Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/fc931040337824af3f22315e94ff26/aih-tih-sc-d5fda9-R1_A23YTGFLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/3c2102d3e3dafc0babc5cce8250211/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/fc931040337824af3f22315e94ff26/aih-tih-sc-d5fda9-R1_A23YTGFLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/3c2102d3e3dafc0babc5cce8250211/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/cc3d6434ccb65ccba6b880fcebae3d/aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.HNm9yYpVS4/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary -sample contains 28784902 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir -J /tmp/nxf.HNm9yYpVS4/aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.Chimeric.out.junction -O /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.HNm9yYpVS4/aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=31578.95/min [20000], rate=34285.71/min [30000], rate=38297.87/min [40000], rate=42857.14/min [50000], rate=47619.05/min [60000], rate=52173.91/min [70000], rate=49411.76/min [80000], rate=47058.82/min [90000], rate=47368.42/min [100000], rate=47244.09/min [110000], rate=48175.18/min [120000], rate=48648.65/min [130000], rate=50000.00/min [140000], rate=51851.85/min [150000], rate=53571.43/min [160000], rate=54857.14/min [170000], rate=56043.96/min [180000], rate=57142.86/min [190000], rate=58461.54/min [200000], rate=60301.51/min [210000], rate=61764.71/min [220000], rate=63157.89/min [230000], rate=64186.05/min [240000], rate=64864.86/min [250000], rate=66666.67/min [260000], rate=67826.09/min [270000], rate=69230.77/min [280000], rate=69709.54/min [290000], rate=70731.71/min [300000], rate=71428.57/min [310000], rate=72373.54/min [320000], rate=72727.27/min [330000], rate=73062.73/min [340000], rate=73381.29/min [350000], rate=73943.66/min [360000], rate=73720.14/min [370000], rate=72077.92/min [380000], rate=70807.45/min [390000], rate=70059.88/min [400000], rate=69565.22/min [410000], rate=69491.53/min [420000], rate=70000.00/min -building interval tree based on /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=133333.33/min [30000], rate=150000.00/min [40000], rate=150000.00/min [50000], rate=150000.00/min [60000], rate=144000.00/min [70000], rate=155555.56/min [80000], rate=145454.55/min [90000], rate=150000.00/min [100000], rate=150000.00/min [110000], rate=150000.00/min [120000], rate=146938.78/min [130000], rate=147169.81/min [140000], rate=129230.77/min [150000], rate=108433.73/min [160000], rate=95049.50/min [170000], rate=86440.68/min [180000], rate=80597.01/min [190000], rate=76510.07/min [200000], rate=74534.16/min [210000], rate=72832.37/min [220000], rate=71739.13/min [230000], rate=70769.23/min [240000], rate=70935.96/min [250000], rate=71090.05/min [260000], rate=72222.22/min [270000], rate=72000.00/min [280000], rate=71489.36/min [290000], rate=71311.48/min [300000], rate=71713.15/min [310000], rate=72093.02/min [320000], rate=73003.80/min [330000], rate=71739.13/min [340000], rate=70588.24/min [350000], rate=69536.42/min [360000], rate=69230.77/min [370000], rate=68944.10/min [380000], rate=69090.91/min [390000], rate=69436.20/min [400000], rate=69565.22/min [410000], rate=68715.08/min -building interval tree based on /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=42857.14/min [20000], rate=38709.68/min [30000], rate=41860.47/min [40000], rate=48979.59/min [50000], rate=49180.33/min [60000], rate=48648.65/min [70000], rate=50000.00/min [80000], rate=51612.90/min [90000], rate=54000.00/min [100000], rate=56074.77/min [110000], rate=56896.55/min [120000], rate=56250.00/min [130000], rate=55714.29/min [140000], rate=56000.00/min [150000], rate=56603.77/min [160000], rate=58181.82/min [170000], rate=59649.12/min [180000], rate=59016.39/min [190000], rate=58461.54/min [200000], rate=58252.43/min [210000], rate=58333.33/min [220000], rate=58407.08/min [230000], rate=58974.36/min [240000], rate=59504.13/min [250000], rate=60728.74/min [260000], rate=61417.32/min [270000], rate=60902.26/min [280000], rate=60649.82/min [290000], rate=61052.63/min [300000], rate=62283.74/min [310000], rate=63481.23/min [320000], rate=63157.89/min [330000], rate=63057.32/min [340000], rate=63157.89/min [350000], rate=63444.11/min [360000], rate=64670.66/min [370000], rate=65294.12/min [380000], rate=65142.86/min [390000], rate=65000.00/min [400000], rate=65217.39/min [410000], rate=65951.74/min -building interval tree based on /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=33333.33/min [20000], rate=38709.68/min [30000], rate=45000.00/min [40000], rate=54545.45/min [50000], rate=58823.53/min [60000], rate=62068.97/min [70000], rate=62686.57/min [80000], rate=64000.00/min [90000], rate=64285.71/min [100000], rate=66666.67/min [110000], rate=68041.24/min [120000], rate=67289.72/min [130000], rate=67241.38/min [140000], rate=68292.68/min [150000], rate=68702.29/min [160000], rate=67605.63/min [170000], rate=66666.67/min [180000], rate=65853.66/min [190000], rate=65142.86/min [200000], rate=64864.86/min [210000], rate=64615.38/min [220000], rate=64705.88/min [230000], rate=65094.34/min [240000], rate=64864.86/min [250000], rate=64935.06/min [260000], rate=65271.97/min [270000], rate=66122.45/min [280000], rate=64864.86/min [290000], rate=63736.26/min [300000], rate=62937.06/min [310000], rate=62416.11/min [320000], rate=62337.66/min [330000], rate=62264.15/min [340000], rate=62006.08/min [350000], rate=62314.54/min [360000], rate=62790.70/min [370000], rate=63247.86/min [380000], rate=64044.94/min [390000], rate=64462.81/min [400000], rate=63324.54/min [410000], rate=62436.55/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir --filt_file /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 0.00 reads per min processed... 6000000.00 reads per min processed... 4500000.00 reads per min processed... 4000000.00 reads per min processed... 3750000.00 reads per min processed... 3272727.27 reads per min processed... 3230769.23 reads per min processed... 3200000.00 reads per min processed... 3375000.00 reads per min processed... 3529411.76 reads per min processed... 3473684.21 reads per min processed... 3428571.43 reads per min processed... 3545454.55 reads per min processed... 3500000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.HNm9yYpVS4/aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.Chimeric.out.junction --tmpdir /tmp --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --max_promiscuity 10 --min_pct_dom_promiscuity 20 --min_novel_junction_support 1 --min_alt_pct_junction 10 --aggregate_novel_junction_dist 5 --min_spanning_frags_only 1 --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -41134.964754 EM: Round [1] log likelihood: -41099.337213 EM: Round [2] log likelihood: -41083.299978 EM: Round [3] log likelihood: -41074.977764 EM: Round [4] log likelihood: -41070.414868 EM: Round [5] log likelihood: -41067.860660 EM: Round [6] log likelihood: -41066.406034 EM: Round [7] log likelihood: -41065.556822 EM: Round [8] log likelihood: -41065.044744 EM: Round [9] log likelihood: -41064.724484 EM: Round [10] log likelihood: -41064.516530 EM: Round [11] log likelihood: -41064.376468 EM: Round [12] log likelihood: -41064.278809 EM: Round [13] log likelihood: -41064.208489 EM: Round [14] log likelihood: -41064.156335 EM: Round [15] log likelihood: -41064.116597 EM: Round [16] log likelihood: -41064.085572 EM: Round [17] log likelihood: -41064.060813 EM: Round [18] log likelihood: -41064.040661 EM: Round [19] log likelihood: -41064.023972 EM: Round [20] log likelihood: -41064.009936 EM: Round [21] log likelihood: -41063.997970 EM: Round [22] log likelihood: -41063.987649 EM: Round [23] log likelihood: -41063.978652 EM: Round [24] log likelihood: -41063.970741 EM: Round [25] log likelihood: -41063.963729 EM: Round [26] log likelihood: -41063.957470 EM: Round [27] log likelihood: -41063.951851 EM: Round [28] log likelihood: -41063.946780 EM: Round [29] log likelihood: -41063.942181 EM: Round [30] log likelihood: -41063.937994 EM: Round [31] log likelihood: -41063.934168 EM: Round [32] log likelihood: -41063.930660 EM: Round [33] log likelihood: -41063.927434 EM: Round [34] log likelihood: -41063.924460 EM: Round [35] log likelihood: -41063.921711 EM: Round [36] log likelihood: -41063.919165 EM: Round [37] log likelihood: -41063.916803 EM: Round [38] log likelihood: -41063.914607 EM: Round [39] log likelihood: -41063.912562 EM: Round [40] log likelihood: -41063.910655 EM: Round [41] log likelihood: -41063.908874 EM: Round [42] log likelihood: -41063.907209 EM: Round [43] log likelihood: -41063.905651 EM: Round [44] log likelihood: -41063.904190 EM: Round [45] log likelihood: -41063.902820 EM: Round [46] log likelihood: -41063.901534 EM: Round [47] log likelihood: -41063.900326 EM: Round [48] log likelihood: -41063.899189 EM: Round [49] log likelihood: -41063.898120 EM: Round [50] log likelihood: -41063.897113 EM: Round [51] log likelihood: -41063.896164 EM: Round [52] log likelihood: -41063.895269 EM: Round [53] log likelihood: -41063.894425 EM: Round [54] log likelihood: -41063.893629 EM: Round [55] log likelihood: -41063.892877 EM: Round [56] log likelihood: -41063.892166 EM: Round [57] log likelihood: -41063.891494 EM: Round [58] log likelihood: -41063.890859 EM: Round [59] log likelihood: -41063.890258 EM: Round [60] log likelihood: -41063.889690 EM: Round [61] log likelihood: -41063.889151 EM: Round [62] log likelihood: -41063.888642 EM: Round [63] log likelihood: -41063.888159 EM: Round [64] log likelihood: -41063.887701 EM: Round [65] log likelihood: -41063.887267 EM: Round [66] log likelihood: -41063.886856 EM: Round [67] log likelihood: -41063.886466 EM: Round [68] log likelihood: -41063.886096 EM: Round [69] log likelihood: -41063.885745 EM: Round [70] log likelihood: -41063.885412 EM: Round [71] log likelihood: -41063.885095 EM: Round [72] log likelihood: -41063.884794 EM: Round [73] log likelihood: -41063.884509 EM: Round [74] log likelihood: -41063.884237 EM: Round [75] log likelihood: -41063.883979 EM: Round [76] log likelihood: -41063.883734 EM: Round [77] log likelihood: -41063.883501 EM: Round [78] log likelihood: -41063.883279 EM: Round [79] log likelihood: -41063.883068 EM: Round [80] log likelihood: -41063.882867 EM: Round [81] log likelihood: -41063.882676 EM: Round [82] log likelihood: -41063.882494 EM: Round [83] log likelihood: -41063.882321 EM: Round [84] log likelihood: -41063.882156 EM: Round [85] log likelihood: -41063.881999 EM: Round [86] log likelihood: -41063.881849 EM: Round [87] log likelihood: -41063.881706 EM: Round [88] log likelihood: -41063.881570 EM: Round [89] log likelihood: -41063.881441 EM: Round [90] log likelihood: -41063.881317 EM: Round [91] log likelihood: -41063.881199 EM: Round [92] log likelihood: -41063.881087 EM: Round [93] log likelihood: -41063.880979 EM: Round [94] log likelihood: -41063.880877 EM: Round [95] log likelihood: -41063.880779 EM: Stopping iterations at round 95 due to insufficient improvement in likelihood. EM: Starting log likelihood: -41125.554447 EM: Round [1] log likelihood: -41094.311658 EM: Round [2] log likelihood: -41080.583487 EM: Round [3] log likelihood: -41073.477730 EM: Round [4] log likelihood: -41069.573208 EM: Round [5] log likelihood: -41067.376626 EM: Round [6] log likelihood: -41066.117163 EM: Round [7] log likelihood: -41065.376343 EM: Round [8] log likelihood: -41064.926256 EM: Round [9] log likelihood: -41064.642726 EM: Round [10] log likelihood: -41064.457347 EM: Round [11] log likelihood: -41064.331655 EM: Round [12] log likelihood: -41064.243447 EM: Round [13] log likelihood: -41064.179535 EM: Round [14] log likelihood: -41064.131853 EM: Round [15] log likelihood: -41064.095325 EM: Round [16] log likelihood: -41064.066669 EM: Round [17] log likelihood: -41064.043706 EM: Round [18] log likelihood: -41064.024957 EM: Round [19] log likelihood: -41064.009393 EM: Round [20] log likelihood: -41063.996285 EM: Round [21] log likelihood: -41063.985106 EM: Round [22] log likelihood: -41063.975466 EM: Round [23] log likelihood: -41063.967074 EM: Round [24] log likelihood: -41063.959709 EM: Round [25] log likelihood: -41063.953196 EM: Round [26] log likelihood: -41063.947403 EM: Round [27] log likelihood: -41063.942220 EM: Round [28] log likelihood: -41063.937560 EM: Round [29] log likelihood: -41063.933353 EM: Round [30] log likelihood: -41063.929540 EM: Round [31] log likelihood: -41063.926073 EM: Round [32] log likelihood: -41063.922909 EM: Round [33] log likelihood: -41063.920015 EM: Round [34] log likelihood: -41063.917360 EM: Round [35] log likelihood: -41063.914919 EM: Round [36] log likelihood: -41063.912670 EM: Round [37] log likelihood: -41063.910594 EM: Round [38] log likelihood: -41063.908673 EM: Round [39] log likelihood: -41063.906894 EM: Round [40] log likelihood: -41063.905243 EM: Round [41] log likelihood: -41063.903708 EM: Round [42] log likelihood: -41063.902280 EM: Round [43] log likelihood: -41063.900949 EM: Round [44] log likelihood: -41063.899707 EM: Round [45] log likelihood: -41063.898547 EM: Round [46] log likelihood: -41063.897463 EM: Round [47] log likelihood: -41063.896448 EM: Round [48] log likelihood: -41063.895497 EM: Round [49] log likelihood: -41063.894605 EM: Round [50] log likelihood: -41063.893768 EM: Round [51] log likelihood: -41063.892981 EM: Round [52] log likelihood: -41063.892242 EM: Round [53] log likelihood: -41063.891547 EM: Round [54] log likelihood: -41063.890892 EM: Round [55] log likelihood: -41063.890276 EM: Round [56] log likelihood: -41063.889694 EM: Round [57] log likelihood: -41063.889146 EM: Round [58] log likelihood: -41063.888629 EM: Round [59] log likelihood: -41063.888140 EM: Round [60] log likelihood: -41063.887678 EM: Round [61] log likelihood: -41063.887242 EM: Round [62] log likelihood: -41063.886829 EM: Round [63] log likelihood: -41063.886438 EM: Round [64] log likelihood: -41063.886069 EM: Round [65] log likelihood: -41063.885718 EM: Round [66] log likelihood: -41063.885386 EM: Round [67] log likelihood: -41063.885072 EM: Round [68] log likelihood: -41063.884774 EM: Round [69] log likelihood: -41063.884491 EM: Round [70] log