-ctat genome lib [/tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.brWW81FQZF/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.brWW81FQZF/./star-fusion.preliminary -sample contains 51694326 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir -J /tmp/nxf.brWW81FQZF/tih_rna_sample_00679_B23MVV7LT4_1.Chimeric.out.junction -O /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.brWW81FQZF/tih_rna_sample_00679_B23MVV7LT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=37500.00/min [20000], rate=41379.31/min [30000], rate=43902.44/min [40000], rate=48000.00/min [50000], rate=51724.14/min [60000], rate=52941.18/min [70000], rate=51219.51/min [80000], rate=50000.00/min [90000], rate=49090.91/min [100000], rate=48780.49/min [110000], rate=49624.06/min [120000], rate=50704.23/min [130000], rate=51655.63/min [140000], rate=52830.19/min [150000], rate=53892.22/min [160000], rate=55172.41/min [170000], rate=56666.67/min [180000], rate=55384.62/min [190000], rate=54545.45/min [200000], rate=53811.66/min [210000], rate=52941.18/min [220000], rate=52589.64/min [230000], rate=52075.47/min [240000], rate=51612.90/min [250000], rate=51546.39/min [260000], rate=51827.24/min [270000], rate=52258.06/min [280000], rate=52830.19/min [290000], rate=53538.46/min [300000], rate=53412.46/min [310000], rate=52394.37/min [320000], rate=51752.02/min [330000], rate=51697.13/min [340000], rate=51515.15/min [350000], rate=51470.59/min [360000], rate=51428.57/min [370000], rate=51388.89/min [380000], rate=51351.35/min [390000], rate=51541.85/min [400000], rate=51724.14/min [410000], rate=51898.73/min [420000], rate=52173.91/min [430000], rate=52545.82/min [440000], rate=53118.71/min [450000], rate=53571.43/min [460000], rate=53281.85/min [470000], rate=53007.52/min [480000], rate=53038.67/min [490000], rate=53068.59/min [500000], rate=53097.35/min [510000], rate=53125.00/min [520000], rate=53333.33/min [530000], rate=53535.35/min [540000], rate=53910.15/min [550000], rate=54545.45/min [560000], rate=55172.41/min [570000], rate=55700.33/min [580000], rate=55858.75/min [590000], rate=55660.38/min [600000], rate=55555.56/min [610000], rate=55538.69/min [620000], rate=55522.39/min [630000], rate=55752.21/min [640000], rate=55976.68/min [650000], rate=56358.38/min [660000], rate=56733.52/min [670000], rate=56619.72/min [680000], rate=56588.07/min [690000], rate=56480.22/min [700000], rate=56527.59/min [710000], rate=56573.71/min [720000], rate=56842.11/min [730000], rate=57105.61/min [740000], rate=57438.55/min -building interval tree based on /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.13 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=75000.00/min [30000], rate=69230.77/min [40000], rate=68571.43/min [50000], rate=71428.57/min [60000], rate=75000.00/min [70000], rate=68852.46/min [80000], rate=65753.42/min [90000], rate=64285.71/min [100000], rate=64516.13/min [110000], rate=65346.53/min [120000], rate=66055.05/min [130000], rate=67241.38/min [140000], rate=69421.49/min [150000], rate=71428.57/min [160000], rate=69565.22/min [170000], rate=68456.38/min [180000], rate=67924.53/min [190000], rate=68263.47/min [200000], rate=69364.16/min [210000], rate=70000.00/min [220000], rate=67346.94/min [230000], rate=64788.73/min [240000], rate=63157.89/min [250000], rate=61728.40/min [260000], rate=60231.66/min [270000], rate=58695.65/min [280000], rate=58333.33/min [290000], rate=58000.00/min [300000], rate=57692.31/min [310000], rate=57230.77/min [320000], rate=57142.86/min [330000], rate=56896.55/min [340000], rate=56509.70/min [350000], rate=56451.61/min [360000], rate=56544.50/min [370000], rate=56488.55/min [380000], rate=56575.68/min [390000], rate=56521.74/min [400000], rate=56206.09/min [410000], rate=56422.02/min [420000], rate=56629.21/min [430000], rate=56578.95/min [440000], rate=56410.26/min [450000], rate=56250.00/min [460000], rate=56211.81/min [470000], rate=56175.30/min [480000], rate=56250.00/min [490000], rate=56321.84/min [500000], rate=56390.98/min [510000], rate=56983.24/min [520000], rate=57352.94/min [530000], rate=56483.13/min [540000], rate=55670.10/min [550000], rate=55276.38/min [560000], rate=55081.97/min [570000], rate=54895.67/min [580000], rate=54631.08/min [590000], rate=54377.88/min [600000], rate=54135.34/min [610000], rate=54062.04/min [620000], rate=53835.02/min [630000], rate=53617.02/min [640000], rate=53481.89/min [650000], rate=53497.94/min [660000], rate=53658.54/min [670000], rate=53887.40/min [680000], rate=54183.27/min [690000], rate=54402.10/min [700000], rate=54616.38/min [710000], rate=54755.78/min [720000], rate=55031.85/min [730000], rate=55163.73/min [740000], rate=55430.71/min -building interval tree based on /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.13 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=44444.44/min [30000], rate=40909.09/min [40000], rate=40000.00/min [50000], rate=40000.00/min [60000], rate=40449.44/min [70000], rate=39622.64/min [80000], rate=39344.26/min [90000], rate=39416.06/min [100000], rate=40000.00/min [110000], rate=40740.74/min [120000], rate=41379.31/min [130000], rate=42162.16/min [140000], rate=43298.97/min [150000], rate=44776.12/min [160000], rate=44036.70/min [170000], rate=42323.65/min [180000], rate=41064.64/min [190000], rate=40425.53/min [200000], rate=40404.04/min [210000], rate=40384.62/min [220000], rate=40243.90/min [230000], rate=40350.88/min [240000], rate=40449.44/min [250000], rate=40650.41/min [260000], rate=41052.63/min [270000], rate=41538.46/min [280000], rate=41895.26/min [290000], rate=42647.06/min [300000], rate=43269.23/min [310000], rate=43971.63/min [320000], rate=44755.24/min [330000], rate=45622.12/min [340000], rate=46153.85/min [350000], rate=46563.19/min [360000], rate=47058.82/min [370000], rate=47639.48/min [380000], rate=48101.27/min [390000], rate=48851.77/min [400000], rate=49281.31/min [410000], rate=50000.00/min [420000], rate=50704.23/min [430000], rate=51292.25/min [440000], rate=51764.71/min [450000], rate=52224.37/min [460000], rate=52571.43/min [470000], rate=53007.52/min [480000], rate=53531.60/min [490000], rate=54044.12/min [500000], rate=54545.45/min [510000], rate=54937.16/min [520000], rate=55221.24/min [530000], rate=55594.41/min [540000], rate=55958.55/min [550000], rate=56122.45/min [560000], rate=56470.59/min [570000], rate=56905.16/min [580000], rate=57049.18/min [590000], rate=57096.77/min [600000], rate=57416.27/min [610000], rate=57728.71/min [620000], rate=58034.32/min [630000], rate=57886.68/min [640000], rate=57057.95/min [650000], rate=56358.38/min [660000], rate=56011.32/min [670000], rate=55601.66/min [680000], rate=55284.55/min [690000], rate=55200.00/min [700000], rate=55118.11/min [710000], rate=55109.96/min [720000], rate=55313.70/min [730000], rate=55583.76/min [740000], rate=55500.00/min -building interval tree based on /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.13 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=85714.29/min [30000], rate=94736.84/min [40000], rate=100000.00/min [50000], rate=96774.19/min [60000], rate=100000.00/min [70000], rate=102439.02/min [80000], rate=104347.83/min [90000], rate=108000.00/min [100000], rate=109090.91/min [110000], rate=108196.72/min [120000], rate=110769.23/min [130000], rate=111428.57/min [140000], rate=110526.32/min [150000], rate=111111.11/min [160000], rate=111627.91/min [170000], rate=113333.33/min [180000], rate=100000.00/min [190000], rate=88372.09/min [200000], rate=79470.20/min [210000], rate=72832.37/min [220000], rate=68041.24/min [230000], rate=63888.89/min [240000], rate=61016.95/min [250000], rate=59288.54/min [260000], rate=57992.57/min [270000], rate=56643.36/min [280000], rate=55813.95/min [290000], rate=54889.59/min [300000], rate=54380.66/min [310000], rate=53913.04/min [320000], rate=53333.33/min [330000], rate=53083.11/min [340000], rate=53125.00/min [350000], rate=53299.49/min [360000], rate=53731.34/min [370000], rate=54411.76/min [380000], rate=54807.69/min [390000], rate=54929.58/min [400000], rate=55045.87/min [410000], rate=54666.67/min [420000], rate=54782.61/min [430000], rate=54893.62/min [440000], rate=55114.82/min [450000], rate=55214.72/min [460000], rate=55533.20/min [470000], rate=55952.38/min [480000], rate=56470.59/min [490000], rate=55471.70/min [500000], rate=55045.87/min [510000], rate=54351.69/min [520000], rate=53700.52/min [530000], rate=53355.70/min [540000], rate=53114.75/min [550000], rate=53054.66/min [560000], rate=52830.19/min [570000], rate=52696.46/min [580000], rate=52488.69/min [590000], rate=52212.39/min [600000], rate=52173.91/min [610000], rate=52285.71/min [620000], rate=52542.37/min [630000], rate=52793.30/min [640000], rate=52530.78/min [650000], rate=51724.14/min [660000], rate=51295.34/min [670000], rate=51015.23/min [680000], rate=50809.46/min [690000], rate=50673.19/min [700000], rate=50541.52/min [710000], rate=50473.93/min [720000], rate=50526.32/min [730000], rate=50635.84/min [740000], rate=50742.86/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir --filt_file /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.brWW81FQZF/./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... 3600000.00 reads per min processed... 3428571.43 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 2823529.41 reads per min processed... 2700000.00 reads per min processed... 2727272.73 reads per min processed... 2750000.00 reads per min processed... 2666666.67 reads per min processed... 2689655.17 reads per min processed... 2709677.42 reads per min processed... 2647058.82 reads per min processed... 2742857.14 reads per min processed... 2833333.33 reads per min processed... 2769230.77 reads per min processed... 2780487.80 reads per min processed... 2790697.67 reads per min processed... 2800000.00 reads per min processed... 2808510.64 reads per min processed... 2816326.53 reads per min processed... 2769230.77 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.brWW81FQZF/tih_rna_sample_00679_B23MVV7LT4_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.brWW81FQZF/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -108355.415637 EM: Round [1] log likelihood: -108295.512936 EM: Round [2] log likelihood: -108270.032508 EM: Round [3] log likelihood: -108257.258897 EM: Round [4] log likelihood: -108250.432773 EM: Round [5] log likelihood: -108246.667635 EM: Round [6] log likelihood: -108244.531300 EM: Round [7] log likelihood: -108243.277153 EM: Round [8] log likelihood: -108242.510815 EM: Round [9] log likelihood: -108242.021813 EM: Round [10] log likelihood: -108241.695913 EM: Round [11] log likelihood: -108241.469618 EM: Round [12] log likelihood: -108241.306591 EM: Round [13] log likelihood: -108241.185344 EM: Round [14] log likelihood: -108241.092718 EM: Round [15] log likelihood: -108241.020363 EM: Round [16] log likelihood: -108240.962791 EM: Round [17] log likelihood: -108240.916275 EM: Round [18] log likelihood: -108240.878208 EM: Round [19] log likelihood: -108240.846716 EM: Round [20] log likelihood: -108240.820417 EM: Round [21] log likelihood: -108240.798276 EM: Round [22] log likelihood: -108240.779502 EM: Round [23] log likelihood: -108240.763479 EM: Round [24] log likelihood: -108240.749726 EM: Round [25] log likelihood: -108240.737857 EM: Round [26] log likelihood: -108240.727566 EM: Round [27] log likelihood: -108240.718602 EM: Round [28] log likelihood: -108240.710763 EM: Round [29] log likelihood: -108240.703880 EM: Round [30] log likelihood: -108240.697816 EM: Round [31] log likelihood: -108240.692454 EM: Round [32] log likelihood: -108240.687700 EM: Round [33] log likelihood: -108240.683472 EM: Round [34] log likelihood: -108240.679701 EM: Round [35] log likelihood: -108240.676329 EM: Round [36] log likelihood: -108240.673308 EM: Round [37] log likelihood: -108240.670595 EM: Round [38] log likelihood: -108240.668153 EM: Round [39] log likelihood: -108240.665951 EM: Round [40] log likelihood: -108240.663962 EM: Round [41] log likelihood: -108240.662162 EM: Round [42] log likelihood: -108240.660532 EM: Round [43] log likelihood: -108240.659052 EM: Round [44] log likelihood: -108240.657708 EM: Round [45] log likelihood: -108240.656485 EM: Round [46] log likelihood: -108240.655372 EM: Round [47] log likelihood: -108240.654357 EM: Round [48] log likelihood: -108240.653430 EM: Round [49] log likelihood: -108240.652584 EM: Round [50] log likelihood: -108240.651811 EM: Round [51] log likelihood: -108240.651104 EM: Round [52] log likelihood: -108240.650457 EM: Round [53] log likelihood: -108240.649864 EM: Round [54] log likelihood: -108240.649320 EM: Round [55] log likelihood: -108240.648822 EM: Round [56] log likelihood: -108240.648365 EM: Round [57] log likelihood: -108240.647946 EM: Round [58] log likelihood: -108240.647561 EM: Round [59] log likelihood: -108240.647207 EM: Round [60] log likelihood: -108240.646882 EM: Round [61] log likelihood: -108240.646583 EM: Round [62] log likelihood: -108240.646309 EM: Round [63] log likelihood: -108240.646056 EM: Round [64] log likelihood: -108240.645824 EM: Round [65] log likelihood: -108240.645610 EM: Round [66] log likelihood: -108240.645413 EM: Round [67] log likelihood: -108240.645232 EM: Round [68] log likelihood: -108240.645066 EM: Round [69] log likelihood: -108240.644912 EM: Round [70] log likelihood: -108240.644771 EM: Round [71] log likelihood: -108240.644640 EM: Round [72] log likelihood: -108240.644520 EM: Round [73] log likelihood: -108240.644410 EM: Round [74] log likelihood: -108240.644308 EM: Round [75] log likelihood: -108240.644214 EM: Stopping iterations at round 75 due to insufficient improvement in likelihood. EM: Starting log likelihood: -108317.611637 EM: Round [1] log likelihood: -108265.562592 EM: Round [2] log likelihood: -108243.913863 EM: Round [3] log likelihood: -108233.316823 EM: Round [4] log likelihood: -108227.749634 EM: Round [5] log likelihood: -108224.714919 EM: Round [6] log likelihood: -108223.008145 EM: Round [7] log likelihood: -108222.012820 EM: Round [8] log likelihood: -108221.407189 EM: Round [9] log likelihood: -108221.021191 EM: Round [10] log likelihood: -108220.763379 EM: Round [11] log likelihood: -108220.583407 EM: Round [12] log likelihood: -108220.452730 EM: Round [13] log likelihood: -108220.354611 EM: Round [14] log likelihood: -108220.278868 EM: Round [15] log likelihood: -108220.219065 EM: Round [16] log likelihood: -108220.170977 EM: Round [17] log likelihood: -108220.131727 EM: Round [18] log likelihood: -108220.099294 EM: Round [19] log likelihood: -108220.072215 EM: Round [20] log likelihood: -108220.049405 EM: Round [21] log likelihood: -108220.030041 EM: Round [22] log likelihood: -108220.013491 EM: Round [23] log likelihood: -108219.999260 EM: Round [24] log likelihood: -108219.986956 EM: Round [25] log likelihood: -108219.976263 EM: Round [26] log likelihood: -108219.966929 EM: Round [27] log likelihood: -108219.958747 EM: Round [28] log likelihood: -108219.951546 EM: Round [29] log likelihood: -108219.945186 EM: Round [30] log likelihood: -108219.939551 EM: Round [31] log likelihood: -108219.934541 EM: Round [32] log likelihood: -108219.930076 EM: Round [33] log likelihood: -108219.926085 EM: Round [34] log likelihood: -108219.922510 EM: Round [35] log likelihood: -108219.919300 EM: Round [36] log likelihood: -108219.916411 EM: Round [37] log likelihood: -108219.913806 EM: Round [38] log likelihood: -108219.911454 EM: Round [39] log likelihood: -108219.909326 EM: Round [40] log likelihood: -108219.907398 EM: Round [41] log likelihood: -108219.905649 EM: Round [42] log likelihood: -108219.904060 EM: Round [43] log likelihood: -108219.902614 EM: Round [44] log likelihood: -108219.901298 EM: Round [45] log likelihood: -108219.900098 EM: Round [46] log likelihood: -108219.899004 EM: Round [47] log likelihood: -108219.898004 EM: Round [48] log likelihood: -108219.897091 