-ctat genome lib [/tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.DaP6ZeAZMZ/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary -sample contains 33031530 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir -J /tmp/nxf.DaP6ZeAZMZ/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Chimeric.out.junction -O /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.DaP6ZeAZMZ/aih-tih-sc-24ecfe-R1_A23YTGFLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=46153.85/min [20000], rate=50000.00/min [30000], rate=52941.18/min [40000], rate=55813.95/min [50000], rate=58823.53/min [60000], rate=55384.62/min [70000], rate=50000.00/min [80000], rate=47524.75/min [90000], rate=46153.85/min [100000], rate=46511.63/min [110000], rate=46153.85/min [120000], rate=46451.61/min [130000], rate=46706.59/min [140000], rate=47191.01/min [150000], rate=48913.04/min [160000], rate=49740.93/min [170000], rate=51000.00/min [180000], rate=52173.91/min [190000], rate=52534.56/min [200000], rate=53333.33/min [210000], rate=54077.25/min [220000], rate=55000.00/min [230000], rate=55645.16/min [240000], rate=57831.33/min [250000], rate=59055.12/min [260000], rate=59770.11/min [270000], rate=60447.76/min [280000], rate=60431.65/min [290000], rate=61484.10/min [300000], rate=61855.67/min [310000], rate=63265.31/min [320000], rate=64429.53/min [330000], rate=65131.58/min [340000], rate=65806.45/min [350000], rate=66878.98/min [360000], rate=66873.07/min [370000], rate=67477.20/min [380000], rate=68059.70/min [390000], rate=68621.70/min [400000], rate=69164.27/min [410000], rate=69295.77/min [420000], rate=69421.49/min [430000], rate=69168.90/min [440000], rate=69109.95/min [450000], rate=69230.77/min [460000], rate=69696.97/min [470000], rate=68780.49/min [480000], rate=68085.11/min [490000], rate=67276.89/min [500000], rate=67114.09/min [510000], rate=66666.67/min -building interval tree based on /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=80000.00/min [30000], rate=64285.71/min [40000], rate=60000.00/min [50000], rate=60000.00/min [60000], rate=62068.97/min [70000], rate=59154.93/min [80000], rate=56470.59/min [90000], rate=55670.10/min [100000], rate=57142.86/min [110000], rate=58407.08/min [120000], rate=59504.13/min [130000], rate=60000.00/min [140000], rate=58333.33/min [150000], rate=56603.77/min [160000], rate=55491.33/min [170000], rate=54838.71/min [180000], rate=54545.45/min [190000], rate=54807.69/min [200000], rate=55813.95/min [210000], rate=56502.24/min [220000], rate=55462.18/min [230000], rate=54330.71/min [240000], rate=53731.34/min [250000], rate=53380.78/min [260000], rate=53242.32/min [270000], rate=53289.47/min [280000], rate=53846.15/min [290000], rate=54545.45/min [300000], rate=54878.05/min [310000], rate=55357.14/min [320000], rate=55976.68/min [330000], rate=55774.65/min [340000], rate=55434.78/min [350000], rate=55408.97/min [360000], rate=55813.95/min [370000], rate=56632.65/min [380000], rate=57721.52/min [390000], rate=58064.52/min [400000], rate=58111.38/min [410000], rate=58293.84/min [420000], rate=58604.65/min [430000], rate=59310.34/min [440000], rate=60136.67/min [450000], rate=60538.12/min [460000], rate=60393.87/min [470000], rate=60127.93/min [480000], rate=60251.05/min [490000], rate=60618.56/min [500000], rate=61475.41/min [510000], rate=61818.18/min -building interval tree based on /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=85714.29/min [30000], rate=81818.18/min [40000], rate=82758.62/min [50000], rate=75000.00/min [60000], rate=70588.24/min [70000], rate=70000.00/min [80000], rate=71641.79/min [90000], rate=75000.00/min [100000], rate=78947.37/min [110000], rate=81481.48/min [120000], rate=85714.29/min [130000], rate=87640.45/min [140000], rate=91304.35/min [150000], rate=93750.00/min [160000], rate=92307.69/min [170000], rate=87179.49/min [180000], rate=84375.00/min [190000], rate=83823.53/min [200000], rate=82758.62/min [210000], rate=79245.28/min [220000], rate=76744.19/min [230000], rate=74193.55/min [240000], rate=72000.00/min [250000], rate=70754.72/min [260000], rate=70270.27/min [270000], rate=69527.90/min [280000], rate=68571.43/min [290000], rate=68235.29/min [300000], rate=68965.52/min [310000], rate=67883.21/min [320000], rate=65753.42/min [330000], rate=64285.71/min [340000], rate=63551.40/min [350000], rate=62686.57/min [360000], rate=61891.12/min [370000], rate=61157.02/min [380000], rate=60800.00/min [390000], rate=60154.24/min [400000], rate=59553.35/min [410000], rate=58851.67/min [420000], rate=58468.68/min [430000], rate=58503.40/min [440000], rate=58797.33/min [450000], rate=58951.97/min [460000], rate=59740.26/min [470000], rate=60000.00/min [480000], rate=59137.58/min [490000], rate=58102.77/min [500000], rate=57581.57/min [510000], rate=56983.24/min -building interval tree based on /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=100000.00/min [30000], rate=120000.00/min [40000], rate=126315.79/min [50000], rate=136363.64/min [60000], rate=133333.33/min [70000], rate=131250.00/min [80000], rate=137142.86/min [90000], rate=138461.54/min [100000], rate=146341.46/min [110000], rate=140425.53/min [120000], rate=141176.47/min [130000], rate=136842.11/min [140000], rate=140000.00/min [150000], rate=138461.54/min [160000], rate=133333.33/min [170000], rate=132467.53/min [180000], rate=133333.33/min [190000], rate=135714.29/min [200000], rate=134831.46/min [210000], rate=115596.33/min [220000], rate=99248.12/min [230000], rate=88461.54/min [240000], rate=81355.93/min [250000], rate=75757.58/min [260000], rate=72222.22/min [270000], rate=69527.90/min [280000], rate=67469.88/min [290000], rate=65909.09/min [300000], rate=64981.95/min [310000], rate=64583.33/min [320000], rate=64864.86/min [330000], rate=64495.11/min [340000], rate=63949.84/min [350000], rate=63636.36/min [360000], rate=63529.41/min [370000], rate=63428.57/min [380000], rate=63333.33/min [390000], rate=61578.95/min [400000], rate=60453.40/min [410000], rate=59708.74/min [420000], rate=59294.12/min [430000], rate=58769.93/min [440000], rate=58536.59/min [450000], rate=58568.33/min [460000], rate=58723.40/min [470000], rate=57905.54/min [480000], rate=57370.52/min [490000], rate=56866.54/min [500000], rate=56497.18/min [510000], rate=56561.92/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir --filt_file /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.DaP6ZeAZMZ/./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... 3428571.43 reads per min processed... 3333333.33 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 2823529.41 reads per min processed... 2842105.26 reads per min processed... 2857142.86 reads per min processed... 3000000.00 reads per min processed... 3130434.78 reads per min processed... 3120000.00 reads per min processed... 3111111.11 reads per min processed... 3103448.28 reads per min processed... 3096774.19 reads per min processed... 3090909.09 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.DaP6ZeAZMZ/aih-tih-sc-24ecfe-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.DaP6ZeAZMZ/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -94203.146465 EM: Round [1] log likelihood: -94046.630710 EM: Round [2] log likelihood: -93994.543201 EM: Round [3] log likelihood: -93969.960261 EM: Round [4] log likelihood: -93956.940408 EM: Round [5] log likelihood: -93949.706439 EM: Round [6] log likelihood: -93945.548597 EM: Round [7] log likelihood: -93943.072455 EM: Round [8] log likelihood: -93941.539389 EM: Round [9] log likelihood: -93940.551495 EM: Round [10] log likelihood: -93939.889879 EM: Round [11] log likelihood: -93939.430826 EM: Round [12] log likelihood: -93939.102189 EM: Round [13] log likelihood: -93938.860461 EM: Round [14] log likelihood: -93938.678492 EM: Round [15] log likelihood: -93938.538779 EM: Round [16] log likelihood: -93938.429684 EM: Round [17] log likelihood: -93938.343246 EM: Round [18] log likelihood: -93938.273888 EM: Round [19] log likelihood: -93938.217611 EM: Round [20] log likelihood: -93938.171493 EM: Round [21] log likelihood: -93938.133365 EM: Round [22] log likelihood: -93938.101590 EM: Round [23] log likelihood: -93938.074914 EM: Round [24] log likelihood: -93938.052370 EM: Round [25] log likelihood: -93938.033200 EM: Round [26] log likelihood: -93938.016806 EM: Round [27] log likelihood: -93938.002710 EM: Round [28] log likelihood: -93937.990530 EM: Round [29] log likelihood: -93937.979954 EM: Round [30] log likelihood: -93937.970729 EM: Round [31] log likelihood: -93937.962649 EM: Round [32] log likelihood: -93937.955540 EM: Round [33] log likelihood: -93937.949262 EM: Round [34] log likelihood: -93937.943695 EM: Round [35] log likelihood: -93937.938740 EM: Round [36] log likelihood: -93937.934314 EM: Round [37] log likelihood: -93937.930346 EM: Round [38] log likelihood: -93937.926776 EM: Round [39] log likelihood: -93937.923553 EM: Round [40] log likelihood: -93937.920634 EM: Round [41] log likelihood: -93937.917982 EM: Round [42] log likelihood: -93937.915566 EM: Round [43] log likelihood: -93937.913357 EM: Round [44] log likelihood: -93937.911332 EM: Round [45] log likelihood: -93937.909470 EM: Round [46] log likelihood: -93937.907755 EM: Round [47] log likelihood: -93937.906169 EM: Round [48] log likelihood: -93937.904701 EM: Round [49] log likelihood: -93937.903338 EM: Round [50] log likelihood: -93937.902070 EM: Round [51] log likelihood: -93937.900887 EM: Round [52] log likelihood: -93937.899782 EM: Round [53] log likelihood: -93937.898748 EM: Round [54] log likelihood: -93937.897779 EM: Round [55] log likelihood: -93937.896869 EM: Round [56] log likelihood: -93937.896013 EM: Round [57] log likelihood: -93937.895206 EM: Round [58] log likelihood: -93937.894446 EM: Round [59] log likelihood: -93937.893728 EM: Round [60] log likelihood: -93937.893049 EM: Round [61] log likelihood: -93937.892406 EM: Round [62] log likelihood: -93937.891797 EM: Round [63] log likelihood: -93937.891220 EM: Round [64] log likelihood: -93937.890672 EM: Round [65] log likelihood: -93937.890151 EM: Round [66] log likelihood: -93937.889656 EM: Round [67] log likelihood: -93937.889185 EM: Round [68] log likelihood: -93937.888737 EM: Round [69] log likelihood: -93937.888310 EM: Round [70] log likelihood: -93937.887903 EM: Round [71] log likelihood: -93937.887515 EM: Round [72] log likelihood: -93937.887145 EM: Round [73] log likelihood: -93937.886791 EM: Round [74] log likelihood: -93937.886453 EM: Round [75] log likelihood: -93937.886131 EM: Round [76] log likelihood: -93937.885822 EM: Round [77] log likelihood: -93937.885528 EM: Round [78] log likelihood: -93937.885246 EM: Round [79] log likelihood: -93937.884976 EM: Round [80] log likelihood: -93937.884718 EM: Round [81] log likelihood: -93937.884471 EM: Round [82] log likelihood: -93937.884234 EM: Round [83] log likelihood: -93937.884007 EM: Round [84] log likelihood: -93937.883790 EM: Round [85] log likelihood: -93937.883582 EM: Round [86] log likelihood: -93937.883382 EM: Round [87] log likelihood: -93937.883191 EM: Round [88] log likelihood: -93937.883008 EM: Round [89] log likelihood: -93937.882832 EM: Round [90] log likelihood: -93937.882663 EM: Round [91] log likelihood: -93937.882501 EM: Round [92] log likelihood: -93937.882345 EM: Round [93] log likelihood: -93937.882196 EM: Round [94] log likelihood: -93937.882053 EM: Round [95] log likelihood: -93937.881915 EM: Round [96] log likelihood: -93937.881783 EM: Round [97] log likelihood: -93937.881656 EM: Round [98] log likelihood: -93937.881534 EM: Round [99] log likelihood: -93937.881417 EM: Round [100] log likelihood: -93937.881304 EM: Round [101] log likelihood: -93937.881196 EM: Round [102] log likelihood: -93937.881092 EM: Round [103] log likelihood: -93937.880992 EM: Round [104] log likelihood: -93937.880896 EM: Stopping iterations at round 104 due to insufficient improvement in likelihood. EM: Starting log likelihood: -93819.677135 EM: Round [1] log likelihood: -93711.654871 EM: Round [2] log likelihood: -93675.040445 EM: Round [3] log likelihood: -93657.848388 EM: Round [4] log likelihood: -93648.817764 EM: Round [5] log likelihood: -93643.844359 EM: Round [6] log likelihood: -93641.014773 EM: Round [7] log likelihood: -93639.349386 EM: Round [8] log likelihood: -93638.331305 EM: Round [9] log likelihood: -93637.683287 EM: Round [10] log likelihood: -93637.253784 EM: Round [11] log likelihood: -93636.957940 EM: Round [12] log likelihood: -93636.746881 EM: Round [13] log likelihood: -93636.591568 EM: Round [14] log likelihood: -93636.474178 EM: Round [15] log likelihood: -93636.383408 EM: Round [16] log likelihood: -93636.311856 EM: Round [17] log likelihood: -93636.254525 EM: Round [18] log likelihood: -93636.207948 EM: Round [19] log likelihood: -93636.169654 EM: Round [20] log likelihood: -93636.137847 EM: Round [21] log likelihood: -93636.111190 EM: Round [22] log likelihood: -93636.088673 EM: Round [23] log likelihood: -93636.069519 EM: Round [24] log likelihood: -93636.053123 EM: Round [25] log likelihood: -93636.039007 EM: Round [26] log likelihood: -93636.026791 EM: Round [27] log likelihood: -93636.016167 EM: Round [28] log likelihood: -93636.006886 EM: Round [29] log likelihood: -93635.998744 EM: Round [30] log likelihood: -93635.991571 EM: Round [31] log likelihood: -93635.985228 EM: Round [32] log likelihood: -93635.979598 EM: Round [33] log likelihood: -93635.974583 EM: Round [34] log likelihood: -93635.970100 EM: Round [35] log likelihood: -93635.966079 EM: Round [36] log likelihood: -93635.962461 EM: Round [37] log likelihood: -93635.959194 EM: Round [38] log likelihood: -93635.956236 EM: Round [39] log likelihood: -93635.953548 EM: Round [40] log likelihood: -93635.951100 EM: Round [41] log likelihood: -93635.948863 EM: Round [42] log likelihood: -93635.946813 EM: Round [43] log likelihood: -93635.944930 EM: Round [44] log likelihood: -93635.943196 EM: Round [45] log likelihood: -93635.941594 EM: Round [46] log likelihood: -93635.940112 EM: Round [47] log likelihood: -93635.938736 EM: Round [48] log likelihood: -93635.937457 EM: Round [49] log likelihood: -93635.936266 EM: Round [50] log likelihood: -93635.935153 EM: Round [51] log likelihood: -93635.934113 EM: Round [52] log likelihood: -93635.933138 EM: Round [53] log likelihood: -93635.932223 EM: Round [54] log likelihood: -93635.931362 EM: Round [55] log likelihood: -93635.930553 EM: Round [56] log likelihood: -93635.929789 EM: Round [57] log likelihood: -93635.929068 EM: Round [58] log likelihood: -93635.928387 EM: Round [59] log likelihood: -93635.927742 EM: Round [60] log likelihood: -93635.927132 EM: Round [61] log likelihood: -93635.926553 EM: Round [62] log likelihood: -93635.926003 EM: Round [63] log likelihood: -93635.925481 EM: Round [64] log likelihood: -93635.924985 EM: Round [65] log likelihood: -93635.924513 EM: Round [66] log likelihood: -93635.924064 EM: Round [67] log likelihood: -93635.923636 EM: Round [68] log likelihood: -93635.923228 EM: Round [69] log likelihood: -93635.922839 EM: Round [70] log likelihood: -93635.922468 EM: Round [71] log likelihood: -93635.922114 EM: Round [72] log likelihood: -93635.921775 EM: Round [73] log likelihood: -93635.921452 EM: Round [74] log likelihood: -93635.921143 EM: Round [75] log likelihood: -93635.920848 EM: Round [76] log likelihood: -93635.920565 EM: Round [77] log likelihood: -93635.920295 EM: Round [78] log likelihood: -93635.920036 EM: Round [79] log likelihood: -93635.919788 EM: Round [80] log likelihood: -93635.919551 EM: Round [81] log likelihood: -93635.919324 EM: Round [82] log likelihood: -93635.919106 EM: Round [83] log likelihood: -93635.918897 EM: Round [84] log likelihood: -93635.918698 EM: Round [85] log likelihood: -93635.918506 EM: Round [86] log likelihood: -93635.918322 EM: Round [87] log likelihood: -93635.918146 EM: Round [88] log likelihood: -93635.917977 EM: Round [89] log likelihood: -93635.917814 EM: Round [90] log likelihood: -93635.917659 EM: Round [91] log likelihood: -93635.917509 EM: Round [92] log likelihood: -93635.917366 EM: Round [93] log likelihood: -93635.917228 EM: Round [94] log likelihood: -93635.917096 EM: Round [95] log likelihood: -93635.916969 EM: Round [96] log likelihood: -93635.916847 EM: Round [97] log likelihood: -93635.916730 EM: Round [98] log likelihood: -93635.916617 EM: Round [99] log likelihood: -93635.916509 EM: Round [100] log likelihood: -93635.916405 EM: Round [101] log likelihood: -93635.916305 EM: Stopping iterations at round 101 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.DaP6ZeAZMZ/./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.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.DaP6ZeAZMZ/./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.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 33031530 > /tmp/nxf.DaP6ZeAZMZ/./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.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir > /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir --annotate /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.DaP6ZeAZMZ/./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.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir -done, see /tmp/nxf.DaP6ZeAZMZ/./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.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.DaP6ZeAZMZ/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 525, filtered: 5106) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.DaP6ZeAZMZ/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.DaP6ZeAZMZ/./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.DaP6ZeAZMZ/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000243753.5] WARNING, no entry stored in dbm for [ENSG00000181126.13] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000224086.6] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000285756.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000285756.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000285756.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000285756.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000285756.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000285756.2] WARNING, no entry stored in dbm for [ENSG00000276758.1] 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 [ENSG00000286168.2] WARNING, no entry stored in dbm for [ENSG00000230305.2] WARNING, no entry stored in dbm for [ENSG00000259203.2] WARNING, no entry stored in dbm for [ENSG00000244257.5] WARNING, no entry stored in dbm for [ENSG00000251301.7] WARNING, no entry stored in dbm for [ENSG00000229205.5] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000286387.1] WARNING, no entry stored in dbm for [ENSG00000256282.1] WARNING, no entry stored in dbm for [ENSG00000248205.1] WARNING, no entry stored in dbm for [ENSG00000204623.9] WARNING, no