-ctat genome lib [/tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.m2StCavQz7/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.m2StCavQz7/./star-fusion.preliminary -sample contains 143717665 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir -J /tmp/nxf.m2StCavQz7/dna_s760.Chimeric.out.junction -O /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.m2StCavQz7/dna_s760.Chimeric.out.junction -building interval tree based on /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=52173.91/min [30000], rate=48648.65/min [40000], rate=47058.82/min [50000], rate=45454.55/min [60000], rate=45000.00/min [70000], rate=45161.29/min [80000], rate=44859.81/min [90000], rate=45378.15/min [100000], rate=46511.63/min [110000], rate=46808.51/min [120000], rate=47368.42/min [130000], rate=47852.76/min [140000], rate=48554.91/min [150000], rate=49450.55/min [160000], rate=49230.77/min [170000], rate=47222.22/min [180000], rate=45762.71/min [190000], rate=44705.88/min [200000], rate=43795.62/min [210000], rate=43448.28/min [220000], rate=43564.36/min [230000], rate=43670.89/min [240000], rate=43769.00/min [250000], rate=44117.65/min [260000], rate=44571.43/min [270000], rate=45000.00/min [280000], rate=45405.41/min [290000], rate=45789.47/min [300000], rate=46391.75/min [310000], rate=46969.70/min [320000], rate=47290.64/min [330000], rate=46698.11/min [340000], rate=46681.92/min [350000], rate=46666.67/min [360000], rate=46551.72/min [370000], rate=46638.66/min [380000], rate=46721.31/min [390000], rate=46800.00/min [400000], rate=47151.28/min [410000], rate=47398.84/min [420000], rate=47637.05/min [430000], rate=47955.39/min [440000], rate=48175.18/min [450000], rate=47957.37/min [460000], rate=47916.67/min [470000], rate=47796.61/min [480000], rate=47840.53/min [490000], rate=47960.85/min [500000], rate=48000.00/min [510000], rate=48113.21/min [520000], rate=48297.21/min [530000], rate=48401.83/min [540000], rate=48502.99/min [550000], rate=48672.57/min [560000], rate=48979.59/min [570000], rate=49279.54/min [580000], rate=49361.70/min [590000], rate=49235.05/min [600000], rate=49180.33/min [610000], rate=49193.55/min [620000], rate=49271.52/min [630000], rate=49347.26/min [640000], rate=49420.85/min [650000], rate=49618.32/min [660000], rate=49748.74/min [670000], rate=49875.93/min [680000], rate=50000.00/min [690000], rate=50242.72/min [700000], rate=50480.77/min [710000], rate=50653.98/min [720000], rate=50883.39/min -building interval tree based on /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=42857.14/min [20000], rate=44444.44/min [30000], rate=46153.85/min [40000], rate=47058.82/min [50000], rate=49180.33/min [60000], rate=50704.23/min [70000], rate=52500.00/min [80000], rate=52173.91/min [90000], rate=51923.08/min [100000], rate=51724.14/min [110000], rate=52380.95/min [120000], rate=52554.74/min [130000], rate=52702.70/min [140000], rate=53846.15/min [150000], rate=54878.05/min [160000], rate=57485.03/min [170000], rate=60000.00/min [180000], rate=60335.20/min [190000], rate=60000.00/min [200000], rate=60301.51/min [210000], rate=60576.92/min [220000], rate=60000.00/min [230000], rate=59740.26/min [240000], rate=59751.04/min [250000], rate=59523.81/min [260000], rate=59315.59/min [270000], rate=59340.66/min [280000], rate=58741.26/min [290000], rate=57049.18/min [300000], rate=55900.62/min [310000], rate=55029.59/min [320000], rate=54084.51/min [330000], rate=53513.51/min [340000], rate=53125.00/min [350000], rate=52631.58/min [360000], rate=51923.08/min [370000], rate=51627.91/min [380000], rate=51467.27/min [390000], rate=51315.79/min [400000], rate=51391.86/min [410000], rate=51356.99/min [420000], rate=51639.34/min [430000], rate=51807.23/min [440000], rate=52173.91/min [450000], rate=52224.37/min [460000], rate=51879.70/min [470000], rate=51553.93/min [480000], rate=51428.57/min [490000], rate=51219.51/min [500000], rate=51194.54/min [510000], rate=51170.57/min [520000], rate=51063.83/min [530000], rate=51043.34/min [540000], rate=51023.62/min [550000], rate=51083.59/min [560000], rate=51141.55/min [570000], rate=51351.35/min [580000], rate=51327.43/min [590000], rate=51453.49/min [600000], rate=51063.83/min [610000], rate=50622.41/min [620000], rate=50202.43/min [630000], rate=49868.07/min [640000], rate=49548.39/min [650000], rate=49304.68/min [660000], rate=49070.63/min [670000], rate=48905.11/min [680000], rate=48920.86/min [690000], rate=48936.17/min [700000], rate=49065.42/min [710000], rate=49248.55/min [720000], rate=49427.92/min -building interval tree based on /tmp/nxf.m2StCavQz7/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=66666.67/min [30000], rate=64285.71/min [40000], rate=55813.95/min [50000], rate=50847.46/min [60000], rate=48648.65/min [70000], rate=48275.86/min [80000], rate=48979.59/min [90000], rate=50000.00/min [100000], rate=50420.17/min [110000], rate=49624.06/min [120000], rate=49315.07/min [130000], rate=48447.20/min [140000], rate=48000.00/min [150000], rate=47872.34/min [160000], rate=48000.00/min [170000], rate=48571.43/min [180000], rate=49315.07/min [190000], rate=50220.26/min [200000], rate=50420.17/min [210000], rate=51428.57/min [220000], rate=50574.71/min [230000], rate=50000.00/min [240000], rate=49484.54/min [250000], rate=49180.33/min [260000], rate=48902.82/min [270000], rate=49090.91/min [280000], rate=49266.86/min [290000], rate=49431.82/min [300000], rate=49723.76/min [310000], rate=50134.77/min [320000], rate=49870.13/min [330000], rate=49253.73/min [340000], rate=48687.35/min [350000], rate=48387.10/min [360000], rate=48322.15/min [370000], rate=48260.87/min [380000], rate=48000.00/min [390000], rate=47755.10/min [400000], rate=47808.76/min [410000], rate=47953.22/min [420000], rate=48183.56/min [430000], rate=48496.24/min [440000], rate=48708.49/min [450000], rate=48824.59/min [460000], rate=48936.17/min [470000], rate=49214.66/min [480000], rate=49569.71/min [490000], rate=49915.11/min [500000], rate=49668.87/min [510000], rate=49196.14/min [520000], rate=48750.00/min [530000], rate=48475.61/min [540000], rate=48502.99/min [550000], rate=48316.25/min [560000], rate=48206.60/min [570000], rate=48236.95/min [580000], rate=48400.56/min [590000], rate=48760.33/min [600000], rate=48714.48/min [610000], rate=48348.75/min [620000], rate=48062.02/min [630000], rate=47848.10/min [640000], rate=47642.68/min [650000], rate=47387.61/min [660000], rate=47255.37/min [670000], rate=47127.78/min [680000], rate=47058.82/min [690000], rate=46992.05/min [700000], rate=46927.37/min [710000], rate=46864.69/min [720000], rate=46905.54/min -building interval tree based on /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=150000.00/min [20000], rate=120000.00/min [30000], rate=94736.84/min [40000], rate=109090.91/min [50000], rate=100000.00/min [60000], rate=60000.00/min [70000], rate=45652.17/min [80000], rate=40336.13/min [90000], rate=37762.24/min [100000], rate=36363.64/min [110000], rate=35294.12/min [120000], rate=34615.38/min [130000], rate=34361.23/min [140000], rate=34426.23/min [150000], rate=34351.15/min [160000], rate=34532.37/min [170000], rate=34693.88/min [180000], rate=34951.46/min [190000], rate=34969.33/min [200000], rate=34782.61/min [210000], rate=34710.74/min [220000], rate=35013.26/min [230000], rate=35294.12/min [240000], rate=35732.01/min [250000], rate=36231.88/min [260000], rate=36705.88/min [270000], rate=37327.19/min [280000], rate=37752.81/min [290000], rate=38495.58/min [300000], rate=38876.89/min [310000], rate=39075.63/min [320000], rate=39344.26/min [330000], rate=39600.00/min [340000], rate=40078.59/min [350000], rate=40462.43/min [360000], rate=40831.76/min [370000], rate=41111.11/min [380000], rate=41379.31/min [390000], rate=41785.71/min [400000], rate=42179.26/min [410000], rate=42708.33/min [420000], rate=43224.70/min [430000], rate=43143.81/min [440000], rate=42857.14/min [450000], rate=42654.03/min [460000], rate=42526.96/min [470000], rate=42598.19/min [480000], rate=42603.55/min [490000], rate=42608.70/min [500000], rate=42674.25/min [510000], rate=42857.14/min [520000], rate=43093.92/min [530000], rate=43265.31/min [540000], rate=43548.39/min [550000], rate=43708.61/min [560000], rate=43467.01/min [570000], rate=43401.02/min [580000], rate=43337.48/min [590000], rate=43170.73/min [600000], rate=43010.75/min [610000], rate=43008.23/min [620000], rate=43205.57/min [630000], rate=43298.97/min [640000], rate=43438.91/min [650000], rate=43673.01/min [660000], rate=43902.44/min [670000], rate=44224.42/min [680000], rate=44492.91/min [690000], rate=44660.19/min [700000], rate=44871.79/min [710000], rate=45127.12/min [720000], rate=45378.15/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir --filt_file /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 3000000.00 reads per min processed... 4000000.00 reads per min processed... 4500000.00 reads per min processed... 4000000.00 reads per min processed... 4285714.29 reads per min processed... 4500000.00 reads per min processed... 4200000.00 reads per min processed... 4363636.36 reads per min processed... 4500000.00 reads per min processed... 4285714.29 reads per min processed... 4400000.00 reads per min processed... 4500000.00 reads per min processed... 4588235.29 reads per min processed... 4421052.63 reads per min processed... 4500000.00 reads per min processed... 4571428.57 reads per min processed... 4636363.64 reads per min processed... 4695652.17 reads per min processed... 4750000.00 reads per min processed... 4615384.62 reads per min processed... 4666666.67 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.m2StCavQz7/dna_s760.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.m2StCavQz7/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -165494.376868 EM: Round [1] log likelihood: -165407.531308 EM: Round [2] log likelihood: -165381.165897 EM: Round [3] log likelihood: -165370.034167 EM: Round [4] log likelihood: -165364.501207 EM: Round [5] log likelihood: -165361.471309 EM: Round [6] log likelihood: -165359.690341 EM: Round [7] log likelihood: -165358.578849 EM: Round [8] log likelihood: -165357.847349 EM: Round [9] log likelihood: -165357.342930 EM: Round [10] log likelihood: -165356.980855 EM: Round [11] log likelihood: -165356.712002 EM: Round [12] log likelihood: -165356.506645 EM: Round [13] log likelihood: -165356.346057 EM: Round [14] log likelihood: -165356.217984 EM: Round [15] log likelihood: -165356.114138 EM: Round [16] log likelihood: -165356.028738 EM: Round [17] log likelihood: -165355.957645 EM: Round [18] log likelihood: -165355.897827 EM: Round [19] log likelihood: -165355.847019 EM: Round [20] log likelihood: -165355.803499 EM: Round [21] log likelihood: -165355.765938 EM: Round [22] log likelihood: -165355.733298 EM: Round [23] log likelihood: -165355.704758 EM: Round [24] log likelihood: -165355.679661 EM: Round [25] log likelihood: -165355.657478 EM: Round [26] log likelihood: -165355.637777 EM: Round [27] log likelihood: -165355.620204 EM: Round [28] log likelihood: -165355.604468 EM: Round [29] log likelihood: -165355.590325 EM: Round [30] log likelihood: -165355.577570 EM: Round [31] log likelihood: -165355.566033 EM: Round [32] log likelihood: -165355.555568 EM: Round [33] log likelihood: -165355.546049 EM: Round [34] log likelihood: -165355.537371 EM: Round [35] log likelihood: -165355.529442 EM: Round [36] log likelihood: -165355.522182 EM: Round [37] log likelihood: -165355.515522 EM: Round [38] log likelihood: -165355.509401 EM: Round [39] log likelihood: -165355.503768 EM: Round [40] log likelihood: -165355.498575 EM: Round [41] log likelihood: -165355.493781 EM: Round [42] log likelihood: -165355.489350 EM: Round [43] log likelihood: -165355.485249 EM: Round [44] log likelihood: -165355.481450 EM: Round [45] log likelihood: -165355.477926 EM: Round [46] log likelihood: -165355.474654 EM: Round [47] log likelihood: -165355.471615 EM: Round [48] log likelihood: -165355.468788 EM: Round [49] log likelihood: -165355.466157 EM: Round [50] log likelihood: -165355.463706 EM: Round [51] log likelihood: -165355.461422 EM: Round [52] log likelihood: -165355.459292 EM: Round [53] log likelihood: -165355.457304 EM: Round [54] log likelihood: -165355.455447 EM: Round [55] log likelihood: -165355.453713 EM: Round [56] log likelihood: -165355.452092 EM: Round [57] log likelihood: -165355.450577 EM: Round [58] log likelihood: -165355.449159 EM: Round [59] log likelihood: -165355.447832 EM: Round [60] log likelihood: -165355.446590 EM: Round [61] log likelihood: -165355.445426 EM: Round [62] log likelihood: -165355.444336 EM: Round [63] log likelihood: -165355.443315 EM: Round [64] log likelihood: -165355.442357 EM: Round [65] log likelihood: -165355.441459 EM: Round [66] log likelihood: -165355.440617 EM: Round [67] log likelihood: -165355.439827 EM: Round [68] log likelihood: -165355.439086 EM: Round [69] log likelihood: -165355.438391 EM: Round [70] log likelihood: -165355.437738 EM: Round [71] log likelihood: -165355.437125 EM: Round [72] log likelihood: -165355.436549 EM: Round [73] log likelihood: -165355.436009 EM: Round [74] log likelihood: -165355.435501 EM: Round [75] log likelihood: -165355.435024 EM: Round [76] log likelihood: -165355.434576 EM: Round [77] log likelihood: -165355.434155 EM: Round [78] log likelihood: -165355.433759 EM: Round [79] log likelihood: -165355.433387 EM: Round [80] log likelihood: -165355.433038 EM: Round [81] log likelihood: -165355.432709 EM: Round [82] log likelihood: -165355.432400 EM: Round [83] log likelihood: -165355.432110 EM: Round [84] log likelihood: -165355.431837 EM: Round [85] log likelihood: -165355.431580 EM: Round [86] log likelihood: -165355.431339 EM: Round [87] log likelihood: -165355.431112 EM: Round [88] log likelihood: -165355.430898 EM: Round [89] log likelihood: -165355.430698 EM: Round [90] log likelihood: -165355.430509 EM: Round [91] log likelihood: -165355.430331 EM: Round [92] log likelihood: -165355.430164 EM: Round [93] log likelihood: -165355.430007 EM: Round [94] log likelihood: -165355.429859 EM: Round [95] log likelihood: -165355.429720 EM: Round [96] log likelihood: -165355.429589 EM: Round [97] log likelihood: -165355.429466 EM: Round [98] log likelihood: -165355.429350 EM: Round [99] log likelihood: -165355.429241 EM: Round [100] log likelihood: -165355.429139 EM: Round [101] log likelihood: -165355.429043 EM: Stopping iterations at round 101 due to insufficient improvement in likelihood. EM: Starting log likelihood: -165488.373087 EM: Round [1] log likelihood: -165403.193982 EM: Round [2] log likelihood: -165378.046574 EM: Round [3] log likelihood: -165367.787716 EM: Round [4] log likelihood: -165362.838060 EM: Round [5] log likelihood: -165360.188109 EM: Round [6] log likelihood: -165358.657460 EM: Round [7] log likelihood: -165357.716926 EM: Round [8] log likelihood: -165357.107826 EM: Round [9] log likelihood: -165356.695340 EM: Round [10] log likelihood: -165356.405320 EM: Round [11] log likelihood: -165356.194967 EM: Round [12] log likelihood: -165356.038452 EM: Round [13] log likelihood: -165355.919530 EM: Round [14] log likelihood: -165355.827604 EM: Round [15] log likelihood: -165355.755523 EM: Round [16] log likelihood: -165355.698319 EM: Round [17] log likelihood: -165355.652457 EM: Round [18] log likelihood: -165355.615363 EM: Round [19] log likelihood: -165355.585129 EM: Round [20] log likelihood: -165355.560319 EM: Round [21] log likelihood: -165355.539836 EM: Round [22] log likelihood: -165355.522834 EM: Round [23] log likelihood: -165355.508652 EM: Round [24] log likelihood: -165355.496770 EM: Round [25] log likelihood: -165355.486774 EM: Round [26] log likelihood: -165355.478335 EM: Round [27] log likelihood: -165355.471186 EM: Round [28] log likelihood: -165355.465111 EM: Round [29] log likelihood: -165355.459935 EM: Round [30] log likelihood: -165355.455513 EM: Round [31] log likelihood: -165355.451727 EM: Round [32] log likelihood: -165355.448478 EM: Round [33] log likelihood: -165355.445686 EM: Round [34] log likelihood: -165355.443280 EM: Round [35] log likelihood: -165355.441206 EM: Round [36] log likelihood: -165355.439414 EM: Round [37] log likelihood: -165355.437864 EM: Round [38] log likelihood: -165355.436522 EM: Round [39] log likelihood: -165355.435358 EM: Round [40] log likelihood: -165355.434348 EM: Round [41] log likelihood: -165355.433471 EM: Round [42] log likelihood: -165355.432709 EM: Round [43] log likelihood: -165355.432046 EM: Round [44] log likelihood: -165355.431469 EM: Round [45] log likelihood: -165355.430966 EM: Round [46] log likelihood: -165355.430528 EM: Round [47] log likelihood: -165355.430146 EM: Round [48] log likelihood: -165355.429813 EM: Round [49] log likelihood: -165355.429522 EM: Round [50] log likelihood: -165355.429268 EM: Round [51] log likelihood: -165355.429047 EM: Round [52] log likelihood: -165355.428853 EM: Round [53] log likelihood: -165355.428684 EM: Round [54] log likelihood: -165355.428536 EM: Round [55] log likelihood: -165355.428407 EM: Round [56] log likelihood: -165355.428294 EM: Round [57] log likelihood: -165355.428196 EM: Stopping iterations at round 57 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.m2StCavQz7/./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.m2StCavQz7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.m2StCavQz7/./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.m2StCavQz7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 143717665 > /tmp/nxf.m2StCavQz7/./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.m2StCavQz7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir > /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir --annotate /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.m2StCavQz7/./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.m2StCavQz7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir -done, see /tmp/nxf.m2StCavQz7/./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.m2StCavQz7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.m2StCavQz7/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 324, filtered: 12446) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.m2StCavQz7/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.m2StCavQz7/./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.m2StCavQz7/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000213280.2] WARNING, no entry stored in dbm for [ENSG00000267408.1] 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 [ENSG00000270788.1] WARNING, no entry