log likelihood: -167637.804206 EM: Round [61] log likelihood: -167637.803933 EM: Round [62] log likelihood: -167637.803676 EM: Round [63] log likelihood: -167637.803434 EM: Round [64] log likelihood: -167637.803204 EM: Round [65] log likelihood: -167637.802986 EM: Round [66] log likelihood: -167637.802780 EM: Round [67] log likelihood: -167637.802584 EM: Round [68] log likelihood: -167637.802397 EM: Round [69] log likelihood: -167637.802220 EM: Round [70] log likelihood: -167637.802051 EM: Round [71] log likelihood: -167637.801890 EM: Round [72] log likelihood: -167637.801736 EM: Round [73] log likelihood: -167637.801589 EM: Round [74] log likelihood: -167637.801449 EM: Round [75] log likelihood: -167637.801314 EM: Round [76] log likelihood: -167637.801186 EM: Round [77] log likelihood: -167637.801063 EM: Round [78] log likelihood: -167637.800945 EM: Round [79] log likelihood: -167637.800831 EM: Round [80] log likelihood: -167637.800723 EM: Round [81] log likelihood: -167637.800618 EM: Round [82] log likelihood: -167637.800518 EM: Round [83] log likelihood: -167637.800421 EM: Stopping iterations at round 83 due to insufficient improvement in likelihood. EM: Starting log likelihood: -167779.766569 EM: Round [1] log likelihood: -167678.885771 EM: Round [2] log likelihood: -167647.354711 EM: Round [3] log likelihood: -167634.062519 EM: Round [4] log likelihood: -167627.330867 EM: Round [5] log likelihood: -167623.527362 EM: Round [6] log likelihood: -167621.223634 EM: Round [7] log likelihood: -167619.758429 EM: Round [8] log likelihood: -167618.790876 EM: Round [9] log likelihood: -167618.131945 EM: Round [10] log likelihood: -167617.671173 EM: Round [11] log likelihood: -167617.341400 EM: Round [12] log likelihood: -167617.100473 EM: Round [13] log likelihood: -167616.921205 EM: Round [14] log likelihood: -167616.785628 EM: Round [15] log likelihood: -167616.681601 EM: Round [16] log likelihood: -167616.600746 EM: Round [17] log likelihood: -167616.537174 EM: Round [18] log likelihood: -167616.486673 EM: Round [19] log likelihood: -167616.446178 EM: Round [20] log likelihood: -167616.413432 EM: Round [21] log likelihood: -167616.386747 EM: Round [22] log likelihood: -167616.364845 EM: Round [23] log likelihood: -167616.346752 EM: Round [24] log likelihood: -167616.331712 EM: Round [25] log likelihood: -167616.319138 EM: Round [26] log likelihood: -167616.308567 EM: Round [27] log likelihood: -167616.299635 EM: Round [28] log likelihood: -167616.292049 EM: Round [29] log likelihood: -167616.285575 EM: Round [30] log likelihood: -167616.280024 EM: Round [31] log likelihood: -167616.275242 EM: Round [32] log likelihood: -167616.271105 EM: Round [33] log likelihood: -167616.267511 EM: Round [34] log likelihood: -167616.264374 EM: Round [35] log likelihood: -167616.261625 EM: Round [36] log likelihood: -167616.259206 EM: Round [37] log likelihood: -167616.257068 EM: Round [38] log likelihood: -167616.255173 EM: Round [39] log likelihood: -167616.253485 EM: Round [40] log likelihood: -167616.251977 EM: Round [41] log likelihood: -167616.250624 EM: Round [42] log likelihood: -167616.249406 EM: Round [43] log likelihood: -167616.248306 EM: Round [44] log likelihood: -167616.247309 EM: Round [45] log likelihood: -167616.246403 EM: Round [46] log likelihood: -167616.245577 EM: Round [47] log likelihood: -167616.244821 EM: Round [48] log likelihood: -167616.244127 EM: Round [49] log likelihood: -167616.243489 EM: Round [50] log likelihood: -167616.242901 EM: Round [51] log likelihood: -167616.242357 EM: Round [52] log likelihood: -167616.241853 EM: Round [53] log likelihood: -167616.241384 EM: Round [54] log likelihood: -167616.240949 EM: Round [55] log likelihood: -167616.240542 EM: Round [56] log likelihood: -167616.240162 EM: Round [57] log likelihood: -167616.239806 