entry stored in dbm for [ENSG00000286215.1] WARNING, no entry stored in dbm for [ENSG00000287100.1] WARNING, no entry stored in dbm for [ENSG00000254485.5] WARNING, no entry stored in dbm for [ENSG00000261526.2] WARNING, no entry stored in dbm for [ENSG00000225840.2] WARNING, no entry stored in dbm for [ENSG00000241369.6] WARNING, no entry stored in dbm for [ENSG00000228303.1] WARNING, no entry stored in dbm for [ENSG00000228125.2] WARNING, no entry stored in dbm for [ENSG00000250125.4] WARNING, no entry stored in dbm for [ENSG00000287274.1] WARNING, no entry stored in dbm for [ENSG00000277125.1] WARNING, no entry stored in dbm for [ENSG00000267272.5] WARNING, no entry stored in dbm for [ENSG00000241899.1] WARNING, no entry stored in dbm for [ENSG00000277449.1] WARNING, no entry stored in dbm for [ENSG00000261054.1] WARNING, no entry stored in dbm for [ENSG00000261656.6] WARNING, no entry stored in dbm for [ENSG00000287882.1] WARNING, no entry stored in dbm for [ENSG00000267046.1] WARNING, no entry stored in dbm for [ENSG00000224597.10] WARNING, no entry stored in dbm for [ENSG00000280594.1] WARNING, no entry stored in dbm for [ENSG00000257702.3] WARNING, no entry stored in dbm for [ENSG00000201527.1] WARNING, no entry stored in dbm for [ENSG00000184809.13] WARNING, no entry stored in dbm for [ENSG00000275826.1] WARNING, no entry stored in dbm for [ENSG00000204044.6] WARNING, no entry stored in dbm for [ENSG00000255839.1] WARNING, no entry stored in dbm for [ENSG00000226903.2] WARNING, no entry stored in dbm for [ENSG00000188002.10] WARNING, no entry stored in dbm for [ENSG00000224616.3] WARNING, no entry stored in dbm for [ENSG00000265018.6] WARNING, no entry stored in dbm for [ENSG00000230629.2] WARNING, no entry stored in dbm for [ENSG00000228000.1] WARNING, no entry stored in dbm for [ENSG00000238015.2] WARNING, no entry stored in dbm for [ENSG00000263006.6] WARNING, no entry stored in dbm for [ENSG00000239899.3] WARNING, no entry stored in dbm for [ENSG00000241175.3] WARNING, no entry stored in dbm for [ENSG00000244056.3] WARNING, no entry stored in dbm for [ENSG00000265813.2] WARNING, no entry stored in dbm for [ENSG00000237361.3] WARNING, no entry stored in dbm for [ENSG00000244513.7] WARNING, no entry stored in dbm for [ENSG00000277011.1] WARNING, no entry stored in dbm for [ENSG00000260930.2] WARNING, no entry stored in dbm for [ENSG00000273125.2] WARNING, no entry stored in dbm for [ENSG00000224607.4] WARNING, no entry stored in dbm for [ENSG00000288581.1] WARNING, no entry stored in dbm for [ENSG00000240677.1] WARNING, no entry stored in dbm for [ENSG00000224729.6] WARNING, no entry stored in dbm for [ENSG00000205361.8] WARNING, no entry stored in dbm for [ENSG00000233929.1] WARNING, no entry stored in dbm for [ENSG00000205360.6] WARNING, no entry stored in dbm for [ENSG00000218283.2] WARNING, no entry stored in dbm for [ENSG00000225133.1] WARNING, no entry stored in dbm for [ENSG00000223566.1] WARNING, no entry stored in dbm for [ENSG00000283805.1] WARNING, no entry stored in dbm for [ENSG00000197880.9] WARNING, no entry stored in dbm for [ENSG00000248323.7] 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 [ENSG00000248505.2] WARNING, no entry stored in dbm for [ENSG00000248489.2] WARNING, no entry stored in dbm for [ENSG00000236008.3] WARNING, no entry stored in dbm for [ENSG00000229694.7] WARNING, no entry stored in dbm for [ENSG00000248231.1] WARNING, no entry stored in dbm for [ENSG00000235374.2] WARNING, no entry stored in dbm for [ENSG00000231183.4] WARNING, no entry stored in dbm for [ENSG00000287008.1] WARNING, no entry stored in dbm for [ENSG00000281706.3] WARNING, no entry stored in dbm for [ENSG00000233891.8] WARNING, no entry stored in dbm for [ENSG00000229657.2] WARNING, no