-ctat genome lib [/tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.w8G1RAj1YG/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary -sample contains 40165314 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir -J /tmp/nxf.w8G1RAj1YG/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.w8G1RAj1YG/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=63157.89/min [30000], rate=47368.42/min [40000], rate=41379.31/min [50000], rate=39473.68/min [60000], rate=38297.87/min [70000], rate=38888.89/min [80000], rate=39669.42/min [90000], rate=40909.09/min [100000], rate=41666.67/min [110000], rate=42580.65/min [120000], rate=44171.78/min [130000], rate=45614.04/min [140000], rate=46927.37/min [150000], rate=48387.10/min [160000], rate=50000.00/min [170000], rate=51776.65/min [180000], rate=53465.35/min [190000], rate=55072.46/min [200000], rate=57142.86/min [210000], rate=58604.65/min [220000], rate=59459.46/min [230000], rate=60792.95/min [240000], rate=61802.58/min [250000], rate=62761.51/min [260000], rate=64197.53/min [270000], rate=65587.04/min [280000], rate=66932.27/min [290000], rate=69047.62/min [300000], rate=71428.57/min [310000], rate=73517.79/min [320000], rate=74131.27/min [330000], rate=74436.09/min [340000], rate=75276.75/min [350000], rate=76642.34/min [360000], rate=77142.86/min [370000], rate=77894.74/min [380000], rate=77815.70/min [390000], rate=78260.87/min [400000], rate=78688.52/min [410000], rate=79099.68/min [420000], rate=80254.78/min [430000], rate=81904.76/min [440000], rate=83544.30/min [450000], rate=84905.66/min [460000], rate=85185.19/min [470000], rate=85196.37/min [480000], rate=85970.15/min [490000], rate=86725.66/min [500000], rate=86956.52/min [510000], rate=87931.03/min [520000], rate=88135.59/min [530000], rate=87845.30/min [540000], rate=88043.48/min [550000], rate=87765.96/min [560000], rate=88188.98/min [570000], rate=89062.50/min [580000], rate=89230.77/min [590000], rate=90076.34/min [600000], rate=90000.00/min [610000], rate=90370.37/min [620000], rate=90731.71/min [630000], rate=90430.62/min [640000], rate=90566.04/min [650000], rate=90487.24/min [660000], rate=90617.85/min [670000], rate=90744.92/min [680000], rate=89670.33/min [690000], rate=88272.92/min [700000], rate=87500.00/min [710000], rate=86585.37/min [720000], rate=85544.55/min [730000], rate=84555.98/min [740000], rate=84250.47/min [750000], rate=83798.88/min [760000], rate=83363.80/min [770000], rate=82944.34/min [780000], rate=82978.72/min [790000], rate=82722.51/min [800000], rate=82474.23/min [810000], rate=82512.73/min -building interval tree based on /tmp/nxf.w8G1RAj1YG/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=54545.45/min [30000], rate=54545.45/min [40000], rate=60000.00/min [50000], rate=60000.00/min [60000], rate=60000.00/min [70000], rate=60869.57/min [80000], rate=61538.46/min [90000], rate=63529.41/min [100000], rate=65934.07/min [110000], rate=67346.94/min [120000], rate=66055.05/min [130000], rate=65000.00/min [140000], rate=64615.38/min [150000], rate=64285.71/min [160000], rate=64429.53/min [170000], rate=64556.96/min [180000], rate=65454.55/min [190000], rate=67058.82/min [200000], rate=68965.52/min [210000], rate=70786.52/min [220000], rate=72527.47/min [230000], rate=74193.55/min [240000], rate=73846.15/min [250000], rate=73529.41/min [260000], rate=72897.20/min [270000], rate=72645.74/min [280000], rate=72727.27/min [290000], rate=72500.00/min [300000], rate=72289.16/min [310000], rate=72373.54/min [320000], rate=73003.80/min [330000], rate=73333.33/min [340000], rate=73913.04/min [350000], rate=74733.10/min [360000], rate=74740.48/min [370000], rate=73509.93/min [380000], rate=73076.92/min [390000], rate=72222.22/min [400000], rate=71856.29/min [410000], rate=71720.12/min [420000], rate=71186.44/min [430000], rate=71074.38/min [440000], rate=70588.24/min [450000], rate=70680.63/min [460000], rate=70408.16/min [470000], rate=70324.19/min [480000], rate=70761.67/min [490000], rate=71186.44/min [500000], rate=71942.45/min [510000], rate=71830.99/min [520000], rate=71395.88/min [530000], rate=70982.14/min [540000], rate=70588.24/min [550000], rate=70663.81/min [560000], rate=70736.84/min [570000], rate=70807.45/min [580000], rate=71165.64/min [590000], rate=71227.36/min [600000], rate=71005.92/min [610000], rate=70930.23/min [620000], rate=70722.43/min [630000], rate=70654.21/min [640000], rate=70718.23/min [650000], rate=70909.09/min [660000], rate=71095.15/min [670000], rate=71657.75/min [680000], rate=72340.43/min [690000], rate=72631.58/min [700000], rate=73043.48/min [710000], rate=72696.25/min [720000], rate=72483.22/min [730000], rate=72636.82/min [740000], rate=72549.02/min [750000], rate=72580.65/min [760000], rate=72727.27/min [770000], rate=73101.27/min [780000], rate=73469.39/min [790000], rate=73831.78/min [800000], rate=74303.41/min [810000], rate=74425.73/min -building interval tree based on /tmp/nxf.w8G1RAj1YG/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=92307.69/min [30000], rate=100000.00/min [40000], rate=96000.00/min [50000], rate=103448.28/min [60000], rate=112500.00/min [70000], rate=113513.51/min [80000], rate=126315.79/min [90000], rate=125581.40/min [100000], rate=122448.98/min [110000], rate=120000.00/min [120000], rate=116129.03/min [130000], rate=116417.91/min [140000], rate=120000.00/min [150000], rate=118421.05/min [160000], rate=124675.32/min [170000], rate=124390.24/min [180000], rate=121348.31/min [190000], rate=120000.00/min [200000], rate=121212.12/min [210000], rate=118867.92/min [220000], rate=122222.22/min [230000], rate=123214.29/min [240000], rate=124137.93/min [250000], rate=123966.94/min [260000], rate=123809.52/min [270000], rate=124615.38/min [280000], rate=124444.44/min [290000], rate=126086.96/min [300000], rate=127659.57/min [310000], rate=126530.61/min [320000], rate=114970.06/min [330000], rate=108791.21/min [340000], rate=103553.30/min [350000], rate=100000.00/min [360000], rate=96860.99/min [370000], rate=92887.03/min [380000], rate=89411.76/min [390000], rate=86666.67/min [400000], rate=84805.65/min [410000], rate=82828.28/min [420000], rate=81553.40/min [430000], rate=80373.83/min [440000], rate=79279.28/min [450000], rate=78034.68/min [460000], rate=77310.92/min [470000], rate=77049.18/min [480000], rate=76595.74/min [490000], rate=76562.50/min [500000], rate=76726.34/min [510000], rate=77078.09/min [520000], rate=77419.35/min [530000], rate=77184.47/min [540000], rate=77142.86/min [550000], rate=77102.80/min [560000], rate=76712.33/min [570000], rate=76681.61/min [580000], rate=76483.52/min [590000], rate=76457.88/min [600000], rate=76595.74/min [610000], rate=76729.56/min [620000], rate=77018.63/min [630000], rate=76056.34/min [640000], rate=75590.55/min [650000], rate=74856.05/min [660000], rate=74157.30/min [670000], rate=73897.06/min [680000], rate=73779.39/min [690000], rate=73274.34/min [700000], rate=72916.67/min [710000], rate=72696.25/min [720000], rate=72483.22/min [730000], rate=72396.69/min [740000], rate=72430.67/min [750000], rate=72580.65/min [760000], rate=72843.45/min [770000], rate=73101.27/min [780000], rate=72783.83/min [790000], rate=72256.10/min [800000], rate=71856.29/min [810000], rate=71787.30/min -building