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/4e/b1019604c268951935f18d13c8099d/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/92/f449d8b120a24e15822fc7eb25ef75/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/fd6c5b24bcb3db550ef95837154601/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/b1019604c268951935f18d13c8099d/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/fd6c5b24bcb3db550ef95837154601/.command.run ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.KHsOoY8TVX/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary -sample contains 13073429 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir -J /tmp/nxf.KHsOoY8TVX/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction -O /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.KHsOoY8TVX/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Chimeric.out.junction -building interval tree based on /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=60000.00/min [20000], rate=48000.00/min [30000], rate=50000.00/min [40000], rate=47058.82/min [50000], rate=34482.76/min [60000], rate=30769.23/min [70000], rate=29787.23/min [80000], rate=30379.75/min [90000], rate=31764.71/min [100000], rate=32786.89/min [110000], rate=32195.12/min [120000], rate=31304.35/min [130000], rate=30952.38/min [140000], rate=31460.67/min [150000], rate=32258.06/min [160000], rate=33333.33/min [170000], rate=33663.37/min [180000], rate=32335.33/min [190000], rate=31147.54/min [200000], rate=30612.24/min [210000], rate=30215.83/min [220000], rate=30414.75/min [230000], rate=30598.67/min [240000], rate=29937.63/min [250000], rate=29411.76/min [260000], rate=29433.96/min [270000], rate=29616.09/min [280000], rate=29629.63/min [290000], rate=29541.60/min [300000], rate=29801.32/min [310000], rate=30145.87/min [320000], rate=30524.64/min [330000], rate=31083.20/min [340000], rate=31627.91/min [350000], rate=31626.51/min [360000], rate=31764.71/min [370000], rate=31988.47/min [380000], rate=32478.63/min -building interval tree based on /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=22222.22/min [20000], rate=15189.87/min [30000], rate=16071.43/min [40000], rate=17391.30/min [50000], rate=19480.52/min [60000], rate=21428.57/min [70000], rate=23204.42/min [80000], rate=25000.00/min [90000], rate=26600.99/min [100000], rate=28037.38/min [110000], rate=28448.28/min [120000], rate=28800.00/min [130000], rate=28676.47/min [140000], rate=30107.53/min [150000], rate=31034.48/min [160000], rate=31372.55/min [170000], rate=31677.02/min [180000], rate=31213.87/min [190000], rate=31754.87/min [200000], rate=32520.33/min [210000], rate=32898.17/min [220000], rate=33249.37/min [230000], rate=33495.15/min [240000], rate=33566.43/min [250000], rate=33860.05/min [260000], rate=34135.67/min [270000], rate=34541.58/min [280000], rate=35000.00/min [290000], rate=34869.74/min [300000], rate=34749.03/min [310000], rate=35094.34/min [320000], rate=33982.30/min [330000], rate=32512.32/min [340000], rate=31481.48/min [350000], rate=31722.05/min [360000], rate=31764.71/min [370000], rate=31759.66/min [380000], rate=32022.47/min -building interval tree based on /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=28571.43/min [20000], rate=25000.00/min [30000], rate=28125.00/min [40000], rate=30000.00/min [50000], rate=32258.06/min [60000], rate=33644.86/min [70000], rate=35593.22/min [80000], rate=33103.45/min [90000], rate=31395.35/min [100000], rate=31413.61/min [110000], rate=32673.27/min [120000], rate=34615.38/min [130000], rate=36619.72/min [140000], rate=37333.33/min [150000], rate=37037.04/min [160000], rate=37354.09/min [170000], rate=38345.86/min [180000], rate=37241.38/min [190000], rate=36190.48/min [200000], rate=36036.04/min [210000], rate=36311.24/min [220000], rate=36464.09/min [230000], rate=36411.61/min [240000], rate=35380.84/min [250000], rate=33860.05/min [260000], rate=33766.23/min [270000], rate=33061.22/min [280000], rate=32432.43/min [290000], rate=32103.32/min [300000], rate=32490.97/min [310000], rate=32920.35/min [320000], rate=33333.33/min [330000], rate=32945.09/min [340000], rate=32176.66/min [350000], rate=31296.57/min [360000], rate=31079.14/min [370000], rate=31355.93/min [380000], rate=31448.28/min -building interval tree based on /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=120000.00/min [30000], rate=81818.18/min [40000], rate=82758.62/min [50000], rate=66666.67/min [60000], rate=59016.39/min [70000], rate=56000.00/min [80000], rate=56470.59/min [90000], rate=51428.57/min [100000], rate=50000.00/min [110000], rate=48175.18/min [120000], rate=47682.12/min [130000], rate=45882.35/min [140000], rate=44919.79/min [150000], rate=44117.65/min [160000], rate=43835.62/min [170000], rate=36690.65/min [180000], rate=30594.90/min [190000], rate=27014.22/min [200000], rate=24948.02/min [210000], rate=23684.21/min [220000], rate=23036.65/min [230000], rate=23076.92/min [240000], rate=23338.74/min [250000], rate=23622.05/min [260000], rate=24186.05/min [270000], rate=24434.39/min [280000], rate=24705.88/min [290000], rate=25000.00/min [300000], rate=25568.18/min [310000], rate=26160.34/min [320000], rate=26337.45/min [330000], rate=26648.72/min [340000], rate=27019.87/min [350000], rate=27450.98/min [360000], rate=27943.08/min [370000], rate=28388.75/min [380000], rate=28643.22/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir --filt_file /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.KHsOoY8TVX/./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... 3333333.33 reads per min processed... 3272727.27 reads per min processed... 3500000.00 reads per min processed... 3428571.43 reads per min processed... 3600000.00 reads per min processed... 3529411.76 reads per min processed... 3473684.21 reads per min processed... 3600000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.KHsOoY8TVX/22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.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.KHsOoY8TVX/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -40491.035604 EM: Round [1] log likelihood: -40452.312267 EM: Round [2] log likelihood: -40434.356364 EM: Round [3] log likelihood: -40424.918898 EM: Round [4] log likelihood: -40419.732876 EM: Round [5] log likelihood: -40416.847767 EM: Round [6] log likelihood: -40415.226280 EM: Round [7] log likelihood: -40414.297056 EM: Round [8] log likelihood: -40413.748426 EM: Round [9] log likelihood: -40413.412016 EM: Round [10] log likelihood: -40413.196767 EM: Round [11] log likelihood: -40413.052876 EM: Round [12] log likelihood: -40412.952584 EM: Round [13] log likelihood: -40412.880020 EM: Round [14] log likelihood: -40412.825822 EM: Round [15] log likelihood: -40412.784273 EM: Round [16] log likelihood: -40412.751746 EM: Round [17] log likelihood: -40412.725848 EM: Round [18] log likelihood: -40412.704942 EM: Round [19] log likelihood: -40412.687871 EM: Round [20] log likelihood: -40412.673795 EM: Round [21] log likelihood: -40412.662085 EM: Round [22] log likelihood: -40412.652267 EM: Round [23] log likelihood: -40412.643973 EM: Round [24] log likelihood: -40412.636917 EM: Round [25] log likelihood: -40412.630873 EM: Round [26] log likelihood: -40412.625661 EM: Round [27] log likelihood: -40412.621138 EM: Round [28] log likelihood: -40412.617189 EM: Round [29] log likelihood: -40412.613719 EM: Round [30] log likelihood: -40412.610652 EM: Round [31] log likelihood: -40412.607926 EM: Round [32] log likelihood: -40412.605489 EM: Round [33] log likelihood: -40412.603299 EM: Round [34] log likelihood: -40412.601322 EM: Round [35] log likelihood: -40412.599527 EM: Round [36] log likelihood: -40412.597891 EM: Round [37] log likelihood: -40412.596393 EM: Round [38] log likelihood: -40412.595016 EM: Round [39] log likelihood: -40412.593746 EM: Round [40] log likelihood: -40412.592571 EM: Round [41] log likelihood: -40412.591479 EM: Round [42] log likelihood: -40412.590462 EM: Round [43] log likelihood: -40412.589513 EM: Round [44] log likelihood: -40412.588624 EM: Round [45] log likelihood: -40412.587790 EM: Round [46] log likelihood: -40412.587006 EM: Round [47] log likelihood: -40412.586268 EM: Round [48] log likelihood: -40412.585571 EM: Round [49] log likelihood: -40412.584913 EM: Round [50] log likelihood: -40412.584290 EM: Round [51] log likelihood: -40412.583700 EM: Round [52] log likelihood: -40412.583141 EM: Round [53] log likelihood: -40412.582610 EM: Round [54] log likelihood: -40412.582105 EM: Round [55] log likelihood: -40412.581625 EM: Round [56] log likelihood: -40412.581168 EM: Round [57] log