EM: Round [58] log likelihood: -167616.239472 EM: Round [59] log likelihood: -167616.239159 EM: Round [60] log likelihood: -167616.238864 EM: Round [61] log likelihood: -167616.238585 EM: Round [62] log likelihood: -167616.238323 EM: Round [63] log likelihood: -167616.238075 EM: Round [64] log likelihood: -167616.237840 EM: Round [65] log likelihood: -167616.237617 EM: Round [66] log likelihood: -167616.237406 EM: Round [67] log likelihood: -167616.237206 EM: Round [68] log likelihood: -167616.237015 EM: Round [69] log likelihood: -167616.236834 EM: Round [70] log likelihood: -167616.236661 EM: Round [71] log likelihood: -167616.236496 EM: Round [72] log likelihood: -167616.236339 EM: Round [73] log likelihood: -167616.236189 EM: Round [74] log likelihood: -167616.236046 EM: Round [75] log likelihood: -167616.235909 EM: Round [76] log likelihood: -167616.235777 EM: Round [77] log likelihood: -167616.235651 EM: Round [78] log likelihood: -167616.235531 EM: Round [79] log likelihood: -167616.235415 EM: Round [80] log likelihood: -167616.235304 EM: Round [81] log likelihood: -167616.235198 EM: Round [82] log likelihood: -167616.235095 EM: Round [83] log likelihood: -167616.234997 EM: Stopping iterations at round 83 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.MiLITKzNY1/./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.MiLITKzNY1/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.MiLITKzNY1/./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.MiLITKzNY1/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 118711267 > /tmp/nxf.MiLITKzNY1/./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.MiLITKzNY1/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir > /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir --annotate /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.MiLITKzNY1/./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.MiLITKzNY1/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir -done, see /tmp/nxf.MiLITKzNY1/./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.MiLITKzNY1/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.MiLITKzNY1/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 260, filtered: 12580) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.MiLITKzNY1/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.MiLITKzNY1/./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.MiLITKzNY1/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000286045.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000270788.1] WARNING, no entry stored in dbm for [ENSG00000249274.1] WARNING, no entry stored in dbm for [ENSG00000234106.3] WARNING, no entry stored in dbm for [ENSG00000277146.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000244932.2] WARNING, no entry stored in dbm for [ENSG00000223652.2] WARNING, no entry stored in dbm for [ENSG00000234405.2] WARNING, no entry stored in dbm for [ENSG00000213205.3] WARNING, no entry stored in dbm for [ENSG00000286353.1] WARNING, no entry stored in dbm for [ENSG00000203930.12] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000240710.1] WARNING, no entry stored in dbm for [ENSG00000285413.1] WARNING, no entry stored in dbm for [ENSG00000218890.1] WARNING, no entry stored in dbm for [ENSG00000228445.1] WARNING, no entry stored in dbm for [ENSG00000272770.1] WARNING, no entry stored in dbm for [ENSG00000255248.9] WARNING, no entry stored in dbm for [ENSG00000182165.18] WARNING, no entry stored in dbm for [ENSG00000223566.1] WARNING, no entry stored in dbm for [ENSG00000223566.1] WARNING, no entry stored in dbm for [ENSG00000254661.3] WARNING, no entry stored in dbm for [ENSG00000279696.1] WARNING, no entry stored in dbm for [ENSG00000278131.1] WARNING, no entry stored in dbm for [ENSG00000235927.4] WARNING, no entry stored in dbm for [ENSG00000206147.5] WARNING, no entry stored in dbm for [ENSG00000205433.4] WARNING, no entry stored in dbm for [ENSG00000213655.4] WARNING, no entry stored in dbm for [ENSG00000214121.4] WARNING, no entry stored in dbm for [ENSG00000235486.1] WARNING, no entry stored in dbm for [ENSG00000224086.6] WARNING, no entry stored in dbm for [ENSG00000224789.1] WARNING, no entry stored in dbm for [ENSG00000224977.1] WARNING, no entry stored in dbm for [ENSG00000234072.1] WARNING, no entry stored in dbm for [ENSG00000257480.1] WARNING, no entry stored in dbm for [ENSG00000238222.3] WARNING, no entry stored in dbm for [ENSG00000227533.6] WARNING, no entry stored in dbm for [ENSG00000222030.1] WARNING, no entry stored in dbm for [ENSG00000261824.7] WARNING, no entry stored in dbm for [ENSG00000206192.7] WARNING, no entry stored in dbm for [ENSG00000258011.2] WARNING, no entry stored in dbm for [ENSG00000259673.6] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000235032.1] WARNING, no entry stored in dbm for [ENSG00000287172.1] WARNING, no entry stored in dbm for [ENSG00000274827.4] WARNING, no entry stored in dbm for [ENSG00000229515.1] WARNING, no entry stored in dbm for [ENSG00000285230.2] WARNING, no entry stored in dbm for [ENSG00000259720.2] WARNING, no entry stored in dbm for [ENSG00000223912.1] WARNING, no entry stored in dbm for [ENSG00000206195.11] WARNING, no entry stored in dbm for [ENSG00000233221.7] WARNING, no entry stored in dbm for [ENSG00000260066.1] WARNING, no entry stored in dbm for [ENSG00000254661.3] WARNING, no entry stored in dbm for [ENSG00000271162.1] WARNING, no entry stored in dbm for [ENSG00000237480.3] WARNING, no entry stored in dbm for [ENSG00000254863.2] WARNING, no entry stored in dbm for [ENSG00000259719.6] WARNING, no entry stored in dbm for [ENSG00000279159.1] WARNING, no entry stored in dbm for [ENSG00000229106.1] WARNING, no entry stored in dbm for [ENSG00000197023.6] WARNING, no entry stored in dbm for [ENSG00000229106.1] WARNING, no entry stored in dbm for [ENSG00000250442.1] WARNING, no entry stored in dbm for [ENSG00000281357.3] WARNING, no entry stored in dbm for [ENSG00000282965.1] WARNING, no entry stored in dbm for [ENSG00000251297.1] WARNING, no entry stored in dbm for [ENSG00000241838.3] WARNING, no entry stored in dbm for [ENSG00000229473.2] WARNING, no entry stored in dbm for [ENSG00000243064.8] WARNING, no entry stored in dbm for [ENSG00000230908.2] WARNING, no entry stored in dbm for [ENSG00000226409.3] WARNING, no entry stored in dbm for [ENSG00000235314.1] WARNING, no entry stored in dbm for [ENSG00000285742.1] WARNING, no entry stored in dbm for [ENSG00000287266.1] WARNING, no entry stored in dbm for [ENSG00000286005.1] WARNING, no entry stored in dbm for [ENSG00000286196.1] WARNING, no entry stored in dbm for [ENSG00000233406.5] WARNING, no entry stored in dbm for [ENSG00000271573.1] WARNING, no entry stored in dbm for [ENSG00000286063.1] WARNING, no entry stored in dbm for [ENSG00000237686.7] WARNING, no entry stored in dbm for [ENSG00000271609.1] WARNING, no entry stored in dbm for [ENSG00000233029.3] WARNING, no entry stored in dbm for [ENSG00000213431.4] WARNING, no entry stored in dbm for [ENSG00000286876.1] WARNING, no entry stored in dbm for [ENSG00000271795.1] WARNING, no entry stored in dbm for [ENSG00000286271.2] WARNING, no entry stored in dbm for [ENSG00000257261.6] WARNING, no entry stored in dbm for [ENSG00000260249.3] WARNING, no entry stored in dbm for [ENSG00000285841.1] WARNING, no entry stored in dbm for [ENSG00000243004.6] WARNING, no entry stored in dbm for [ENSG00000237294.1] WARNING, no entry stored in dbm for [ENSG00000280054.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] * STAR-Fusion complete. See output: /tmp/nxf.MiLITKzNY1/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)