-ctat genome lib [/tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.bNamvMJxvK/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary -sample contains 72117083 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir -J /tmp/nxf.bNamvMJxvK/aih-tih-sc-976eb1-R1_B23WHYVLT4_1.Chimeric.out.junction -O /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.bNamvMJxvK/aih-tih-sc-976eb1-R1_B23WHYVLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=42857.14/min [20000], rate=38709.68/min [30000], rate=40909.09/min [40000], rate=42105.26/min [50000], rate=43478.26/min [60000], rate=45569.62/min [70000], rate=47191.01/min [80000], rate=47524.75/min [90000], rate=48214.29/min [100000], rate=48000.00/min [110000], rate=49253.73/min [120000], rate=50349.65/min [130000], rate=49681.53/min [140000], rate=48275.86/min [150000], rate=46632.12/min [160000], rate=45497.63/min [170000], rate=44736.84/min [180000], rate=44444.44/min [190000], rate=44186.05/min [200000], rate=43795.62/min [210000], rate=43598.62/min [220000], rate=44000.00/min [230000], rate=44230.77/min [240000], rate=44444.44/min [250000], rate=44510.39/min [260000], rate=44827.59/min [270000], rate=45125.35/min [280000], rate=45901.64/min [290000], rate=46524.06/min [300000], rate=47120.42/min [310000], rate=47814.91/min [320000], rate=48241.21/min [330000], rate=48768.47/min [340000], rate=49038.46/min [350000], rate=49645.39/min [360000], rate=50232.56/min [370000], rate=50800.92/min [380000], rate=51351.35/min [390000], rate=52348.99/min [400000], rate=53097.35/min [410000], rate=53829.32/min [420000], rate=54427.65/min [430000], rate=54893.62/min [440000], rate=55462.18/min [450000], rate=56016.60/min [460000], rate=56907.22/min [470000], rate=57433.81/min [480000], rate=58064.52/min [490000], rate=58682.63/min [500000], rate=59288.54/min [510000], rate=59765.62/min [520000], rate=60231.66/min [530000], rate=60919.54/min [540000], rate=61480.08/min [550000], rate=61913.70/min [560000], rate=62107.21/min [570000], rate=62408.76/min [580000], rate=62589.93/min [590000], rate=62433.86/min [600000], rate=62500.00/min [610000], rate=62778.73/min [620000], rate=62944.16/min [630000], rate=63105.18/min [640000], rate=63261.94/min [650000], rate=63517.92/min [660000], rate=63157.89/min [670000], rate=62422.36/min [680000], rate=61911.99/min [690000], rate=61424.33/min [700000], rate=60957.91/min [710000], rate=60511.36/min [720000], rate=60335.20/min [730000], rate=60082.30/min [740000], rate=59919.03/min [750000], rate=59760.96/min [760000], rate=59764.09/min [770000], rate=59844.56/min [780000], rate=60077.02/min [790000], rate=60305.34/min [800000], rate=60000.00/min [810000], rate=59852.22/min [820000], rate=59636.36/min [830000], rate=59569.38/min [840000], rate=59504.13/min -building interval tree based on /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=60000.00/min [20000], rate=63157.89/min [30000], rate=60000.00/min [40000], rate=50000.00/min [50000], rate=49180.33/min [60000], rate=48000.00/min [70000], rate=47191.01/min [80000], rate=47058.82/min [90000], rate=47787.61/min [100000], rate=48000.00/min [110000], rate=46153.85/min [120000], rate=46753.25/min [130000], rate=47272.73/min [140000], rate=47727.27/min [150000], rate=48387.10/min [160000], rate=49484.54/min [170000], rate=50495.05/min [180000], rate=50467.29/min [190000], rate=49781.66/min [200000], rate=49792.53/min [210000], rate=49411.76/min [220000], rate=48708.49/min [230000], rate=48591.55/min [240000], rate=48648.65/min [250000], rate=48701.30/min [260000], rate=48902.82/min [270000], rate=49090.91/min [280000], rate=49411.76/min [290000], rate=50000.00/min [300000], rate=50561.80/min [310000], rate=51098.90/min [320000], rate=51752.02/min [330000], rate=51428.57/min [340000], rate=50746.27/min [350000], rate=50480.77/min [360000], rate=50467.29/min [370000], rate=50454.55/min [380000], rate=50554.32/min [390000], rate=50759.22/min [400000], rate=50847.46/min [410000], rate=51037.34/min [420000], rate=51323.83/min [430000], rate=51292.25/min [440000], rate=51361.87/min [450000], rate=51526.72/min [460000], rate=51782.36/min [470000], rate=52029.52/min [480000], rate=52363.64/min [490000], rate=52782.76/min [500000], rate=53285.97/min [510000], rate=53217.39/min [520000], rate=53061.22/min [530000], rate=52911.81/min [540000], rate=52941.18/min [550000], rate=52969.50/min [560000], rate=53080.57/min [570000], rate=53271.03/min [580000], rate=53620.96/min [590000], rate=54045.80/min [600000], rate=54462.93/min [610000], rate=54954.95/min [620000], rate=55439.64/min [630000], rate=55917.16/min [640000], rate=56387.67/min [650000], rate=56603.77/min [660000], rate=56410.26/min [670000], rate=56223.78/min [680000], rate=56275.86/min [690000], rate=56173.68/min [700000], rate=56224.90/min [710000], rate=56274.77/min [720000], rate=56396.87/min [730000], rate=56662.35/min [740000], rate=56996.15/min [750000], rate=57251.91/min [760000], rate=57430.73/min [770000], rate=57320.10/min [780000], rate=57212.71/min [790000], rate=57246.38/min [800000], rate=57279.24/min [810000], rate=57446.81/min [820000], rate=57746.48/min [830000], rate=57974.39/min [840000], rate=58198.61/min -building interval tree based on /tmp/nxf.bNamvMJxvK/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=48000.00/min [30000], rate=48648.65/min [40000], rate=52173.91/min [50000], rate=54545.45/min [60000], rate=57142.86/min [70000], rate=58333.33/min [80000], rate=60000.00/min [90000], rate=61363.64/min [100000], rate=61224.49/min [110000], rate=62264.15/min [120000], rate=62608.70/min [130000], rate=59090.91/min [140000], rate=58333.33/min [150000], rate=58064.52/min [160000], rate=58536.59/min [170000], rate=59302.33/min [180000], rate=60000.00/min [190000], rate=60962.57/min [200000], rate=60000.00/min [210000], rate=59433.96/min [220000], rate=58928.57/min [230000], rate=58974.36/min [240000], rate=59016.39/min [250000], rate=59760.96/min [260000], rate=60465.12/min [270000], rate=61363.64/min [280000], rate=60649.82/min [290000], rate=59385.67/min [300000], rate=58823.53/min [310000], rate=58125.00/min [320000], rate=57831.33/min [330000], rate=57391.30/min [340000], rate=57303.37/min [350000], rate=57220.71/min [360000], rate=56992.08/min [370000], rate=56923.08/min [380000], rate=56575.68/min [390000], rate=56385.54/min [400000], rate=56470.59/min [410000], rate=56292.91/min [420000], rate=56124.72/min [430000], rate=56455.14/min [440000], rate=56410.26/min [450000], rate=56485.36/min [460000], rate=56673.51/min [470000], rate=56854.84/min [480000], rate=57029.70/min [490000], rate=56756.76/min [500000], rate=56926.00/min [510000], rate=56983.24/min [520000], rate=56934.31/min [530000], rate=56887.30/min [540000], rate=56942.00/min [550000], rate=57192.37/min [560000], rate=57534.25/min [570000], rate=57966.10/min [580000], rate=57711.44/min [590000], rate=57096.77/min [600000], rate=56782.33/min [610000], rate=56307.69/min [620000], rate=56024.10/min [630000], rate=55834.56/min [640000], rate=55571.64/min [650000], rate=55397.73/min [660000], rate=55230.13/min [670000], rate=55371.90/min [680000], rate=55359.57/min [690000], rate=55200.00/min [700000], rate=55190.54/min [710000], rate=55252.92/min [720000], rate=55455.71/min [730000], rate=55725.19/min [740000], rate=55919.40/min [750000], rate=56109.73/min [760000], rate=56296.30/min [770000], rate=56410.26/min [780000], rate=56727.27/min [790000], rate=56902.76/min [800000], rate=56603.77/min [810000], rate=56380.51/min [820000], rate=56036.45/min [830000], rate=55829.60/min -building interval tree based on /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=109090.91/min [30000], rate=112500.00/min [40000], rate=120000.00/min [50000], rate=120000.00/min [60000], rate=120000.00/min [70000], rate=116666.67/min [80000], rate=117073.17/min [90000], rate=120000.00/min [100000], rate=122448.98/min [110000], rate=122222.22/min [120000], rate=118032.79/min [130000], rate=116417.91/min [140000], rate=116666.67/min [150000], rate=112500.00/min [160000], rate=109090.91/min [170000], rate=108510.64/min [180000], rate=108000.00/min [190000], rate=106542.06/min [200000], rate=85714.29/min [210000], rate=77300.61/min [220000], rate=71351.35/min [230000], rate=66346.15/min [240000], rate=63436.12/min [250000], rate=60728.74/min [260000], rate=58867.92/min [270000], rate=57243.82/min [280000], rate=56565.66/min [290000], rate=55591.05/min [300000], rate=55045.87/min [310000], rate=54545.45/min [320000], rate=54237.29/min [330000], rate=53804.35/min [340000], rate=53543.31/min [350000], rate=53571.43/min [360000], rate=52811.74/min [370000], rate=52482.27/min [380000], rate=52655.89/min [390000], rate=52702.70/min [400000], rate=52516.41/min [410000], rate=52340.43/min [420000], rate=52390.85/min [430000], rate=52760.74/min [440000], rate=52905.81/min [450000], rate=53045.19/min [460000], rate=53179.19/min [470000], rate=53409.09/min [480000], rate=53831.78/min [490000], rate=54143.65/min [500000], rate=54545.45/min [510000], rate=54545.45/min [520000], rate=54355.40/min [530000], rate=54358.97/min [540000], rate=54271.36/min [550000], rate=54455.45/min [560000], rate=54368.93/min [570000], rate=54545.45/min [580000], rate=54631.08/min [590000], rate=54798.76/min [600000], rate=55130.17/min [610000], rate=55454.55/min [620000], rate=55772.11/min [630000], rate=56166.42/min [640000], rate=55813.95/min [650000], rate=55476.53/min [660000], rate=55230.13/min [670000], rate=55144.03/min [680000], rate=54912.52/min [690000], rate=54834.44/min [700000], rate=54830.29/min [710000], rate=54755.78/min [720000], rate=54683.54/min [730000], rate=54409.94/min [740000], rate=54278.73/min [750000], rate=54151.62/min [760000], rate=54156.77/min [770000], rate=54352.94/min [780000], rate=54545.45/min [790000], rate=54671.28/min [800000], rate=54483.54/min [810000], rate=54301.68/min [820000], rate=54244.76/min [830000], rate=54071.66/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir --filt_file /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.bNamvMJxvK/./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... 4000000.00 reads per min processed... 3750000.00 reads per min processed... 4000000.00 reads per min processed... 3818181.82 reads per min processed... 4000000.00 reads per min processed... 3857142.86 reads per min processed... 3750000.00 reads per min processed... 3666666.67 reads per min processed... 3600000.00 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... 3777777.78 reads per min processed... 3857142.86 reads per min processed... 3931034.48 reads per min processed... 3870967.74 reads per min processed... 3937500.00 reads per min processed... 3882352.94 reads per min processed... 3942857.14 reads per min processed... 3891891.89 reads per min processed... 3846153.85 reads per min processed... 3804878.05 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.bNamvMJxvK/aih-tih-sc-976eb1-R1_B23WHYVLT4_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.bNamvMJxvK/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -65203.105648 EM: Round [1] log likelihood: -65179.880319 EM: Round [2] log likelihood: -65170.350464 EM: Round [3] log likelihood: -65165.645867 EM: Round [4] log likelihood: -65163.093910 EM: Round [5] log likelihood: -65161.632305 EM: Round [6] log likelihood: -65160.757794 EM: Round [7] log likelihood: -65160.209853 EM: Round [8] log likelihood: -65159.849145 EM: Round [9] log likelihood: -65159.599834 EM: Round [10] log likelihood: -65159.419761 EM: Round [11] log likelihood: -65159.284790 EM: Round [12] log likelihood: -65159.180581 EM: Round [13] log likelihood: -65159.098241 EM: Round [14] log likelihood: -65159.032011 EM: Round [15] log likelihood: -65158.977992 EM: Round [16] log likelihood: -65158.933443 EM: Round [17] log likelihood: -65158.896373 