Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/f0e508e3231f0e24fdfcb4cf9109f4/ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz 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/49/726b26a493226c1ac7073cb772f169/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/f0e508e3231f0e24fdfcb4cf9109f4/ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/726b26a493226c1ac7073cb772f169/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/12b2994b64a78d3012fdce6b89194e/ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.jeoHw0KcYS/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary -sample contains 14655979 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir -J /tmp/nxf.jeoHw0KcYS/ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.jeoHw0KcYS/ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=70588.24/min [30000], rate=75000.00/min [40000], rate=82758.62/min [50000], rate=85714.29/min [60000], rate=87804.88/min [70000], rate=93333.33/min [80000], rate=96000.00/min [90000], rate=98181.82/min [100000], rate=100000.00/min [110000], rate=100000.00/min [120000], rate=101408.45/min [130000], rate=102631.58/min [140000], rate=103703.70/min [150000], rate=104651.16/min [160000], rate=105494.51/min [170000], rate=106250.00/min [180000], rate=105882.35/min [190000], rate=106542.06/min [200000], rate=107142.86/min [210000], rate=106779.66/min [220000], rate=105600.00/min [230000], rate=104545.45/min [240000], rate=102857.14/min [250000], rate=101351.35/min [260000], rate=97500.00/min [270000], rate=92571.43/min [280000], rate=90810.81/min [290000], rate=89690.72/min [300000], rate=87804.88/min [310000], rate=85321.10/min [320000], rate=83842.79/min [330000], rate=82500.00/min [340000], rate=82591.09/min [350000], rate=82031.25/min [360000], rate=80597.01/min [370000], rate=78169.01/min [380000], rate=76254.18/min [390000], rate=75483.87/min -building interval tree based on /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=75000.00/min [20000], rate=92307.69/min [30000], rate=90000.00/min [40000], rate=96000.00/min [50000], rate=96774.19/min [60000], rate=94736.84/min [70000], rate=97674.42/min [80000], rate=102127.66/min [90000], rate=110204.08/min [100000], rate=109090.91/min [110000], rate=110000.00/min [120000], rate=110769.23/min [130000], rate=109859.15/min [140000], rate=107692.31/min [150000], rate=105882.35/min [160000], rate=105494.51/min [170000], rate=97142.86/min [180000], rate=90756.30/min [190000], rate=87022.90/min [200000], rate=83916.08/min [210000], rate=81818.18/min [220000], rate=81481.48/min [230000], rate=81656.80/min [240000], rate=79120.88/min [250000], rate=76923.08/min [260000], rate=75728.16/min [270000], rate=74311.93/min [280000], rate=74336.28/min [290000], rate=71020.41/min [300000], rate=67924.53/min [310000], rate=66906.47/min [320000], rate=65306.12/min [330000], rate=64285.71/min [340000], rate=61631.42/min [350000], rate=60344.83/min [360000], rate=59504.13/min [370000], rate=58575.20/min [380000], rate=58015.27/min [390000], rate=57212.71/min [400000], rate=55172.41/min -building interval tree based on /tmp/nxf.jeoHw0KcYS/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=92307.69/min [30000], rate=81818.18/min [40000], rate=85714.29/min [50000], rate=96774.19/min [60000], rate=97297.30/min [70000], rate=93333.33/min [80000], rate=92307.69/min [90000], rate=94736.84/min [100000], rate=92307.69/min [110000], rate=86842.11/min [120000], rate=82758.62/min [130000], rate=80412.37/min [140000], rate=80769.23/min [150000], rate=78947.37/min [160000], rate=78688.52/min [170000], rate=79069.77/min [180000], rate=71523.18/min [190000], rate=66666.67/min [200000], rate=64516.13/min [210000], rate=63316.58/min [220000], rate=62857.14/min [230000], rate=63594.47/min [240000], rate=64000.00/min [250000], rate=60000.00/min [260000], rate=55123.67/min [270000], rate=52090.03/min [280000], rate=51219.51/min [290000], rate=51176.47/min [300000], rate=50561.80/min [310000], rate=47448.98/min [320000], rate=45390.07/min [330000], rate=44394.62/min [340000], rate=43404.26/min [350000], rate=43209.88/min [360000], rate=42942.35/min [370000], rate=42940.04/min [380000], rate=43100.19/min [390000], rate=43173.43/min -building interval tree based on /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=150000.00/min [20000], rate=133333.33/min [30000], rate=150000.00/min [40000], rate=160000.00/min [50000], rate=157894.74/min [60000], rate=156521.74/min [70000], rate=161538.46/min [80000], rate=160000.00/min [90000], rate=154285.71/min [100000], rate=157894.74/min [110000], rate=157142.86/min [120000], rate=156521.74/min [130000], rate=159183.67/min [140000], rate=140000.00/min [150000], rate=104651.16/min [160000], rate=88888.89/min [170000], rate=77272.73/min [180000], rate=72000.00/min [190000], rate=67857.14/min [200000], rate=65573.77/min [210000], rate=64615.38/min [220000], rate=64390.24/min [230000], rate=63302.75/min [240000], rate=62882.10/min [250000], rate=61983.47/min [260000], rate=62151.39/min [270000], rate=58695.65/min [280000], rate=53674.12/min [290000], rate=49856.73/min [300000], rate=48648.65/min [310000], rate=48311.69/min [320000], rate=46943.77/min [330000], rate=46808.51/min [340000], rate=46469.25/min [350000], rate=44025.16/min [360000], rate=42857.14/min [370000], rate=42528.74/min [380000], rate=42776.74/min [390000], rate=42700.73/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir --filt_file /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info. 6000000.00 reads per min processed... 4000000.00 reads per min processed... 3600000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 2857142.86 reads per min processed... 2869565.22 reads per min processed... 2880000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.jeoHw0KcYS/ColoN_FFPE_L01_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.jeoHw0KcYS/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -30149.304464 EM: Round [1] log likelihood: -30113.914014 EM: Round [2] log likelihood: -30098.031392 EM: Round [3] log likelihood: -30089.683435 EM: Round [4] log likelihood: -30085.088522 EM: Round [5] log likelihood: -30082.511915 EM: Round [6] log likelihood: -30081.033977 EM: Round [7] log likelihood: -30080.158630 EM: Round [8] log likelihood: -30079.620327 EM: Round [9] log likelihood: -30079.276340 EM: Round [10] log likelihood: -30079.048491 EM: Round [11] log likelihood: -30078.892705 EM: Round [12] log likelihood: -30078.783275 EM: Round [13] log likelihood: -30078.704658 EM: Round [14] log likelihood: -30078.647116 EM: Round [15] log likelihood: -30078.604341 EM: Round [16] log likelihood: -30078.572121 EM: Round [17] log likelihood: -30078.547571 EM: Round [18] log likelihood: -30078.528669 EM: Round [19] log likelihood: -30078.513975 EM: Round [20] log likelihood: -30078.502441 EM: Round [21] log likelihood: -30078.493304 EM: Round [22] log likelihood: -30078.485996 EM: Round [23] log likelihood: -30078.480093 EM: Round [24] log likelihood: -30078.475276 EM: Round [25] log likelihood: -30078.471303 EM: Round [26] log likelihood: -30078.467991 EM: Round [27] log likelihood: -30078.465199 EM: Round [28] log likelihood: -30078.462818 EM: Round [29] log likelihood: -30078.460764 EM: Round [30] log likelihood: -30078.458973 EM: Round [31] log likelihood: -30078.457394 EM: Round [32] log likelihood: -30078.455987 EM: Round [33] log likelihood: -30078.454722 EM: Round [34] log likelihood: -30078.453573 EM: Round [35] log likelihood: -30078.452521 EM: Round [36] log likelihood: -30078.451551 EM: Round [37] log likelihood: -30078.450650 EM: Round [38] log likelihood: -30078.449808 EM: Round [39] log likelihood: -30078.449018 EM: Round [40] log likelihood: -30078.448272 EM: Round [41] log likelihood: -30078.447566 EM: Round [42] log likelihood: -30078.446895 EM: Round [43] log likelihood: -30078.446256 EM: Round [44] log likelihood: -30078.445645 EM: Round [45] log likelihood: -30078.445061 EM: Round [46] log likelihood: -30078.444500 EM: Round [47] log likelihood: -30078.443962 EM: Round [48] log likelihood: -30078.443445 EM: Round [49] log likelihood: -30078.442947 EM: Round [50] log likelihood: -30078.442467 EM: Round [51] log likelihood: -30078.442005 EM: Round [52] log likelihood: -30078.441559 EM: Round [53] log likelihood: -30078.441128 EM: Round [54] log likelihood: -30078.440713 EM: Round [55] log likelihood: -30078.440312 EM: Round [56] log likelihood: -30078.439925 EM: Round [57] log likelihood: -30078.439551 EM: Round [58] log likelihood: -30078.439189 EM: Round [59] log likelihood: -30078.438840 EM: Round [60] log likelihood: -30078.438503 EM: Round [61] log likelihood: -30078.438177 EM: Round [62] log likelihood: -30078.437862 EM: Round [63] log likelihood: -30078.437557 EM: Round [64] log likelihood: -30078.437263 EM: Round [65] log likelihood: -30078.436979 EM: Round [66] log likelihood: -30078.436704 EM: Round [67] log likelihood: -30078.436439 EM: Round [68] log likelihood: -30078.436183 EM: Round [69] log likelihood: -30078.435935 EM: Round [70] log likelihood: -30078.435696 EM: Round [71] log likelihood: -30078.435465 EM: Round [72] log likelihood: -30078.435241 EM: Round [73] log likelihood: -30078.435026 EM: Round [74] log likelihood: -30078.434818 EM: Round [75] log likelihood: -30078.434617 EM: Round [76] log likelihood: -30078.434422 EM: Round [77] log likelihood: -30078.434235 EM: Round [78] log likelihood: -30078.434054 EM: Round [79] log likelihood: -30078.433879 EM: Round [80] log likelihood: -30078.433711 EM: Round [81] log likelihood: -30078.433548 EM: Round [82] log likelihood: -30078.433391 EM: Round [83] log likelihood: -30078.433239 EM: Round [84] log likelihood: -30078.433093 EM: Round [85] log likelihood: -30078.432952 EM: Round [86] log likelihood: -30078.432816 EM: Round [87] log likelihood: -30078.432684 EM: Round [88] log likelihood: -30078.432558 EM: Round [89] log likelihood: -30078.432435 EM: Round [90] log likelihood: -30078.432317 EM: Round [91] log likelihood: -30078.432204 EM: Round [92] log likelihood: -30078.432094 EM: Round [93] log likelihood: -30078.431988 EM: Round [94] log likelihood: -30078.431886 EM: Round [95] log likelihood: -30078.431787 EM: Stopping iterations at round 95 due to insufficient improvement in likelihood. EM: Starting log likelihood: -30064.023186 EM: Round [1] log likelihood: -30033.294368 EM: Round [2] log likelihood: -30020.058687 EM: Round [3] log likelihood: -30013.312791 EM: Round [4] log likelihood: -30009.690094 EM: Round [5] log likelihood: -30007.694195 EM: Round [6] log likelihood: -30006.561279 EM: Round [7] log likelihood: -30005.893234 EM: Round [8] log likelihood: -30005.482416 EM: Round [9] log likelihood: -30005.219176 EM: Round [10] log likelihood: -30005.044089 EM: Round [11] log likelihood: -30004.923830 EM: Round [12] log likelihood: -30004.838983 EM: Round [13] log likelihood: -30004.777789 EM: Round [14] log likelihood: -30004.732851 EM: Round [15] log likelihood: -30004.699358 EM: Round [16] log likelihood: -30004.674079 EM: Round [17] log likelihood: -30004.654789 EM: Round [18] log likelihood: -30004.639923 EM: Round [19] log likelihood: -30004.628357 EM: Round [20] log likelihood: -30004.619275 EM: Round [21] log likelihood: -30004.612076 EM: Round [22] log likelihood: -30004.606314 EM: Round [23] log likelihood: -30004.601655 EM: Round [24] log likelihood: -30004.597846 EM: Round [25] log likelihood: -30004.594697 EM: Round [26] log likelihood: -30004.592062 EM: Round [27] log likelihood: -30004.589830 EM: Round [28] log likelihood: -30004.587915 EM: Round [29] log likelihood: -30004.586252 EM: Round [30] log likelihood: -30004.584788 EM: Round [31] log likelihood: -30004.583486 EM: Round [32] log likelihood: -30004.582314 EM: Round [33] log likelihood: -30004.581247 EM: Round [34] log likelihood: -30004.580268 EM: Round [35] log likelihood: -30004.579361 EM: Round [36] log likelihood: -30004.578515 EM: Round [37] log likelihood: -30004.577721 EM: Round [38] log likelihood: -30004.576971 EM: Round [39] log likelihood: -30004.576260 EM: Round [40] log likelihood: -30004.575582 EM: Round [41] log likelihood: -30004.574935 EM: Round [42] log likelihood: -30004.574315 EM: Round [43] log likelihood: -30004.573719 EM: Round [44] log likelihood: -30004.573146 EM: Round [45] log likelihood: -30004.572595 EM: Round [46] log likelihood: -30004.572062 EM: Round [47] log likelihood: -30004.571549 EM: Round [48] log likelihood: -30004.571052 EM: Round [49] log likelihood: -30004.570573 EM: Round [50] log likelihood: -30004.570109 EM: Round [51] log likelihood: -30004.569660 EM: Round [52] log likelihood: -30004.569226 EM: Round [53] log likelihood: -30004.568806 EM: Round [54] log likelihood: -30004.568399 EM: Round [55] log likelihood: -30004.568006 EM: Round [56] log likelihood: -30004.567625 EM: Round [57] log likelihood: -30004.567257 EM: Round [58] log likelihood: -30004.566900 EM: Round [59] log likelihood: -30004.566555 EM: Round [60] log likelihood: -30004.566221 EM: Round [61] log likelihood: -30004.565898 EM: Round [62] log likelihood: -30004.565586 EM: Round [63] log likelihood: -30004.565284 EM: Round [64] log likelihood: -30004.564991 EM: Round [65] log likelihood: -30004.564709 EM: Round [66] log likelihood: -30004.564435 EM: Round [67] log likelihood: -30004.564171 EM: Round [68] log likelihood: -30004.563915 EM: Round [69] log likelihood: -30004.563669 EM: Round [70] log likelihood: -30004.563430 EM: Round [71] log likelihood: -30004.563199 EM: Round [72] log likelihood: -30004.562976 EM: Round [73] log likelihood: -30004.562761 EM: Round [74] log likelihood: -30004.562553 EM: Round [75] log likelihood: -30004.562352 EM: Round [76] log likelihood: -30004.562158 EM: Round [77] log likelihood: -30004.561971 EM: Round [78] log likelihood: -30004.561790 EM: Round [79] log likelihood: -30004.561615 EM: Round [80] log likelihood: -30004.561446 EM: Round [81] log likelihood: -30004.561284 EM: Round [82] log likelihood: -30004.561126 EM: Round [83] log likelihood: -30004.560975 EM: Round [84] log likelihood: -30004.560828 EM: Round [85] log likelihood: -30004.560687 EM: Round [86] log likelihood: -30004.560551 EM: Round [87] log likelihood: -30004.560419 EM: Round [88] log likelihood: -30004.560292 EM: Round [89] log likelihood: -30004.560170 EM: Round [90] log likelihood: -30004.560051 EM: Round [91] log likelihood: -30004.559937 EM: Round [92] log likelihood: -30004.559827 EM: Round [93] log likelihood: -30004.559721 EM: Round [94] log likelihood: -30004.559619 EM: Round [95] log likelihood: -30004.559521 EM: Stopping iterations at round 95 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.jeoHw0KcYS/./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.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.jeoHw0KcYS/./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.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 14655979 > /tmp/nxf.jeoHw0KcYS/./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.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir > /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir --annotate /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.jeoHw0KcYS/./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.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir -done, see /tmp/nxf.jeoHw0KcYS/./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.