interval tree based on /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=50000.00/min [20000], rate=52173.91/min [30000], rate=50000.00/min [40000], rate=51063.83/min [50000], rate=52631.58/min [60000], rate=54545.45/min [70000], rate=56000.00/min [80000], rate=57831.33/min [90000], rate=59340.66/min [100000], rate=62500.00/min [110000], rate=64077.67/min [120000], rate=65454.55/min [130000], rate=67241.38/min [140000], rate=69421.49/min [150000], rate=69767.44/min [160000], rate=69064.75/min [170000], rate=69387.76/min [180000], rate=70129.87/min [190000], rate=69938.65/min [200000], rate=71856.29/min [210000], rate=73255.81/min [220000], rate=75000.00/min [230000], rate=75000.00/min [240000], rate=75000.00/min [250000], rate=75000.00/min [260000], rate=76470.59/min [270000], rate=76415.09/min [280000], rate=76712.33/min [290000], rate=78026.91/min [300000], rate=78602.62/min [310000], rate=79828.33/min [320000], rate=79668.05/min [330000], rate=78260.87/min [340000], rate=77566.54/min [350000], rate=76642.34/min [360000], rate=76056.34/min [370000], rate=75254.24/min [380000], rate=75000.00/min [390000], rate=75000.00/min [400000], rate=74534.16/min [410000], rate=74096.39/min [420000], rate=73900.29/min [430000], rate=73504.27/min [440000], rate=73130.19/min [450000], rate=72776.28/min [460000], rate=72823.22/min [470000], rate=72868.22/min [480000], rate=73096.45/min [490000], rate=73500.00/min [500000], rate=73710.07/min [510000], rate=74271.84/min [520000], rate=73411.76/min [530000], rate=72272.73/min [540000], rate=71365.64/min [550000], rate=70512.82/min [560000], rate=70000.00/min [570000], rate=69653.77/min [580000], rate=69322.71/min [590000], rate=69140.62/min [600000], rate=69097.89/min [610000], rate=69187.15/min [620000], rate=69273.74/min [630000], rate=69613.26/min [640000], rate=69945.36/min [650000], rate=70143.88/min [660000], rate=70714.29/min [670000], rate=70899.47/min [680000], rate=71204.19/min [690000], rate=70890.41/min [700000], rate=70351.76/min [710000], rate=69836.07/min [720000], rate=69453.38/min [730000], rate=68976.38/min [740000], rate=68837.21/min [750000], rate=68493.15/min [760000], rate=68365.82/min [770000], rate=68141.59/min [780000], rate=68023.26/min [790000], rate=68103.45/min [800000], rate=68085.11/min [810000], rate=68258.43/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir --filt_file /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 12000000.00 reads per min processed... 6000000.00 reads per min processed... 6000000.00 reads per min processed... 5000000.00 reads per min processed... 5142857.14 reads per min processed... 4666666.67 reads per min processed... 4363636.36 reads per min processed... 4500000.00 reads per min processed... 4285714.29 reads per min processed... 3882352.94 reads per min processed... 3789473.68 reads per min processed... 3714285.71 reads per min processed... 3652173.91 reads per min processed... 3750000.00 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... 4000000.00 reads per min processed... 3942857.14 reads per min processed... 3891891.89 reads per min processed... 3947368.42 reads per min processed... 3900000.00 reads per min processed... 