EM: Round [18] log likelihood: -65158.865293 EM: Round [19] log likelihood: -65158.839066 EM: Round [20] log likelihood: -65158.816807 EM: Round [21] log likelihood: -65158.797821 EM: Round [22] log likelihood: -65158.781552 EM: Round [23] log likelihood: -65158.767552 EM: Round [24] log likelihood: -65158.755458 EM: Round [25] log likelihood: -65158.744973 EM: Round [26] log likelihood: -65158.735852 EM: Round [27] log likelihood: -65158.727895 EM: Round [28] log likelihood: -65158.720932 EM: Round [29] log likelihood: -65158.714823 EM: Round [30] log likelihood: -65158.709450 EM: Round [31] log likelihood: -65158.704713 EM: Round [32] log likelihood: -65158.700527 EM: Round [33] log likelihood: -65158.696823 EM: Round [34] log likelihood: -65158.693537 EM: Round [35] log likelihood: -65158.690617 EM: Round [36] log likelihood: -65158.688019 EM: Round [37] log likelihood: -65158.685703 EM: Round [38] log likelihood: -65158.683637 EM: Round [39] log likelihood: -65158.681790 EM: Round [40] log likelihood: -65158.680137 EM: Round [41] log likelihood: -65158.678657 EM: Round [42] log likelihood: -65158.677329 EM: Round [43] log likelihood: -65158.676138 EM: Round [44] log likelihood: -65158.675068 EM: Round [45] log likelihood: -65158.674105 EM: Round [46] log likelihood: -65158.673239 EM: Round [47] log likelihood: -65158.672459 EM: Round [48] log likelihood: -65158.671757 EM: Round [49] log likelihood: -65158.671123 EM: Round [50] log likelihood: -65158.670551 EM: Round [51] log likelihood: -65158.670035 EM: Round [52] log likelihood: -65158.669569 EM: Round [53] log likelihood: -65158.669148 EM: Round [54] log likelihood: -65158.668768 EM: Round [55] log likelihood: -65158.668423 EM: Round [56] log likelihood: -65158.668112 EM: Round [57] log likelihood: -65158.667830 EM: Round [58] log likelihood: -65158.667575 EM: Round [59] log likelihood: -65158.667344 EM: Round [60] log likelihood: -65158.667135 EM: Round [61] log likelihood: -65158.666946 EM: Round [62] log likelihood: -65158.666774 EM: Round [63] log likelihood: -65158.666618 EM: Round [64] log likelihood: -65158.666477 EM: Round [65] log likelihood: -65158.666349 EM: Round [66] log likelihood: -65158.666233 EM: Round [67] log likelihood: -65158.666128 EM: Round [68] log likelihood: -65158.666032 EM: Stopping iterations at round 68 due to insufficient improvement in likelihood. EM: Starting log likelihood: -65200.328696 EM: Round [1] log likelihood: -65178.278062 EM: Round [2] log likelihood: -65169.287275 EM: Round [3] log likelihood: -65164.897552 EM: Round [4] log likelihood: -65162.553158 EM: Round [5] log likelihood: -65161.234588 EM: Round [6] log likelihood: -65160.460640 EM: Round [7] log likelihood: -65159.984584 EM: Round [8] log likelihood: -65159.676161 EM: Round [9] log likelihood: -65159.465545 EM: Round [10] log likelihood: -65159.314573 EM: Round [11] log likelihood: -65159.201791 EM: Round [12] log likelihood: -65159.114696 EM: Round [13] log likelihood: -65159.045679 EM: Round [14] log likelihood: -65158.989898 EM: Round [15] log likelihood: -65158.944125 EM: Round [16] log likelihood: -65158.906117 EM: Round [17] log likelihood: -65158.874257 EM: Round [18] log likelihood: -65158.847343 EM: Round [19] log likelihood: -65158.824458 EM: Round [20] log likelihood: -65158.804890 EM: Round [21] log likelihood: -65158.788076 EM: Round [22] log likelihood: -65158.773564 EM: Round [23] log likelihood: -65158.760991 EM: Round [24] log likelihood: -65158.750057 EM: Round [25] log likelihood: -65158.740518 EM: Round [26] log likelihood: -65158.732171 EM: Round [27] log likelihood: -65158.724847 EM: Round [28] log likelihood: -65158.718404 EM: Round [29] log likelihood: -65158.712723 EM: Round [30] log likelihood: -65158.707702 EM: Round [31] log likelihood: -65158.703257 EM: Round [32] log likelihood: -65158.699313 EM: Round [33] log likelihood: -65158.695807 EM: Round [34] log likelihood: -65158.692687 EM: Round [35] log likelihood: -65158.689905 EM: Round [36] log likelihood: -65158.687422 EM: Round [37] log likelihood: -65158.685202 EM: Round [38] log likelihood: -65158.683216 EM: Round [39] log likelihood: -65158.681435 EM: Round [40] log likelihood: -65158.679839 EM: Round [41] log likelihood: -65158.678405 EM: Round [42] log likelihood: -65158.677117 EM: Round [43] log likelihood: -65158.675959 EM: Round [44] log likelihood: -65158.674916 EM: Round [45] log likelihood: -65158.673977 EM: Round [46] log likelihood: -65158.673131 EM: Round [47] log likelihood: -65158.672368 EM: Round [48] log likelihood: -65158.671679 EM: Round [49] log likelihood: -65158.671057 EM: Round [50] log likelihood: -65158.670496 EM: Round [51] log likelihood: -65158.669988 EM: Round [52] log likelihood: -65158.669529 EM: Round [53] log likelihood: -65158.669114 EM: Round [54] log likelihood: -65158.668739 EM: Round [55] log likelihood: -65158.668399 EM: Round [56] log likelihood: -65158.668091 EM: Round [57] log likelihood: -65158.667813 EM: Round [58] log likelihood: -65158.667560 EM: Round [59] log likelihood: -65158.667331 EM: Round [60] log likelihood: -65158.667124 EM: Round [61] log likelihood: -65158.666936 EM: Round [62] log likelihood: -65158.666766 EM: Round [63] log likelihood: -65158.666611 EM: Round [64] log likelihood: -65158.666471 EM: Round [65] log likelihood: -65158.666344 EM: Round [66] log likelihood: -65158.666229 EM: Round [67] log likelihood: -65158.666124 EM: Round [68] log likelihood: -65158.666029 EM: Stopping iterations at round 68 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.bNamvMJxvK/./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.bNamvMJxvK/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.bNamvMJxvK/./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.bNamvMJxvK/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 72117083 > /tmp/nxf.bNamvMJxvK/./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.bNamvMJxvK/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir > /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir --annotate /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.bNamvMJxvK/./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.bNamvMJxvK/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir -done, see /tmp/nxf.bNamvMJxvK/./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.bNamvMJxvK/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.bNamvMJxvK/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 800, filtered: 5652) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.bNamvMJxvK/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.bNamvMJxvK/./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.bNamvMJxvK/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000180747.15] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000245958.6] WARNING, no entry stored in dbm for [ENSG00000280136.2] 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 [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000262801.6] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000225689.2] WARNING, no entry stored in dbm for [ENSG00000245532.9] WARNING, no entry stored in dbm for [ENSG00000270231.4] WARNING, no entry stored in dbm for [ENSG00000181126.13] WARNING, no entry stored in dbm for [ENSG00000272645.3] WARNING, no entry stored in dbm for [ENSG00000277053.4] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000278887.2] WARNING, no entry stored in dbm for [ENSG00000280828.1] WARNING, no entry stored in dbm for [ENSG00000276805.2] WARNING, no entry stored in dbm for [ENSG00000278621.1] WARNING, no entry stored in dbm for [ENSG00000254485.5] WARNING, no entry stored in dbm for [ENSG00000257403.2] WARNING, no entry stored in dbm for [ENSG00000189149.12] WARNING, no entry stored in dbm for [ENSG00000226472.8] WARNING, no entry stored in dbm for [ENSG00000225264.3] WARNING, no entry stored in dbm for [ENSG00000237004.4] WARNING, no