EM: Round [49] log likelihood: -108219.896256 EM: Round [50] log likelihood: -108219.895491 EM: Round [51] log likelihood: -108219.894791 EM: Round [52] log likelihood: -108219.894150 EM: Round [53] log likelihood: -108219.893561 EM: Round [54] log likelihood: -108219.893022 EM: Round [55] log likelihood: -108219.892527 EM: Round [56] log likelihood: -108219.892073 EM: Round [57] log likelihood: -108219.891656 EM: Round [58] log likelihood: -108219.891272 EM: Round [59] log likelihood: -108219.890920 EM: Round [60] log likelihood: -108219.890596 EM: Round [61] log likelihood: -108219.890299 EM: Round [62] log likelihood: -108219.890025 EM: Round [63] log likelihood: -108219.889773 EM: Round [64] log likelihood: -108219.889541 EM: Round [65] log likelihood: -108219.889328 EM: Round [66] log likelihood: -108219.889131 EM: Round [67] log likelihood: -108219.888950 EM: Round [68] log likelihood: -108219.888784 EM: Round [69] log likelihood: -108219.888631 EM: Round [70] log likelihood: -108219.888489 EM: Round [71] log likelihood: -108219.888359 EM: Round [72] log likelihood: -108219.888239 EM: Round [73] log likelihood: -108219.888129 EM: Round [74] log likelihood: -108219.888027 EM: Round [75] log likelihood: -108219.887933 EM: Stopping iterations at round 75 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.brWW81FQZF/./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.brWW81FQZF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.brWW81FQZF/./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.brWW81FQZF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 51694326 > /tmp/nxf.brWW81FQZF/./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.brWW81FQZF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir > /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir --annotate /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.brWW81FQZF/./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.brWW81FQZF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir -done, see /tmp/nxf.brWW81FQZF/./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.brWW81FQZF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.brWW81FQZF/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 830, filtered: 7625) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.brWW81FQZF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.brWW81FQZF/./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.brWW81FQZF/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000239268.3] 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 [ENSG00000237296.9] 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 [ENSG00000281641.3] WARNING, no entry stored in dbm for [ENSG00000060303.5] WARNING, no entry stored in dbm for [ENSG00000196796.5] WARNING, no entry stored in dbm for [ENSG00000274536.7] WARNING, no entry stored in dbm for [ENSG00000206702.1] WARNING, no entry stored in dbm for [ENSG00000204959.4] WARNING, no entry stored in dbm for [ENSG00000271162.1] WARNING, no entry stored in dbm for [ENSG00000196796.5] WARNING, no entry stored in dbm for [ENSG00000261499.2] WARNING, no entry stored in dbm for [ENSG00000229930.1] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000224016.2] WARNING, no entry stored in dbm for [ENSG00000261342.1] WARNING, no entry stored in dbm for [ENSG00000237004.4] WARNING, no entry stored in dbm for [ENSG00000228303.1] WARNING, no entry stored in dbm for [ENSG00000232354.8] WARNING, no entry stored in dbm for [ENSG00000222005.9] WARNING, no entry stored in dbm for [ENSG00000286943.1] WARNING, no entry stored in dbm for [ENSG00000282458.1] WARNING, no entry stored in dbm for [ENSG00000234769.7] WARNING, no entry stored in dbm for [ENSG00000232615.4] WARNING, no entry stored in dbm for [ENSG00000254287.1] WARNING, no entry stored in dbm for [ENSG00000127957.18] WARNING, no entry stored in dbm for [ENSG00000277741.4] WARNING, no entry stored in dbm for [ENSG00000235706.8] WARNING, no entry stored in dbm for [ENSG00000285470.1] WARNING, no entry stored in dbm for [ENSG00000205231.1] WARNING, no entry stored in dbm for [ENSG00000258384.1] WARNING, no entry stored in dbm for [ENSG00000270641.1] WARNING, no entry stored in dbm for [ENSG00000232894.1] WARNING, no entry stored in dbm for [ENSG00000248290.1] WARNING, no entry stored in dbm for [ENSG00000259647.1] WARNING, no entry stored in dbm for [ENSG00000230979.3] WARNING, no entry stored in dbm for [ENSG00000249859.12] WARNING, no entry stored in dbm for [ENSG00000175147.13] WARNING, no entry stored in dbm for [ENSG00000267686.2] WARNING, no entry stored in dbm for [ENSG00000128438.10] WARNING, no entry stored in dbm for [ENSG00000253320.7] WARNING, no entry stored in dbm for [ENSG00000247708.8] WARNING, no entry stored in dbm for [ENSG00000234918.1] WARNING, no entry stored in dbm for [ENSG00000237137.1] WARNING, no entry stored in dbm for [ENSG00000277072.5] WARNING, no entry stored in dbm for [ENSG00000254741.1] WARNING, no entry stored in dbm for [ENSG00000235281.2] WARNING, no entry stored in dbm for [ENSG00000269893.8] WARNING, no entry stored in dbm for [ENSG00000286864.1] WARNING, no entry stored in dbm for [ENSG00000251079.6] WARNING, no entry stored in dbm for [ENSG00000269904.2] WARNING, no entry stored in dbm for [ENSG00000262801.6] WARNING, no entry stored in dbm for [ENSG00000245958.6] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000228463.10] WARNING, no entry stored in dbm for [ENSG00000286511.1] WARNING, no entry stored in dbm for [ENSG00000255815.3] WARNING, no entry stored in dbm for [ENSG00000270830.1] WARNING, no entry stored in dbm for [ENSG00000227982.1] WARNING, no entry stored in dbm for [ENSG00000213075.7] WARNING, no entry stored in dbm for [ENSG00000242768.2] WARNING, no entry stored in dbm for [ENSG00000215444.2] WARNING, no entry stored in dbm for [ENSG00000230559.1] WARNING, no entry stored in dbm for [ENSG00000206975.1] WARNING, no entry stored in dbm for [ENSG00000236948.2] WARNING, no entry stored in dbm for [ENSG00000249418.2] WARNING, no entry stored in dbm for [ENSG00000260024.1] WARNING, no entry stored in dbm for [ENSG00000236770.1] WARNING, no entry stored in dbm for [ENSG00000214182.5] WARNING, no entry stored in dbm for [ENSG00000214176.9] WARNING, no entry stored in dbm for [ENSG00000257621.8] WARNING, no entry stored in dbm for [ENSG00000248927.1] WARNING, no entry stored in dbm for [ENSG00000228940.1] WARNING, no entry stored in dbm for [ENSG00000229442.2] WARNING, no entry stored in dbm for [ENSG00000200794.1] WARNING, no entry stored in dbm for [ENSG00000267302.5] WARNING, no entry stored in dbm for [ENSG00000117242.7] WARNING, no entry stored in dbm for [ENSG00000267532.5] WARNING, no entry stored in dbm for [ENSG00000249977.1] WARNING, no entry stored in dbm for [ENSG00000235020.5] WARNING, no entry stored in dbm for [ENSG00000277568.1] WARNING, no entry stored in dbm for [ENSG00000231806.3] WARNING, no entry stored in dbm for [ENSG00000259702.3] WARNING, no entry stored in dbm for [ENSG00000266916.7] WARNING, no entry stored in dbm for [ENSG00000286641.1] WARNING, no entry stored in dbm for [ENSG00000179818.14] WARNING, no entry stored in dbm for [ENSG00000247081.8] WARNING, no entry stored in dbm for [ENSG00000247627.2] WARNING, no entry stored in dbm for [ENSG00000270948.1] WARNING, no entry stored in dbm for [ENSG00000250299.6] WARNING, no entry stored in dbm for [ENSG00000224296.3] WARNING, no entry stored in dbm for [ENSG00000228340.6] WARNING, no entry stored in dbm for [ENSG00000266531.1] WARNING, no entry stored in dbm for [ENSG00000231090.2] WARNING, no entry stored in dbm for [ENSG00000225206.10] WARNING, no entry stored in dbm for [ENSG00000280828.1] WARNING, no entry stored in dbm for [ENSG00000225783.8] WARNING, no entry stored in dbm for [ENSG00000259953.2] WARNING, no entry stored in dbm for [ENSG00000234948.2] WARNING, no entry stored in dbm for [ENSG00000278090.3] WARNING, no entry stored in dbm for [ENSG00000234476.3] WARNING, no entry stored in dbm for [ENSG00000215244.3] WARNING, no entry stored in dbm for [ENSG00000255411.3] WARNING, no entry stored in dbm for [ENSG00000230943.3] WARNING, no entry stored in dbm for [ENSG00000249362.2] WARNING, no entry stored in dbm for [ENSG00000255760.2] WARNING, no entry stored in dbm for [ENSG00000276778.1] WARNING, no entry stored in dbm for [ENSG00000273125.2] WARNING, no entry stored in dbm for [ENSG00000224961.3] WARNING, no entry stored in dbm for [ENSG00000261008.7] WARNING, no entry stored in dbm for [ENSG00000225434.3] WARNING, no entry stored in dbm for [ENSG00000231671.1] WARNING, no entry stored in dbm for [ENSG00000228794.10] 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 [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 [ENSG00000237248.5] WARNING, no entry stored in dbm for [ENSG00000231711.2] WARNING, no entry stored in dbm for [ENSG00000231721.7] WARNING, no entry stored in dbm for [ENSG00000232662.2] WARNING, no entry stored in dbm for [ENSG00000217889.3] WARNING, no entry stored in dbm for [ENSG00000224791.1] WARNING, no entry stored in dbm for [ENSG00000186831.11] WARNING, no entry stored in dbm for [ENSG00000277128.2] WARNING, no entry stored in dbm for [ENSG00000242337.5] WARNING, no entry stored in dbm for [ENSG00000099251.14] WARNING, no entry stored in dbm for [ENSG00000259228.1] WARNING, no entry stored in dbm for [ENSG00000235734.4] WARNING, no entry stored in dbm for [ENSG00000251099.2] WARNING, no entry stored in dbm for [ENSG00000225851.1] WARNING, no entry stored in dbm for [ENSG00000230795.3] WARNING, no entry stored in dbm for [ENSG00000272078.1] WARNING, no entry stored in dbm for [ENSG00000253392.3] WARNING, no entry stored in dbm for [ENSG00000258570.1] WARNING, no entry stored in dbm for [ENSG00000220875.1] WARNING, no entry stored in dbm for [ENSG00000200156.1] WARNING, no entry stored in dbm for [ENSG00000199568.1] WARNING, no entry stored in dbm for [ENSG00000272556.2] WARNING, no entry stored in dbm for [ENSG00000226259.10] WARNING, no entry stored in dbm for [ENSG00000215158.9] WARNING, no entry stored in dbm for [ENSG00000241549.8] WARNING, no entry stored in dbm for [ENSG00000227953.7] WARNING, no entry stored in dbm for [ENSG00000265174.1] WARNING, no entry stored in dbm for [ENSG00000259345.7] WARNING, no entry stored in dbm for [ENSG00000206803.1] WARNING, no entry stored in dbm for [ENSG00000201852.1] WARNING, no entry stored in dbm for [ENSG00000236438.7] WARNING, no entry stored in dbm for [ENSG00000249919.1] WARNING, no entry stored in dbm for [ENSG00000260565.7] WARNING, no entry stored in dbm for [ENSG00000188828.13] WARNING, no entry stored in dbm for [ENSG00000234152.1] WARNING, no entry stored in dbm for [ENSG00000237435.10] WARNING, no entry stored in dbm for [ENSG00000175658.4] WARNING, no entry stored in dbm for [ENSG00000244306.11] WARNING, no entry stored in dbm for [ENSG00000241383.2] WARNING, no entry stored in dbm for [ENSG00000180525.13] WARNING, no entry stored in dbm for [ENSG00000233514.1] WARNING, no entry stored in dbm for [ENSG00000196810.5] WARNING, no entry stored in dbm for [ENSG00000228966.2] WARNING, no entry stored in dbm for [ENSG00000278969.1] WARNING, no entry stored in dbm for [ENSG00000260750.7] WARNING, no entry stored in dbm for [ENSG00000205559.5] WARNING, no entry stored in dbm for [ENSG00000241104.5] WARNING, no entry stored in dbm for [ENSG00000218586.3] WARNING, no entry stored in dbm for [ENSG00000254838.5] WARNING, no entry stored in dbm for [ENSG00000253502.1] WARNING, no entry stored in dbm for [ENSG00000214071.4] WARNING, no entry stored in dbm for [ENSG00000213338.3] WARNING, no entry stored in dbm for [ENSG00000242083.2] WARNING, no entry stored in dbm for [ENSG00000251143.1] WARNING, no entry stored in dbm for [ENSG00000287528.1] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000186481.16] WARNING, no entry stored in dbm for [ENSG00000205464.13] WARNING, no entry