3857142.86 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.w8G1RAj1YG/OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_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.w8G1RAj1YG/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -37852.007352 EM: Round [1] log likelihood: -37788.047288 EM: Round [2] log likelihood: -37758.964094 EM: Round [3] log likelihood: -37744.179274 EM: Round [4] log likelihood: -37736.266019 EM: Round [5] log likelihood: -37731.886301 EM: Round [6] log likelihood: -37729.379484 EM: Round [7] log likelihood: -37727.889478 EM: Round [8] log likelihood: -37726.967907 EM: Round [9] log likelihood: -37726.375413 EM: Round [10] log likelihood: -37725.980744 EM: Round [11] log likelihood: -37725.709546 EM: Round [12] log likelihood: -37725.518180 EM: Round [13] log likelihood: -37725.380104 EM: Round [14] log likelihood: -37725.278602 EM: Round [15] log likelihood: -37725.202811 EM: Round [16] log likelihood: -37725.145459 EM: Round [17] log likelihood: -37725.101560 EM: Round [18] log likelihood: -37725.067616 EM: Round [19] log likelihood: -37725.041131 EM: Round [20] log likelihood: -37725.020294 EM: Round [21] log likelihood: -37725.003773 EM: Round [22] log likelihood: -37724.990578 EM: Round [23] log likelihood: -37724.979966 EM: Round [24] log likelihood: -37724.971373 EM: Round [25] log likelihood: -37724.964370 EM: Round [26] log likelihood: -37724.958625 EM: Round [27] log likelihood: -37724.953883 EM: Round [28] log likelihood: -37724.949943 EM: Round [29] log likelihood: -37724.946649 EM: Round [30] log likelihood: -37724.943878 EM: Round [31] log likelihood: -37724.941533 EM: Round [32] log likelihood: -37724.939537 EM: Round [33] log likelihood: -37724.937826 EM: Round [34] log likelihood: -37724.936352 EM: Round [35] log likelihood: -37724.935074 EM: Round [36] log likelihood: -37724.933960 EM: Round [37] log likelihood: -37724.932984 EM: Round [38] log likelihood: -37724.932123 EM: Round [39] log likelihood: -37724.931361 EM: Round [40] log likelihood: -37724.930683 EM: Round [41] log likelihood: -37724.930076 EM: Round [42] log likelihood: -37724.929532 EM: Round [43] log likelihood: -37724.929040 EM: Round [44] log likelihood: -37724.928596 EM: Round [45] log likelihood: -37724.928192 EM: Round [46] log likelihood: -37724.927824 EM: Round [47] log likelihood: -37724.927487 EM: Round [48] log likelihood: -37724.927178 EM: Round [49] log likelihood: -37724.926894 EM: Round [50] log likelihood: -37724.926632 EM: Round [51] log likelihood: -37724.926390 EM: Round [52] log likelihood: -37724.926166 EM: Round [53] log likelihood: -37724.925959 EM: Round [54] log likelihood: -37724.925766 EM: Round [55] log likelihood: -37724.925586 EM: Round [56] log likelihood: -37724.925419 EM: Round [57] log likelihood: -37724.925263 EM: Round [58] log likelihood: -37724.925117 EM: Round [59] log likelihood: -37724.924980 EM: Round [60] log likelihood: -37724.924852 EM: Round [61] log likelihood: -37724.924732 EM: Round [62] log likelihood: -37724.924620 EM: Round [63] log likelihood: -37724.924514 EM: Round [64] log likelihood: -37724.924415 EM: Stopping iterations at round 64 due to insufficient improvement in likelihood. EM: Starting log likelihood: -37837.336363 EM: Round [1] log likelihood: -37779.160295 EM: Round [2] log likelihood: -37753.423124 EM: Round [3] log likelihood: -37740.656259 EM: Round [4] log likelihood: -37733.963989 EM: Round [5] log likelihood: -37730.333412 EM: Round [6] log likelihood: -37728.298553 EM: Round [7] log likelihood: -37727.115438 EM: Round [8] log likelihood: -37726.399776 EM: Round [9] log likelihood: -37725.949446 EM: Round [10] log likelihood: -37725.655445 EM: Round [11] log likelihood: -37725.457130 EM: Round [12] log likelihood: -37725.319567 EM: Round [13] log likelihood: -37725.221887 EM: Round [14] log likelihood: -37725.151176 EM: Round [15] log likelihood: -37725.099162 EM: Round [16] log likelihood: -37725.060390 EM: Round [17] log likelihood: -37725.031160 EM: Round [18] log likelihood: -37725.008905 EM: Round [19] log