likelihood: -40412.580733 EM: Round [58] log likelihood: -40412.580319 EM: Round [59] log likelihood: -40412.579923 EM: Round [60] log likelihood: -40412.579546 EM: Round [61] log likelihood: -40412.579186 EM: Round [62] log likelihood: -40412.578843 EM: Round [63] log likelihood: -40412.578515 EM: Round [64] log likelihood: -40412.578201 EM: Round [65] log likelihood: -40412.577901 EM: Round [66] log likelihood: -40412.577615 EM: Round [67] log likelihood: -40412.577340 EM: Round [68] log likelihood: -40412.577078 EM: Round [69] log likelihood: -40412.576827 EM: Round [70] log likelihood: -40412.576587 EM: Round [71] log likelihood: -40412.576358 EM: Round [72] log likelihood: -40412.576138 EM: Round [73] log likelihood: -40412.575927 EM: Round [74] log likelihood: -40412.575725 EM: Round [75] log likelihood: -40412.575532 EM: Round [76] log likelihood: -40412.575347 EM: Round [77] log likelihood: -40412.575170 EM: Round [78] log likelihood: -40412.575000 EM: Round [79] log likelihood: -40412.574837 EM: Round [80] log likelihood: -40412.574681 EM: Round [81] log likelihood: -40412.574531 EM: Round [82] log likelihood: -40412.574388 EM: Round [83] log likelihood: -40412.574251 EM: Round [84] log likelihood: -40412.574119 EM: Round [85] log likelihood: -40412.573992 EM: Round [86] log likelihood: -40412.573871 EM: Round [87] log likelihood: -40412.573755 EM: Round [88] log likelihood: -40412.573644 EM: Round [89] log likelihood: -40412.573537 EM: Round [90] log likelihood: -40412.573434 EM: Round [91] log likelihood: -40412.573336 EM: Stopping iterations at round 91 due to insufficient improvement in likelihood. EM: Starting log likelihood: -40481.606931 EM: Round [1] log likelihood: -40447.086911 EM: Round [2] log likelihood: -40431.295311 EM: Round [3] log likelihood: -40423.046059 EM: Round [4] log likelihood: -40418.548847 EM: Round [5] log likelihood: -40416.072025 EM: Round [6] log likelihood: -40414.695561 EM: Round [7] log likelihood: -40413.916454 EM: Round [8] log likelihood: -40413.462905 EM: Round [9] log likelihood: -40413.189401 EM: Round [10] log likelihood: -40413.017865 EM: Round [11] log likelihood: -40412.905871 EM: Round [12] log likelihood: -40412.829890 EM: Round [13] log likelihood: -40412.776522 EM: Round [14] log likelihood: -40412.737888 EM: Round [15] log likelihood: -40412.709196 EM: Round [16] log likelihood: -40412.687423 EM: Round [17] log likelihood: -40412.670595 EM: Round [18] log likelihood: -40412.657381 EM: Round [19] log likelihood: -40412.646855 EM: Round [20] log likelihood: -40412.638360 EM: Round [21] log likelihood: -40412.631421 EM: Round [22] log likelihood: -40412.625683 EM: Round [23] log likelihood: -40412.620886 EM: Round [24] log likelihood: -40412.616828 EM: Round [25] log likelihood: -40412.613360 EM: Round [26] log likelihood: -40412.610362 EM: Round [27] log likelihood: -40412.607746 EM: Round [28] log likelihood: -40412.605440 EM: Round [29] log likelihood: -40412.603390 EM: Round [30] log likelihood: -40412.601550 EM: Round [31] log likelihood: -40412.599886 EM: Round [32] log likelihood: -40412.598371 EM: Round [33] log likelihood: -40412.596982 EM: Round [34] log likelihood: -40412.595702 EM: Round [35] log likelihood: -40412.594515 EM: Round [36] log likelihood: -40412.593410 EM: Round [37] log likelihood: -40412.592377 EM: Round [38] log likelihood: -40412.591408 EM: Round [39] log likelihood: -40412.590497 EM: Round [40] log likelihood: -40412.589637 EM: Round [41] log likelihood: -40412.588824 EM: Round [42] log likelihood: -40412.588053 EM: Round [43] log likelihood: -40412.587322 EM: Round [44] log likelihood: -40412.586627 EM: Round [45] log likelihood: -40412.585966 EM: Round [46] log likelihood: -40412.585336 EM: Round [47] log likelihood: -40412.584735 EM: Round [48] log likelihood: -40412.584162 EM: Round [49] log likelihood: -40412.583615 EM: Round [50] log likelihood: -40412.583092 EM: Round [51] log likelihood: -40412.582592 EM: Round [52] log likelihood: -40412.582114 EM: Round [53] log likelihood: -40412.581657 EM: Round [54] log likelihood: -40412.581219 EM: Round [55] log likelihood: -40412.580800 EM: Round [56] log likelihood: -40412.580399 EM: Round [57] log likelihood: -40412.580015 EM: Round [58] log likelihood: -40412.579647 EM: Round [59] log