stored in dbm for [ENSG00000278594.1] WARNING, no entry stored in dbm for [ENSG00000277103.1] WARNING, no entry stored in dbm for [ENSG00000217801.10] WARNING, no entry stored in dbm for [ENSG00000230001.1] WARNING, no entry stored in dbm for [ENSG00000286215.1] WARNING, no entry stored in dbm for [ENSG00000286887.1] WARNING, no entry stored in dbm for [ENSG00000225850.3] WARNING, no entry stored in dbm for [ENSG00000288583.1] WARNING, no entry stored in dbm for [ENSG00000287368.1] WARNING, no entry stored in dbm for [ENSG00000258458.8] WARNING, no entry stored in dbm for [ENSG00000230490.3] WARNING, no entry stored in dbm for [ENSG00000230615.7] WARNING, no entry stored in dbm for [ENSG00000287904.1] WARNING, no entry stored in dbm for [ENSG00000286757.2] WARNING, no entry stored in dbm for [ENSG00000258757.1] WARNING, no entry stored in dbm for [ENSG00000255375.3] WARNING, no entry stored in dbm for [ENSG00000227486.2] WARNING, no entry stored in dbm for [ENSG00000268818.2] WARNING, no entry stored in dbm for [ENSG00000238290.1] WARNING, no entry stored in dbm for [ENSG00000272476.1] WARNING, no entry stored in dbm for [ENSG00000237851.1] WARNING, no entry stored in dbm for [ENSG00000225418.1] WARNING, no entry stored in dbm for [ENSG00000259443.1] WARNING, no entry stored in dbm for [ENSG00000228658.1] WARNING, no entry stored in dbm for [ENSG00000237017.1] WARNING, no entry stored in dbm for [ENSG00000283453.2] WARNING, no entry stored in dbm for [ENSG00000229930.1] WARNING, no entry stored in dbm for [ENSG00000261441.1] WARNING, no entry stored in dbm for [ENSG00000235421.1] WARNING, no entry stored in dbm for [ENSG00000286182.1] WARNING, no entry stored in dbm for [ENSG00000277332.1] WARNING, no entry stored in dbm for [ENSG00000251314.2] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000251264.1] WARNING, no entry stored in dbm for [ENSG00000279118.1] WARNING, no entry stored in dbm for [ENSG00000269292.1] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000224016.2] WARNING, no entry stored in dbm for [ENSG00000286545.1] WARNING, no entry stored in dbm for [ENSG00000268362.6] WARNING, no entry stored in dbm for [ENSG00000265936.1] WARNING, no entry stored in dbm for [ENSG00000214259.3] WARNING, no entry stored in dbm for [ENSG00000280828.1] WARNING, no entry stored in dbm for [ENSG00000287226.1] WARNING, no entry stored in dbm for [ENSG00000286133.2] WARNING, no entry stored in dbm for [ENSG00000286891.1] WARNING, no entry stored in dbm for [ENSG00000259605.3] WARNING, no entry stored in dbm for [ENSG00000280828.1] WARNING, no entry stored in dbm for [ENSG00000283674.3] WARNING, no entry stored in dbm for [ENSG00000287860.1] WARNING, no entry stored in dbm for [ENSG00000254728.1] WARNING, no entry stored in dbm for [ENSG00000288549.1] WARNING, no entry stored in dbm for [ENSG00000288549.1] WARNING, no entry stored in dbm for [ENSG00000248613.1] WARNING, no entry stored in dbm for [ENSG00000251471.1] WARNING, no entry stored in dbm for [ENSG00000286037.1] 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 [ENSG00000249476.2] WARNING, no entry stored in dbm for [ENSG00000259106.1] WARNING, no entry stored in dbm for [ENSG00000287446.1] WARNING, no entry stored in dbm for [ENSG00000278959.1] WARNING, no entry stored in dbm for [ENSG00000269745.1] WARNING, no entry stored in dbm for [ENSG00000269745.1] WARNING, no entry stored in dbm for [ENSG00000279218.1] WARNING, no entry stored in dbm for [ENSG00000256988.2] WARNING, no entry stored in dbm for [ENSG00000274712.2] WARNING, no entry stored in dbm for [ENSG00000226624.1] WARNING, no entry stored in dbm for [ENSG00000213885.4] WARNING, no entry stored in dbm for [ENSG00000254610.3] WARNING, no entry stored in dbm for [ENSG00000277283.1] WARNING, no entry stored in dbm for [ENSG00000250132.6] WARNING, no entry stored in dbm for [ENSG00000251794.1] * STAR-Fusion complete. See output: /tmp/nxf.brWW81FQZF/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)