likelihood: -37724.991814 EM: Round [20] log likelihood: -37724.978583 EM: Round [21] log likelihood: -37724.968264 EM: Round [22] log likelihood: -37724.960160 EM: Round [23] log likelihood: -37724.953751 EM: Round [24] log likelihood: -37724.948649 EM: Round [25] log likelihood: -37724.944561 EM: Round [26] log likelihood: -37724.941263 EM: Round [27] log likelihood: -37724.938586 EM: Round [28] log likelihood: -37724.936397 EM: Round [29] log likelihood: -37724.934596 EM: Round [30] log likelihood: -37724.933104 EM: Round [31] log likelihood: -37724.931859 EM: Round [32] log likelihood: -37724.930814 EM: Round [33] log likelihood: -37724.929929 EM: Round [34] log likelihood: -37724.929176 EM: Round [35] log likelihood: -37724.928531 EM: Round [36] log likelihood: -37724.927974 EM: Round [37] log likelihood: -37724.927490 EM: Round [38] log likelihood: -37724.927067 EM: Round [39] log likelihood: -37724.926695 EM: Round [40] log likelihood: -37724.926366 EM: Round [41] log likelihood: -37724.926073 EM: Round [42] log likelihood: -37724.925811 EM: Round [43] log likelihood: -37724.925576 EM: Round [44] log likelihood: -37724.925364 EM: Round [45] log likelihood: -37724.925171 EM: Round [46] log likelihood: -37724.924996 EM: Round [47] log likelihood: -37724.924836 EM: Round [48] log likelihood: -37724.924689 EM: Round [49] log likelihood: -37724.924554 EM: Round [50] log likelihood: -37724.924430 EM: Round [51] log likelihood: -37724.924315 EM: Round [52] log likelihood: -37724.924208 EM: Round [53] log likelihood: -37724.924109 EM: Stopping iterations at round 53 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.w8G1RAj1YG/./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.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.w8G1RAj1YG/./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.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 40165314 > /tmp/nxf.w8G1RAj1YG/./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.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir > /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir --annotate /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.w8G1RAj1YG/./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.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir -done, see /tmp/nxf.w8G1RAj1YG/./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.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.w8G1RAj1YG/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 229, filtered: 3018) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.w8G1RAj1YG/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.w8G1RAj1YG/./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.w8G1RAj1YG/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000227288.3] WARNING, no entry stored in dbm for [ENSG00000241735.2] WARNING, no entry stored in dbm for [ENSG00000247081.8] WARNING, no entry stored in dbm for [ENSG00000237686.7] WARNING, no entry stored in dbm for [ENSG00000239268.3] WARNING, no entry stored in dbm for [ENSG00000259294.1] WARNING, no entry stored in dbm for [ENSG00000259291.2] WARNING, no entry stored in dbm for [ENSG00000287535.1] WARNING, no entry stored in dbm for [ENSG00000264920.2] WARNING, no entry stored in dbm for [ENSG00000276092.1] WARNING, no entry stored in dbm for [ENSG00000267248.3] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000230454.1] WARNING, no entry stored in dbm for [ENSG00000205583.13] WARNING, no entry stored in dbm for [ENSG00000208023.3] WARNING, no entry stored in dbm for [ENSG00000272143.1] WARNING, no entry stored in dbm for [ENSG00000283426.1] WARNING, no entry stored in dbm for [ENSG00000185485.14] WARNING, no entry stored in dbm for [ENSG00000273599.1] WARNING, no entry stored in dbm for [ENSG00000279179.1] WARNING, no entry stored in dbm for [ENSG00000237232.9] WARNING, no entry stored in dbm for [ENSG00000233979.1] WARNING, no entry stored in dbm for [ENSG00000265798.6] WARNING, no entry stored in dbm for [ENSG00000278834.1] WARNING, no entry stored in dbm for [ENSG00000236116.1] WARNING, no entry stored in dbm for [ENSG00000273143.