likelihood: -40412.579294 EM: Round [60] log likelihood: -40412.578956 EM: Round [61] log likelihood: -40412.578632 EM: Round [62] log likelihood: -40412.578322 EM: Round [63] log likelihood: -40412.578025 EM: Round [64] log likelihood: -40412.577740 EM: Round [65] log likelihood: -40412.577466 EM: Round [66] log likelihood: -40412.577204 EM: Round [67] log likelihood: -40412.576953 EM: Round [68] log likelihood: -40412.576712 EM: Round [69] log likelihood: -40412.576481 EM: Round [70] log likelihood: -40412.576259 EM: Round [71] log likelihood: -40412.576047 EM: Round [72] log likelihood: -40412.575843 EM: Round [73] log likelihood: -40412.575647 EM: Round [74] log likelihood: -40412.575460 EM: Round [75] log likelihood: -40412.575280 EM: Round [76] log likelihood: -40412.575108 EM: Round [77] log likelihood: -40412.574942 EM: Round [78] log likelihood: -40412.574783 EM: Round [79] log likelihood: -40412.574631 EM: Round [80] log likelihood: -40412.574485 EM: Round [81] log likelihood: -40412.574344 EM: Round [82] log likelihood: -40412.574210 EM: Round [83] log likelihood: -40412.574081 EM: Round [84] log likelihood: -40412.573957 EM: Round [85] log likelihood: -40412.573838 EM: Round [86] log likelihood: -40412.573724 EM: Round [87] log likelihood: -40412.573614 EM: Round [88] log likelihood: -40412.573509 EM: Round [89] log likelihood: -40412.573408 EM: Round [90] log likelihood: -40412.573311 EM: Stopping iterations at round 90 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.KHsOoY8TVX/./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.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.KHsOoY8TVX/./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.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 13073429 > /tmp/nxf.KHsOoY8TVX/./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.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir > /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir --annotate /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.KHsOoY8TVX/./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.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir -done, see /tmp/nxf.KHsOoY8TVX/./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.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.KHsOoY8TVX/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 375, filtered: 3724) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.KHsOoY8TVX/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.KHsOoY8TVX/./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.KHsOoY8TVX/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000257476.1] WARNING, no entry stored in dbm for [ENSG00000199883.1] WARNING, no entry stored in dbm for [ENSG00000202241.1] WARNING, no entry stored in dbm for [ENSG00000200867.1] WARNING, no entry stored in dbm for [ENSG00000202241.1] WARNING, no entry stored in dbm for [ENSG00000200783.1] WARNING, no entry stored in dbm for [ENSG00000202241.1] WARNING, no entry stored in dbm for [ENSG00000230305.2] WARNING, no entry stored in dbm for [ENSG00000259020.3] WARNING, no entry stored in dbm for [ENSG00000093100.13] WARNING, no entry stored in dbm for [ENSG00000236643.1] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000272848.2] WARNING, no entry stored in dbm for [ENSG00000146556.14] WARNING, no entry stored in dbm for [ENSG00000186312.10] WARNING, no entry stored in dbm for [ENSG00000270641.1] WARNING, no entry stored in dbm for [ENSG00000225914.3] WARNING, no entry stored in dbm for [ENSG00000240549.2] WARNING, no entry stored in dbm for [ENSG00000224914.4] WARNING, no entry stored in dbm for [ENSG00000231528.3] WARNING, no entry stored in dbm for [ENSG00000225292.2] WARNING, no entry stored in dbm for [ENSG00000270576.1] WARNING, no entry stored in dbm for [ENSG00000286786.1] WARNING, no entry stored in dbm for [ENSG00000286884.1] WARNING, no entry stored in dbm for [ENSG00000204044.6] WARNING, no entry stored in dbm for [ENSG00000231304.2] WARNING, no entry stored in dbm for [ENSG00000237232.9] WARNING, no entry stored in dbm for [ENSG00000275265.1] WARNING, no entry stored in dbm for [ENSG00000250379.1] WARNING, no entry stored in dbm for [ENSG00000213891.3] WARNING, no entry stored in dbm for [ENSG00000207334.1] WARNING, no entry stored in dbm for [ENSG00000200048.1] WARNING, no entry stored in dbm for [ENSG00000243562.3] WARNING, no entry stored in dbm for [ENSG00000242971.3] WARNING, no entry stored in dbm for [ENSG00000239437.3] WARNING, no entry stored in dbm for [ENSG00000266420.2] WARNING, no entry stored in dbm for [ENSG00000239726.3] WARNING, no entry stored in dbm for [ENSG00000278771.1] WARNING, no entry stored in dbm for [ENSG00000244642.3] WARNING, no entry stored in dbm for [ENSG00000243035.3] WARNING, no entry stored in dbm for [ENSG00000201600.1] WARNING, no entry stored in dbm for [ENSG00000280124.1] WARNING, no entry stored in dbm for [ENSG00000230461.9] WARNING, no entry stored in dbm for [ENSG00000274602.5] WARNING, no entry stored in dbm for [ENSG00000232556.1] WARNING, no entry stored in dbm for [ENSG00000277270.2] WARNING, no entry stored in dbm for [ENSG00000254285.3] WARNING, no entry stored in dbm for [ENSG00000245694.10] WARNING, no entry stored in dbm for [ENSG00000285855.1] WARNING, no entry stored in dbm for [ENSG00000250961.2] WARNING, no entry stored in dbm for [ENSG00000180066.10] WARNING, no entry stored in dbm for [ENSG00000272197.2] WARNING, no entry stored in dbm for [ENSG00000276956.1] WARNING, no entry stored in dbm for [ENSG00000239942.2] WARNING, no entry stored in dbm for [ENSG00000266467.2] WARNING, no entry stored in dbm for [ENSG00000268545.1] WARNING, no entry stored in dbm for [ENSG00000225422.4] WARNING, no entry stored in dbm for [ENSG00000249476.2] WARNING, no entry stored in dbm for [ENSG00000267519.6] WARNING, no entry stored in dbm for [ENSG00000237986.4] WARNING, no entry stored in dbm for [ENSG00000229893.2] WARNING, no entry stored in dbm for [ENSG00000205611.5] WARNING, no entry stored in dbm for [ENSG00000227036.8] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000267244.5] WARNING, no entry stored in dbm for [ENSG00000253647.1] WARNING, no entry stored in dbm for [ENSG00000249286.1] WARNING, no entry stored in dbm for [ENSG00000214045.3] WARNING, no entry stored in dbm for [ENSG00000276550.4] WARNING, no entry stored in dbm for [ENSG00000225851.1] WARNING, no entry stored in dbm for [ENSG00000275216.2] WARNING, no entry stored in dbm for [ENSG00000236206.2] WARNING, no entry stored in dbm for [ENSG00000250208.6] WARNING, no entry stored in dbm for [ENSG00000088340.17] WARNING, no entry stored in dbm for [ENSG00000248429.5] WARNING, no entry stored in dbm for [ENSG00000248290.1] WARNING, no entry stored in dbm for [ENSG00000241743.4] WARNING, no entry stored in dbm for [ENSG00000254285.3] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000239521.9] WARNING, no entry stored in dbm for [ENSG00000181577.16] WARNING, no entry stored in dbm for [ENSG00000224413.1] WARNING, no entry stored in dbm for [ENSG00000233995.1] WARNING, no entry stored in dbm for [ENSG00000233995.1] WARNING, no entry stored in dbm for [ENSG00000233995.1] WARNING, no entry stored in dbm for [ENSG00000233995.1] WARNING, no entry stored in dbm for [ENSG00000285608.1] WARNING, no entry stored in dbm for [ENSG00000234026.1] WARNING, no entry stored in dbm for [ENSG00000274691.1] WARNING, no entry stored in dbm for [ENSG00000224691.1] WARNING, no entry stored in dbm for [ENSG00000242779.7] WARNING, no entry stored in dbm for [ENSG00000236526.1] WARNING, no entry stored in dbm for [ENSG00000249306.6] WARNING, no entry stored in dbm for [ENSG00000231536.1] WARNING, no entry stored in dbm for [ENSG00000266865.6] WARNING, no entry stored in dbm for [ENSG00000214999.3] WARNING, no entry stored in dbm for [ENSG00000261924.1] WARNING, no entry stored in dbm for [ENSG00000241770.1] WARNING, no entry stored in dbm for [ENSG00000254285.3] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000265401.1] WARNING, no entry stored in dbm for [ENSG00000265401.1] WARNING, no entry stored in dbm for [ENSG00000173209.23] WARNING, no entry stored in dbm for [ENSG00000243620.2] WARNING, no entry stored in dbm for [ENSG00000285336.1] WARNING, no entry stored in dbm for [ENSG00000257337.7] WARNING, no entry stored in dbm for [ENSG00000261265.1] WARNING, no entry stored in dbm for [ENSG00000186148.13] WARNING, no entry stored in dbm for [ENSG00000225792.2] * STAR-Fusion complete. See output: /tmp/nxf.KHsOoY8TVX/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)