stored in dbm for [ENSG00000249274.1] WARNING, no entry stored in dbm for [ENSG00000229739.4] 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 [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000288002.1] 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 [IGH-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000277702.1] WARNING, no entry stored in dbm for [ENSG00000277146.1] 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 [ENSG00000255276.1] WARNING, no entry stored in dbm for [ENSG00000257139.1] WARNING, no entry stored in dbm for [ENSG00000255276.1] WARNING, no entry stored in dbm for [ENSG00000257139.1] WARNING, no entry stored in dbm for [ENSG00000255276.1] WARNING, no entry stored in dbm for [ENSG00000257139.1] WARNING, no entry stored in dbm for [ENSG00000255276.1] WARNING, no entry stored in dbm for [ENSG00000257139.1] WARNING, no entry stored in dbm for [ENSG00000287721.1] WARNING, no entry stored in dbm for [ENSG00000254543.1] 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 [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 [ENSG00000279641.1] 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 [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000248441.7] WARNING, no entry stored in dbm for [ENSG00000269235.2] WARNING, no entry stored in dbm for [ENSG00000185182.14] WARNING, no entry stored in dbm for [ENSG00000249963.1] WARNING, no entry stored in dbm for [ENSG00000270641.1] WARNING, no entry stored in dbm for [ENSG00000253563.2] 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 [ENSG00000234405.2] WARNING, no entry stored in dbm for [ENSG00000234405.2] WARNING, no entry stored in dbm for [ENSG00000237356.7] WARNING, no entry stored in dbm for [ENSG00000235917.1] WARNING, no entry stored in dbm for [ENSG00000238062.6] WARNING, no entry stored in dbm for [ENSG00000245498.7] WARNING, no entry stored in dbm for [ENSG00000232044.7] WARNING, no entry stored in dbm for [ENSG00000282668.1] WARNING, no entry stored in dbm for [ENSG00000238116.2] WARNING, no entry stored in dbm for [ENSG00000229391.7] WARNING, no entry stored in dbm for [ENSG00000223883.2] WARNING, no entry stored in dbm for [ENSG00000228956.8] WARNING, no entry stored in dbm for [ENSG00000249244.1] WARNING, no entry stored in dbm for [ENSG00000257122.5] WARNING, no entry stored in dbm for [ENSG00000258203.5] WARNING, no entry stored in dbm for [ENSG00000249859.12] WARNING, no entry stored in dbm for [ENSG00000203307.2] WARNING, no entry stored in dbm for [ENSG00000250519.7] WARNING, no entry stored in dbm for [ENSG00000256347.1] WARNING, no entry stored in dbm for [ENSG00000250462.8] WARNING, no entry stored in dbm for [ENSG00000172965.17] WARNING, no entry stored in dbm for [ENSG00000261014.2] WARNING, no entry stored in dbm for [ENSG00000237401.8] WARNING, no entry stored in dbm for [ENSG00000224722.3] WARNING, no entry stored in dbm for [ENSG00000258027.2] WARNING, no entry stored in dbm for [ENSG00000231933.7] WARNING, no entry stored in dbm for [ENSG00000233355.7] WARNING, no entry stored in dbm for [ENSG00000215386.13] WARNING, no entry stored in dbm for [ENSG00000261313.2] WARNING, no entry stored in dbm for [ENSG00000224430.2] WARNING, no entry stored in dbm for [ENSG00000236053.1] WARNING, no entry stored in dbm for [ENSG00000198358.4] WARNING, no entry stored in dbm for [ENSG00000232285.1] WARNING, no entry stored in dbm for [ENSG00000233086.8] WARNING, no entry stored in dbm for [ENSG00000256422.6] WARNING, no entry stored in dbm for [ENSG00000260976.2] WARNING, no entry stored in dbm for [ENSG00000203356.2] WARNING, no entry stored in dbm for [ENSG00000236204.6] WARNING, no entry stored in dbm for [ENSG00000223823.1] WARNING, no