entry stored in dbm for [ENSG00000228815.1] WARNING, no entry stored in dbm for [ENSG00000237004.4] WARNING, no entry stored in dbm for [ENSG00000224365.1] WARNING, no entry stored in dbm for [ENSG00000287985.1] WARNING, no entry stored in dbm for [ENSG00000228303.1] WARNING, no entry stored in dbm for [ENSG00000226383.7] WARNING, no entry stored in dbm for [ENSG00000249459.11] WARNING, no entry stored in dbm for [ENSG00000276627.3] WARNING, no entry stored in dbm for [ENSG00000177410.13] WARNING, no entry stored in dbm for [ENSG00000272848.2] WARNING, no entry stored in dbm for [ENSG00000285961.1] WARNING, no entry stored in dbm for [ENSG00000282458.1] WARNING, no entry stored in dbm for [ENSG00000225292.2] WARNING, no entry stored in dbm for [ENSG00000204832.10] WARNING, no entry stored in dbm for [ENSG00000236380.5] WARNING, no entry stored in dbm for [ENSG00000226752.9] WARNING, no entry stored in dbm for [ENSG00000261416.1] WARNING, no entry stored in dbm for [ENSG00000233514.1] WARNING, no entry stored in dbm for [ENSG00000241656.1] WARNING, no entry stored in dbm for [ENSG00000287306.1] WARNING, no entry stored in dbm for [ENSG00000261008.7] WARNING, no entry stored in dbm for [ENSG00000247516.8] WARNING, no entry stored in dbm for [ENSG00000205583.13] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000205583.13] WARNING, no entry stored in dbm for [ENSG00000258704.6] WARNING, no entry stored in dbm for [ENSG00000215448.3] WARNING, no entry stored in dbm for [ENSG00000263821.1] WARNING, no entry stored in dbm for [ENSG00000237037.9] WARNING, no entry stored in dbm for [ENSG00000237037.9] WARNING, no entry stored in dbm for [ENSG00000198763.3] WARNING, no entry stored in dbm for [ENSG00000265735.2] WARNING, no entry stored in dbm for [ENSG00000263740.2] WARNING, no entry stored in dbm for [ENSG00000276168.1] WARNING, no entry stored in dbm for [ENSG00000250039.4] WARNING, no entry stored in dbm for [ENSG00000250337.7] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000287411.1] WARNING, no entry stored in dbm for [ENSG00000286511.1] WARNING, no entry stored in dbm for [ENSG00000247950.7] WARNING, no entry stored in dbm for [ENSG00000234684.7] WARNING, no entry stored in dbm for [ENSG00000146556.14] WARNING, no entry stored in dbm for [ENSG00000281641.3] WARNING, no entry stored in dbm for [ENSG00000287882.1] WARNING, no entry stored in dbm for [ENSG00000230116.1] WARNING, no entry stored in dbm for [ENSG00000200728.1] WARNING, no entry stored in dbm for [ENSG00000185485.14] WARNING, no entry stored in dbm for [ENSG00000240606.3] WARNING, no entry stored in dbm for [ENSG00000275014.1] WARNING, no entry stored in dbm for [ENSG00000078319.10] WARNING, no entry stored in dbm for [ENSG00000257815.7] WARNING, no entry stored in dbm for [ENSG00000259240.1] WARNING, no entry stored in dbm for [ENSG00000286830.1] WARNING, no entry stored in dbm for [ENSG00000234911.2] WARNING, no entry stored in dbm for [ENSG00000263317.1] WARNING, no entry stored in dbm for [ENSG00000272655.2] WARNING, no entry stored in dbm for [ENSG00000225746.13] WARNING, no entry stored in dbm for [ENSG00000267132.1] WARNING, no entry stored in dbm for [ENSG00000251508.1] WARNING, no entry stored in dbm for [ENSG00000255185.6] WARNING, no entry stored in dbm for [ENSG00000226232.8] WARNING, no entry stored in dbm for [ENSG00000205853.12] WARNING, no entry stored in dbm for [ENSG00000253438.4] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000249419.1] WARNING, no entry stored in dbm for [ENSG00000268686.2] WARNING, no entry stored in dbm for [ENSG00000232054.1] WARNING, no entry stored in dbm for [ENSG00000259161.2] WARNING, no entry stored in dbm for [ENSG00000288071.1] WARNING, no entry stored in dbm for [ENSG00000284052.1] WARNING, no entry stored in dbm for [ENSG00000245532.9] WARNING, no entry stored in dbm for [ENSG00000198496.12] WARNING, no entry stored in dbm for [ENSG00000236051.7] WARNING, no