likelihood: -41063.884222 EM: Round [71] log likelihood: -41063.883967 EM: Round [72] log likelihood: -41063.883725 EM: Round [73] log likelihood: -41063.883494 EM: Round [74] log likelihood: -41063.883276 EM: Round [75] log likelihood: -41063.883068 EM: Round [76] log likelihood: -41063.882870 EM: Round [77] log likelihood: -41063.882682 EM: Round [78] log likelihood: -41063.882502 EM: Round [79] log likelihood: -41063.882332 EM: Round [80] log likelihood: -41063.882169 EM: Round [81] log likelihood: -41063.882015 EM: Round [82] log likelihood: -41063.881867 EM: Round [83] log likelihood: -41063.881727 EM: Round [84] log likelihood: -41063.881593 EM: Round [85] log likelihood: -41063.881465 EM: Round [86] log likelihood: -41063.881343 EM: Round [87] log likelihood: -41063.881227 EM: Round [88] log likelihood: -41063.881116 EM: Round [89] log likelihood: -41063.881010 EM: Round [90] log likelihood: -41063.880909 EM: Round [91] log likelihood: -41063.880812 EM: Stopping iterations at round 91 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 28784902 > /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir > /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir --annotate /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir -done, see /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 346, filtered: 3803) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000158482.10] WARNING, no entry stored in dbm for [ENSG00000276721.1] WARNING, no entry stored in dbm for [ENSG00000237390.1] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000225465.10] WARNING, no entry stored in dbm for [ENSG00000196796.5] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000213643.3] WARNING, no entry stored in dbm for [ENSG00000275374.1] WARNING, no entry stored in dbm for [ENSG00000286356.1] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000274343.1] WARNING, no entry stored in dbm for [ENSG00000287356.1] WARNING, no entry stored in dbm for [ENSG00000203709.12] WARNING, no entry stored in dbm for [ENSG00000287920.1] WARNING, no entry stored in dbm for [ENSG00000283426.1] WARNING, no entry stored in dbm for [ENSG00000225689.2] WARNING, no entry stored in dbm for [ENSG00000286630.1] WARNING, no entry stored in dbm for [ENSG00000230423.3] WARNING, no entry stored in dbm for [ENSG00000230937.12] WARNING, no entry stored in dbm for [ENSG00000239881.1] WARNING, no entry stored in dbm for [ENSG00000228665.2] WARNING, no entry stored in dbm for [ENSG00000223508.5] WARNING, no entry stored in dbm for [ENSG00000265735.2] WARNING, no entry stored in dbm for [ENSG00000244112.3] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000202406.1] WARNING, no entry stored in dbm for [ENSG00000222982.1] WARNING, no entry stored in dbm for [ENSG00000201078.1] WARNING, no entry stored in dbm for [ENSG00000199640.1] WARNING, no entry stored in dbm for [ENSG00000199622.1] WARNING, no entry stored in dbm for [ENSG00000199640.1] WARNING, no entry stored in dbm for [ENSG00000199622.1] WARNING, no entry stored in dbm for [ENSG00000202344.1] WARNING, no entry stored in dbm for [ENSG00000222385.1] WARNING, no entry stored in dbm for [ENSG00000202344.1] WARNING, no entry stored in dbm for [ENSG00000255857.6] WARNING, no entry stored in dbm for [ENSG00000196796.5] WARNING, no entry stored in dbm for [ENSG00000288588.1] WARNING, no entry stored in dbm for [ENSG00000203799.13] WARNING, no entry stored in dbm for [ENSG00000258090.1] WARNING, no entry stored in dbm for [ENSG00000186960.12] WARNING, no entry stored in dbm for [ENSG00000263740.2] WARNING, no entry stored in dbm for [ENSG00000215154.6] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000203825.4] WARNING, no entry stored in dbm for [ENSG00000281026.1] WARNING, no entry stored in dbm for [ENSG00000277047.5] WARNING, no entry stored in dbm for [ENSG00000214955.5] WARNING, no entry stored in dbm for [ENSG00000226320.6] WARNING, no entry stored in dbm for [ENSG00000235687.9] WARNING, no entry stored in dbm for [ENSG00000227060.7] WARNING, no entry stored in dbm for [ENSG00000135477.11] WARNING, no entry stored in dbm for [ENSG00000269821.1] WARNING, no entry stored in dbm for [ENSG00000236679.2] WARNING, no entry stored in dbm for [ENSG00000249768.2] WARNING, no entry stored in dbm for [ENSG00000261395.3] WARNING, no entry stored in dbm for [ENSG00000272620.2] WARNING, no entry stored in dbm for [ENSG00000272595.2] WARNING, no entry stored in dbm for [ENSG00000234741.8] WARNING, no entry stored in dbm for [ENSG00000248360.7] WARNING, no entry stored in dbm for [ENSG00000223652.2] WARNING, no entry stored in dbm for [ENSG00000235768.1] WARNING, no entry stored in dbm for [ENSG00000228887.3] WARNING, no entry stored in dbm for [ENSG00000186704.9] WARNING, no entry stored in dbm for [ENSG00000233514.1] WARNING, no entry stored in dbm for [ENSG00000214659.4] WARNING, no entry stored in dbm for [ENSG00000196796.5] WARNING, no entry stored in dbm for [ENSG00000223745.8] WARNING, no entry stored in dbm for [ENSG00000214548.18] WARNING, no entry stored in dbm for [ENSG00000220267.1] WARNING, no entry stored in dbm for [ENSG00000254290.1] WARNING, no entry stored in dbm for [ENSG00000279367.1] WARNING, no entry stored in dbm for [ENSG00000287285.1] WARNING, no entry stored in dbm for [ENSG00000234353.2] WARNING, no entry stored in dbm for [ENSG00000267419.2] WARNING, no entry stored in dbm for [ENSG00000215559.8] WARNING, no entry stored in dbm for [ENSG00000236627.1] WARNING, no entry stored in dbm for [ENSG00000225096.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000228685.1] WARNING, no entry stored in dbm for [ENSG00000234851.4] WARNING, no entry stored in dbm for [ENSG00000237788.1] WARNING, no entry stored in dbm for [ENSG00000241354.2] WARNING, no entry stored in dbm for [ENSG00000214535.3] WARNING, no entry stored in dbm for [ENSG00000203413.3] WARNING, no entry stored in dbm for [ENSG00000215302.8] WARNING, no entry stored in dbm for [ENSG00000231160.10] WARNING, no entry stored in dbm for [ENSG00000250696.5] WARNING, no entry stored in dbm for [ENSG00000224218.1] WARNING, no entry stored in dbm for [ENSG00000282375.1] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000286436.1] WARNING, no entry stored in dbm for [ENSG00000280136.2] WARNING, no entry stored in dbm for [ENSG00000228303.1] WARNING, no entry stored in dbm for [ENSG00000252765.1] WARNING, no entry stored in dbm for [ENSG00000276538.1] WARNING, no entry stored in dbm for [ENSG00000254485.5] WARNING, no entry stored in dbm for [ENSG00000264666.1] WARNING, no entry stored in dbm for [ENSG00000286982.1] WARNING, no entry stored in dbm for [ENSG00000279249.3] WARNING, no entry stored in dbm for [ENSG00000279317.2] WARNING, no entry stored in dbm for [ENSG00000267469.1] WARNING, no entry stored in dbm for [ENSG00000230305.2] WARNING, no entry stored in dbm for [ENSG00000231139.1] WARNING, no entry stored in dbm for [ENSG00000242737.1] WARNING, no entry stored in dbm for [ENSG00000277739.1] * STAR-Fusion complete. See output: /tmp/nxf.HNm9yYpVS4/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)