entry stored in dbm for [ENSG00000250331.2] WARNING, no entry stored in dbm for [ENSG00000274020.4] WARNING, no entry stored in dbm for [ENSG00000251320.1] WARNING, no entry stored in dbm for [ENSG00000254363.6] WARNING, no entry stored in dbm for [ENSG00000258036.2] WARNING, no entry stored in dbm for [ENSG00000236982.1] WARNING, no entry stored in dbm for [ENSG00000241527.1] WARNING, no entry stored in dbm for [ENSG00000262714.1] WARNING, no entry stored in dbm for [ENSG00000229976.2] WARNING, no entry stored in dbm for [ENSG00000285758.2] WARNING, no entry stored in dbm for [ENSG00000278301.1] WARNING, no entry stored in dbm for [ENSG00000279233.1] WARNING, no entry stored in dbm for [ENSG00000248425.1] WARNING, no entry stored in dbm for [ENSG00000266573.6] WARNING, no entry stored in dbm for [ENSG00000196295.12] WARNING, no entry stored in dbm for [ENSG00000260005.6] WARNING, no entry stored in dbm for [ENSG00000286032.1] WARNING, no entry stored in dbm for [ENSG00000225121.2] WARNING, no entry stored in dbm for [ENSG00000228502.1] WARNING, no entry stored in dbm for [ENSG00000260158.1] WARNING, no entry stored in dbm for [ENSG00000253833.1] WARNING, no entry stored in dbm for [ENSG00000256508.2] WARNING, no entry stored in dbm for [ENSG00000213050.5] WARNING, no entry stored in dbm for [ENSG00000237470.3] WARNING, no entry stored in dbm for [ENSG00000251216.2] WARNING, no entry stored in dbm for [ENSG00000254119.5] WARNING, no entry stored in dbm for [ENSG00000229140.11] WARNING, no entry stored in dbm for [ENSG00000259516.2] WARNING, no entry stored in dbm for [ENSG00000279851.2] WARNING, no entry stored in dbm for [ENSG00000224271.7] WARNING, no entry stored in dbm for [ENSG00000273828.2] WARNING, no entry stored in dbm for [ENSG00000260062.3] 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 [ENSG00000233747.1] WARNING, no entry stored in dbm for [ENSG00000259087.5] WARNING, no entry stored in dbm for [ENSG00000281450.1] WARNING, no entry stored in dbm for [ENSG00000273119.1] WARNING, no entry stored in dbm for [ENSG00000255273.1] WARNING, no entry stored in dbm for [ENSG00000204818.4] WARNING, no entry stored in dbm for [ENSG00000242017.1] WARNING, no entry stored in dbm for [ENSG00000261826.1] WARNING, no entry stored in dbm for [ENSG00000271457.1] WARNING, no entry stored in dbm for [ENSG00000226149.6] WARNING, no entry stored in dbm for [ENSG00000220685.3] WARNING, no entry stored in dbm for [ENSG00000280135.1] WARNING, no entry stored in dbm for [ENSG00000280135.1] WARNING, no entry stored in dbm for [ENSG00000280135.1] WARNING, no entry stored in dbm for [ENSG00000258743.6] WARNING, no entry stored in dbm for [ENSG00000229186.4] WARNING, no entry stored in dbm for [ENSG00000273773.1] WARNING, no entry stored in dbm for [ENSG00000277304.1] WARNING, no entry stored in dbm for [ENSG00000197815.4] WARNING, no entry stored in dbm for [ENSG00000279834.1] WARNING, no entry stored in dbm for [ENSG00000215288.5] WARNING, no entry stored in dbm for [ENSG00000280449.1] WARNING, no entry stored in dbm for [ENSG00000255511.1] WARNING, no entry stored in dbm for [ENSG00000176134.5] WARNING, no entry stored in dbm for [ENSG00000255750.6] WARNING, no entry stored in dbm for [ENSG00000240418.1] WARNING, no entry stored in dbm for [ENSG00000257674.1] WARNING, no entry stored in dbm for [ENSG00000278083.1] WARNING, no entry stored in dbm for [ENSG00000279235.1] WARNING, no entry stored in dbm for [ENSG00000229020.4] WARNING, no entry stored in dbm for [ENSG00000213798.3] 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 [IGL-.g@-ext] * STAR-Fusion complete. See output: /tmp/nxf.m2StCavQz7/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)