entry stored in dbm for [ENSG00000285587.1] WARNING, no entry stored in dbm for [ENSG00000214955.5] WARNING, no entry stored in dbm for [ENSG00000236172.7] WARNING, no entry stored in dbm for [ENSG00000196312.15] WARNING, no entry stored in dbm for [ENSG00000229021.2] 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 [ENSG00000255666.7] WARNING, no entry stored in dbm for [ENSG00000257259.3] WARNING, no entry stored in dbm for [ENSG00000277448.1] WARNING, no entry stored in dbm for [ENSG00000281903.2] WARNING, no entry stored in dbm for [ENSG00000237057.3] WARNING, no entry stored in dbm for [ENSG00000248473.2] WARNING, no entry stored in dbm for [ENSG00000279579.3] WARNING, no entry stored in dbm for [ENSG00000215866.8] WARNING, no entry stored in dbm for [ENSG00000247157.7] WARNING, no entry stored in dbm for [ENSG00000230426.4] WARNING, no entry stored in dbm for [ENSG00000235687.9] WARNING, no entry stored in dbm for [ENSG00000235687.9] WARNING, no entry stored in dbm for [ENSG00000235687.9] WARNING, no entry stored in dbm for [ENSG00000241135.6] WARNING, no entry stored in dbm for [ENSG00000203721.7] WARNING, no entry stored in dbm for [ENSG00000235734.4] WARNING, no entry stored in dbm for [ENSG00000225269.3] WARNING, no entry stored in dbm for [ENSG00000266904.6] WARNING, no entry stored in dbm for [ENSG00000259070.7] WARNING, no entry stored in dbm for [ENSG00000215483.11] WARNING, no entry stored in dbm for [ENSG00000280780.2] WARNING, no entry stored in dbm for [ENSG00000230202.1] WARNING, no entry stored in dbm for [ENSG00000236756.4] WARNING, no entry stored in dbm for [ENSG00000232934.8] WARNING, no entry stored in dbm for [ENSG00000281344.1] WARNING, no entry stored in dbm for [ENSG00000233369.7] WARNING, no entry stored in dbm for [ENSG00000227038.3] WARNING, no entry stored in dbm for [ENSG00000251508.1] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000273888.1] WARNING, no entry stored in dbm for [ENSG00000198468.9] WARNING, no entry stored in dbm for [ENSG00000271795.1] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000275431.1] WARNING, no entry stored in dbm for [ENSG00000223353.2] WARNING, no entry stored in dbm for [ENSG00000236438.7] WARNING, no entry stored in dbm for [ENSG00000281649.2] WARNING, no entry stored in dbm for [ENSG00000251504.1] WARNING, no entry stored in dbm for [ENSG00000204623.9] WARNING, no entry stored in dbm for [ENSG00000223773.7] WARNING, no entry stored in dbm for [ENSG00000258897.1] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000287376.1] WARNING, no entry stored in dbm for [ENSG00000226954.1] WARNING, no entry stored in dbm for [ENSG00000186704.9] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000234840.2] WARNING, no entry stored in dbm for [ENSG00000226548.1] WARNING, no entry stored in dbm for [ENSG00000273297.2] WARNING, no entry stored in dbm for [ENSG00000250635.1] WARNING, no entry stored in dbm for [ENSG00000260390.1] WARNING, no entry stored in dbm for [ENSG00000269001.2] WARNING, no entry stored in dbm for [ENSG00000174407.13] WARNING, no entry stored in dbm for [ENSG00000239480.1] WARNING, no entry stored in dbm for [ENSG00000235205.1] WARNING, no entry stored in dbm for [ENSG00000278932.4] WARNING, no entry stored in dbm for [ENSG00000226976.3] WARNING, no entry stored in dbm for [ENSG00000216809.1] WARNING, no entry stored in dbm for [ENSG00000214428.3] WARNING, no entry stored in dbm for [ENSG00000259755.1] WARNING, no entry stored in dbm for [ENSG00000236607.3] WARNING, no entry stored in dbm for [ENSG00000226312.7] WARNING, no entry stored in dbm for [ENSG00000227617.9] WARNING, no entry stored in dbm for [ENSG00000230681.1] WARNING, no entry stored in dbm for [ENSG00000223773.7] WARNING, no entry stored in dbm for [ENSG00000178722.13] WARNING, no entry stored in dbm for [ENSG00000287151.1] WARNING, no entry stored in dbm for [ENSG00000286626.1] WARNING, no entry stored in dbm for [ENSG00000280424.1] WARNING, no entry stored in dbm for [ENSG00000216657.1] WARNING, no entry stored in dbm for [ENSG00000263647.1] WARNING, no entry stored in dbm for [ENSG00000230648.1] WARNING, no entry stored in dbm for [ENSG00000249993.1] WARNING, no entry stored in dbm for [ENSG00000226066.1] WARNING, no entry stored in dbm for [ENSG00000234996.4] WARNING, no entry stored in dbm for [ENSG00000233343.1] WARNING, no entry stored in dbm for [ENSG00000287934.1] WARNING, no entry stored in dbm for [ENSG00000272028.1] WARNING, no entry stored in dbm for [ENSG00000207190.1] WARNING, no entry stored in dbm for [ENSG00000200108.1] WARNING, no entry stored in dbm for [ENSG00000206772.1] WARNING, no entry stored in dbm for [ENSG00000202089.1] WARNING, no entry stored in dbm for [ENSG00000242779.7] WARNING, no entry stored in dbm for [ENSG00000261505.1] WARNING, no entry stored in dbm for [ENSG00000244560.7] WARNING, no entry stored in dbm for [ENSG00000287278.1] WARNING, no entry stored in dbm for [ENSG00000286548.1] WARNING, no entry stored in dbm for [ENSG00000245552.7] WARNING, no entry stored in dbm for [ENSG00000224431.1] WARNING, no entry stored in dbm for [ENSG00000287338.1] WARNING, no entry stored in dbm for [ENSG00000232576.2] WARNING, no entry stored in dbm for [ENSG00000287368.1] WARNING, no entry stored in dbm for [ENSG00000225096.3] WARNING, no entry stored in dbm for [ENSG00000227619.3] WARNING, no entry stored in dbm for [ENSG00000197670.6] WARNING, no entry stored in dbm for [ENSG00000273162.1] WARNING, no entry stored in dbm for [ENSG00000224886.2] WARNING, no entry stored in dbm for [ENSG00000237301.1] WARNING, no entry stored in dbm for [ENSG00000226310.1] WARNING, no entry stored in dbm for [ENSG00000247130.2] WARNING, no entry stored in dbm for [ENSG00000286578.1] WARNING, no entry stored in dbm for [ENSG00000235181.1] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000223809.1] WARNING, no entry stored in dbm for [ENSG00000249592.6] WARNING, no entry stored in dbm for [ENSG00000250999.2] WARNING, no entry stored in dbm for [ENSG00000250999.2] WARNING, no entry stored in dbm for [ENSG00000278212.2] WARNING, no entry stored in dbm for [ENSG00000278791.1] WARNING, no entry stored in dbm for [ENSG00000239572.3] WARNING, no entry stored in dbm for [ENSG00000249684.6] WARNING, no entry stored in dbm for [ENSG00000251314.2] WARNING, no entry stored in dbm for [ENSG00000224016.2] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000259418.1] WARNING, no entry stored in dbm for [ENSG00000264151.6] WARNING, no entry stored in dbm for [ENSG00000279259.1] WARNING, no entry stored in dbm for [ENSG00000253571.1] WARNING, no entry stored in dbm for [ENSG00000260290.2] WARNING, no entry stored in dbm for [ENSG00000266208.1] WARNING, no entry stored in dbm for [ENSG00000229212.8] WARNING, no entry stored in dbm for [ENSG00000260693.1] WARNING, no entry stored in dbm for [ENSG00000251131.2] WARNING, no entry stored in dbm for [ENSG00000259429.5] WARNING, no entry stored in dbm for [ENSG00000259390.4] WARNING, no entry stored in dbm for [ENSG00000272800.3] WARNING, no entry stored in dbm for [ENSG00000259407.1] WARNING, no entry stored in dbm for [ENSG00000281896.1] WARNING, no entry stored in dbm for [ENSG00000274525.1] WARNING, no entry stored in dbm for [ENSG00000269032.1] WARNING, no entry stored in dbm for [ENSG00000184319.16] WARNING, no entry stored in dbm for [ENSG00000287292.1] WARNING, no entry stored in dbm for [ENSG00000235583.2] WARNING, no entry stored in dbm for [ENSG00000255595.5] WARNING, no entry stored in dbm for [ENSG00000258513.1] WARNING, no entry stored in dbm for [ENSG00000279726.2] WARNING, no entry stored in dbm for [ENSG00000277476.1] WARNING, no entry stored in dbm for [ENSG00000262265.2] WARNING, no entry stored in dbm for [ENSG00000247137.9] * STAR-Fusion complete. See output: /tmp/nxf.bNamvMJxvK/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)