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.jeoHw0KcYS/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 228, filtered: 2769) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.jeoHw0KcYS/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.jeoHw0KcYS/./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.jeoHw0KcYS/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000237004.4] 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 [ENSG00000279217.1] 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 [ENSG00000227521.2] WARNING, no entry stored in dbm for [ENSG00000240549.2] WARNING, no entry stored in dbm for [ENSG00000271434.3] WARNING, no entry stored in dbm for [ENSG00000264538.6] 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 [ENSG00000270791.1] WARNING, no entry stored in dbm for [ENSG00000232648.4] WARNING, no entry stored in dbm for [ENSG00000253508.1] WARNING, no entry stored in dbm for [ENSG00000187483.10] WARNING, no entry stored in dbm for [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000241625.3] WARNING, no entry stored in dbm for [ENSG00000241246.3] WARNING, no entry stored in dbm for [ENSG00000201901.1] WARNING, no entry stored in dbm for [ENSG00000199683.1] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000238013.1] WARNING, no entry stored in dbm for [ENSG00000273149.1] WARNING, no entry stored in dbm for [ENSG00000249621.1] WARNING, no entry stored in dbm for [ENSG00000227619.3] WARNING, no entry stored in dbm for [ENSG00000279128.1] WARNING, no entry stored in dbm for [ENSG00000196312.15] WARNING, no entry stored in dbm for [ENSG00000182366.10] WARNING, no entry stored in dbm for [ENSG00000284237.1] WARNING, no entry stored in dbm for [ENSG00000245937.8] WARNING, no entry stored in dbm for [ENSG00000245275.8] WARNING, no entry stored in dbm for [ENSG00000224520.2] WARNING, no entry stored in dbm for [ENSG00000257402.2] WARNING, no entry stored in dbm for [ENSG00000205312.8] WARNING, no entry stored in dbm for [ENSG00000236467.8] WARNING, no entry stored in dbm for [ENSG00000260776.6] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000181126.13] WARNING, no entry stored in dbm for [ENSG00000225978.3] WARNING, no entry stored in dbm for [ENSG00000231721.7] WARNING, no entry stored in dbm for [ENSG00000235240.1] WARNING, no entry stored in dbm for [ENSG00000230849.2] WARNING, no entry stored in dbm for [ENSG00000231900.3] 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 [ENSG00000250345.2] WARNING, no entry stored in dbm for [ENSG00000283907.1] WARNING, no entry stored in dbm for [ENSG00000234028.3] WARNING, no entry stored in dbm for [ENSG00000216906.2] WARNING, no entry stored in dbm for [ENSG00000247373.3] WARNING, no entry stored in dbm for [ENSG00000233221.7] WARNING, no entry stored in dbm for [ENSG00000175147.13] WARNING, no entry stored in dbm for [ENSG00000255717.7] WARNING, no entry stored in dbm for [ENSG00000223704.2] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000273329.1] WARNING, no entry stored in dbm for [ENSG00000261670.1] WARNING, no entry stored in dbm for [ENSG00000277801.1] WARNING, no entry stored in dbm for [ENSG00000271551.2] WARNING, no entry stored in dbm for [ENSG00000271329.1] WARNING, no entry stored in dbm for [ENSG00000226239.2] WARNING, no entry stored in dbm for [ENSG00000230869.1] WARNING, no entry stored in dbm for [ENSG00000282572.2] WARNING, no entry stored in dbm for [ENSG00000277125.1] WARNING, no entry stored in dbm for [ENSG00000286619.1] WARNING, no entry stored in dbm for [ENSG00000269001.2] WARNING, no entry stored in dbm for [ENSG00000288633.1] WARNING, no entry stored in dbm for [ENSG00000187953.10] WARNING, no entry stored in dbm for [ENSG00000264151.6] WARNING, no entry stored in dbm for [ENSG00000257607.1] WARNING, no entry stored in dbm for [ENSG00000234129.8] WARNING, no entry stored in dbm for [ENSG00000234638.1] WARNING, no entry stored in dbm for [ENSG00000259649.4] WARNING, no entry stored in dbm for [ENSG00000226472.8] WARNING, no entry stored in dbm for [ENSG00000279726.2] * STAR-Fusion complete. See output: /tmp/nxf.jeoHw0KcYS/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)