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000270866.1] WARNING, no entry stored in dbm for [ENSG00000272578.5] WARNING, no entry stored in dbm for [ENSG00000229359.2] WARNING, no entry stored in dbm for [ENSG00000248449.2] WARNING, no entry stored in dbm for [ENSG00000277739.1] WARNING, no entry stored in dbm for [ENSG00000283568.1] WARNING, no entry stored in dbm for [ENSG00000273129.2] WARNING, no entry stored in dbm for [ENSG00000273129.2] WARNING, no entry stored in dbm for [ENSG00000259275.4] WARNING, no entry stored in dbm for [ENSG00000258288.1] WARNING, no entry stored in dbm for [ENSG00000227632.2] WARNING, no entry stored in dbm for [ENSG00000256916.1] WARNING, no entry stored in dbm for [ENSG00000279162.1] WARNING, no entry stored in dbm for [ENSG00000279171.1] WARNING, no entry stored in dbm for [ENSG00000231566.2] WARNING, no entry stored in dbm for [ENSG00000270069.1] WARNING, no entry stored in dbm for [ENSG00000257747.2] WARNING, no entry stored in dbm for [ENSG00000259605.3] WARNING, no entry stored in dbm for [ENSG00000218347.2] 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 [ENSG00000225191.1] WARNING, no entry stored in dbm for [ENSG00000184274.3] WARNING, no entry stored in dbm for [ENSG00000228223.3] WARNING, no entry stored in dbm for [ENSG00000280217.1] WARNING, no entry stored in dbm for [ENSG00000287535.1] WARNING, no entry stored in dbm for [ENSG00000197847.12] WARNING, no entry stored in dbm for [ENSG00000250959.2] WARNING, no entry stored in dbm for [ENSG00000265962.1] WARNING, no entry stored in dbm for [ENSG00000255471.1] WARNING, no entry stored in dbm for [ENSG00000228876.4] WARNING, no entry stored in dbm for [ENSG00000281383.1] WARNING, no entry stored in dbm for [ENSG00000280800.1] WARNING, no entry stored in dbm for [ENSG00000281181.1] WARNING, no entry stored in dbm for [ENSG00000280614.1] WARNING, no entry stored in dbm for [ENSG00000244139.3] WARNING, no entry stored in dbm for [ENSG00000214439.4] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [ENSG00000279136.1] WARNING, no entry stored in dbm for [ENSG00000248223.1] WARNING, no entry stored in dbm for [ENSG00000228056.3] WARNING, no entry stored in dbm for [ENSG00000281398.4] WARNING, no entry stored in dbm for [ENSG00000271714.1] WARNING, no entry stored in dbm for [ENSG00000177410.13] WARNING, no entry stored in dbm for [ENSG00000287867.1] WARNING, no entry stored in dbm for [ENSG00000254319.6] WARNING, no entry stored in dbm for [ENSG00000277125.1] WARNING, no entry stored in dbm for [ENSG00000219201.4] WARNING, no entry stored in dbm for [ENSG00000279837.1] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000240519.1] WARNING, no entry stored in dbm for [ENSG00000218175.2] WARNING, no entry stored in dbm for [ENSG00000273270.1] WARNING, no entry stored in dbm for [ENSG00000276122.1] 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 [ENSG00000197813.6] WARNING, no entry stored in dbm for [ENSG00000259663.2] WARNING, no entry stored in dbm for [ENSG00000272568.6] * STAR-Fusion complete. See output: /tmp/nxf.w8G1RAj1YG/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)