entry stored in dbm for [ENSG00000255074.1] WARNING, no entry stored in dbm for [ENSG00000204622.11] WARNING, no entry stored in dbm for [ENSG00000224557.7] WARNING, no entry stored in dbm for [ENSG00000261716.2] WARNING, no entry stored in dbm for [ENSG00000220323.4] WARNING, no entry stored in dbm for [ENSG00000178243.4] WARNING, no entry stored in dbm for [ENSG00000281832.1] WARNING, no entry stored in dbm for [ENSG00000239533.6] WARNING, no entry stored in dbm for [ENSG00000230590.11] WARNING, no entry stored in dbm for [ENSG00000213362.3] WARNING, no entry stored in dbm for [ENSG00000213362.3] WARNING, no entry stored in dbm for [ENSG00000213468.7] WARNING, no entry stored in dbm for [ENSG00000185684.15] WARNING, no entry stored in dbm for [ENSG00000254285.3] WARNING, no entry stored in dbm for [ENSG00000240416.1] WARNING, no entry stored in dbm for [ENSG00000229357.1] WARNING, no entry stored in dbm for [ENSG00000224078.15] WARNING, no entry stored in dbm for [ENSG00000283541.1] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000176593.8] WARNING, no entry stored in dbm for [ENSG00000244712.1] WARNING, no entry stored in dbm for [ENSG00000215874.3] WARNING, no entry stored in dbm for [ENSG00000227742.2] WARNING, no entry stored in dbm for [ENSG00000233145.1] WARNING, no entry stored in dbm for [ENSG00000226835.3] WARNING, no entry stored in dbm for [ENSG00000219807.2] WARNING, no entry stored in dbm for [ENSG00000283285.1] WARNING, no entry stored in dbm for [ENSG00000230006.7] WARNING, no entry stored in dbm for [ENSG00000270504.1] WARNING, no entry stored in dbm for [ENSG00000217801.10] WARNING, no entry stored in dbm for [ENSG00000235922.1] WARNING, no entry stored in dbm for [ENSG00000269934.3] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000234238.2] WARNING, no entry stored in dbm for [ENSG00000255085.8] WARNING, no entry stored in dbm for [ENSG00000226359.1] WARNING, no entry stored in dbm for [ENSG00000237250.3] WARNING, no entry stored in dbm for [ENSG00000130600.19] WARNING, no entry stored in dbm for [ENSG00000254247.1] WARNING, no entry stored in dbm for [ENSG00000282375.1] WARNING, no entry stored in dbm for [ENSG00000228999.4] WARNING, no entry stored in dbm for [ENSG00000240787.1] WARNING, no entry stored in dbm for [ENSG00000286895.1] WARNING, no entry stored in dbm for [ENSG00000239268.3] WARNING, no entry stored in dbm for [ENSG00000253107.1] WARNING, no entry stored in dbm for [ENSG00000253107.1] WARNING, no entry stored in dbm for [ENSG00000262580.5] WARNING, no entry stored in dbm for [ENSG00000279048.1] WARNING, no entry stored in dbm for [ENSG00000277782.1] WARNING, no entry stored in dbm for [ENSG00000254741.1] WARNING, no entry stored in dbm for [ENSG00000251376.1] WARNING, no entry stored in dbm for [ENSG00000250140.1] WARNING, no entry stored in dbm for [ENSG00000268093.1] WARNING, no entry stored in dbm for [ENSG00000270799.1] WARNING, no entry stored in dbm for [ENSG00000240401.9] WARNING, no entry stored in dbm for [ENSG00000267723.1] WARNING, no entry stored in dbm for [ENSG00000280394.1] WARNING, no entry stored in dbm for [ENSG00000225840.2] WARNING, no entry stored in dbm for [ENSG00000240661.3] WARNING, no entry stored in dbm for [ENSG00000259106.1] WARNING, no entry stored in dbm for [ENSG00000277534.1] WARNING, no entry stored in dbm for [ENSG00000274712.2] WARNING, no entry stored in dbm for [ENSG00000273314.1] WARNING, no entry stored in dbm for [ENSG00000230477.1] WARNING, no entry stored in dbm for [ENSG00000280054.1] WARNING, no entry stored in dbm for [ENSG00000259983.1] WARNING, no entry stored in dbm for [ENSG00000272599.2] * STAR-Fusion complete. See output: /tmp/nxf.DaP6ZeAZMZ/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)