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/4f/0734f77412ec58e675bc615016ec7c/aih-tih-sc-0754d2-R1_A23YTGFLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/1e710377721187d00adf408ca01ee0/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/1e710377721187d00adf408ca01ee0/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/0734f77412ec58e675bc615016ec7c/aih-tih-sc-0754d2-R1_A23YTGFLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/dae1d6aa7b1426d476226fd533566f/aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.ZNEdBQDLuY/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary -sample contains 29706015 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir -J /tmp/nxf.ZNEdBQDLuY/aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Chimeric.out.junction -O /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.ZNEdBQDLuY/aih-tih-sc-0754d2-R1_A23YTGFLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=54545.45/min [20000], rate=54545.45/min [30000], rate=54545.45/min [40000], rate=60000.00/min [50000], rate=65217.39/min [60000], rate=65454.55/min [70000], rate=70000.00/min [80000], rate=72727.27/min [90000], rate=76056.34/min [100000], rate=83333.33/min [110000], rate=90410.96/min [120000], rate=97297.30/min [130000], rate=102631.58/min [140000], rate=103703.70/min [150000], rate=105882.35/min [160000], rate=106666.67/min [170000], rate=107368.42/min [180000], rate=108000.00/min [190000], rate=110679.61/min [200000], rate=111111.11/min [210000], rate=110526.32/min [220000], rate=114782.61/min [230000], rate=118965.52/min [240000], rate=123076.92/min [250000], rate=125000.00/min [260000], rate=124800.00/min [270000], rate=124615.38/min [280000], rate=125373.13/min [290000], rate=127941.18/min [300000], rate=127659.57/min [310000], rate=129166.67/min [320000], rate=128000.00/min [330000], rate=126923.08/min [340000], rate=127500.00/min [350000], rate=127272.73/min [360000], rate=126315.79/min [370000], rate=124022.35/min [380000], rate=123243.24/min [390000], rate=122513.09/min [400000], rate=118226.60/min [410000], rate=112844.04/min [420000], rate=110043.67/min [430000], rate=107949.79/min [440000], rate=106024.10/min -building interval tree based on /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=200000.00/min [20000], rate=240000.00/min [30000], rate=225000.00/min [40000], rate=171428.57/min [50000], rate=166666.67/min [60000], rate=180000.00/min [70000], rate=182608.70/min [80000], rate=177777.78/min [90000], rate=192857.14/min [100000], rate=181818.18/min [110000], rate=178378.38/min [120000], rate=180000.00/min [130000], rate=190243.90/min [140000], rate=186666.67/min [150000], rate=191489.36/min [160000], rate=188235.29/min [170000], rate=182142.86/min [180000], rate=177049.18/min [190000], rate=175384.62/min [200000], rate=171428.57/min [210000], rate=172602.74/min [220000], rate=176000.00/min [230000], rate=172500.00/min [240000], rate=167441.86/min [250000], rate=166666.67/min [260000], rate=143119.27/min [270000], rate=123664.12/min [280000], rate=112000.00/min [290000], rate=104819.28/min [300000], rate=98901.10/min [310000], rate=95384.62/min [320000], rate=92307.69/min [330000], rate=90000.00/min [340000], rate=88311.69/min [350000], rate=87500.00/min [360000], rate=87449.39/min [370000], rate=86381.32/min [380000], rate=85714.29/min [390000], rate=85714.29/min [400000], rate=85409.25/min [410000], rate=82828.28/min [420000], rate=81290.32/min [430000], rate=80373.83/min -building interval tree based on /tmp/nxf.ZNEdBQDLuY/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=100000.00/min [30000], rate=75000.00/min [40000], rate=72727.27/min [50000], rate=69767.44/min [60000], rate=65454.55/min [70000], rate=63636.36/min [80000], rate=65753.42/min [90000], rate=67500.00/min [100000], rate=65934.07/min [110000], rate=65346.53/min [120000], rate=62608.70/min [130000], rate=61417.32/min [140000], rate=60000.00/min [150000], rate=60000.00/min [160000], rate=62745.10/min [170000], rate=63750.00/min [180000], rate=62790.70/min [190000], rate=61956.52/min [200000], rate=61538.46/min [210000], rate=61165.05/min [220000], rate=61395.35/min [230000], rate=61883.41/min [240000], rate=62068.97/min [250000], rate=61983.47/min [260000], rate=62400.00/min [270000], rate=63035.02/min [280000], rate=64615.38/min [290000], rate=66159.70/min [300000], rate=67415.73/min [310000], rate=68888.89/min [320000], rate=70072.99/min [330000], rate=70967.74/min [340000], rate=70833.33/min [350000], rate=70469.80/min [360000], rate=70129.87/min [370000], rate=70253.16/min [380000], rate=71250.00/min [390000], rate=71779.14/min [400000], rate=71428.57/min [410000], rate=71304.35/min [420000], rate=71794.87/min [430000], rate=72676.06/min -building interval tree based on /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=57142.86/min [30000], rate=51428.57/min [40000], rate=51063.83/min [50000], rate=50000.00/min [60000], rate=52941.18/min [70000], rate=56756.76/min [80000], rate=59259.26/min [90000], rate=61363.64/min [100000], rate=60606.06/min [110000], rate=61682.24/min [120000], rate=63716.81/min [130000], rate=66666.67/min [140000], rate=67200.00/min [150000], rate=66176.47/min [160000], rate=66666.67/min [170000], rate=66666.67/min [180000], rate=64670.66/min [190000], rate=64406.78/min [200000], rate=63829.79/min [210000], rate=63636.36/min [220000], rate=63461.54/min [230000], rate=64186.05/min [240000], rate=64285.71/min [250000], rate=62761.51/min [260000], rate=61904.76/min [270000], rate=61596.96/min [280000], rate=61090.91/min [290000], rate=61052.63/min [300000], rate=61643.84/min [310000], rate=62207.36/min [320000], rate=63366.34/min [330000], rate=64077.67/min [340000], rate=62769.23/min [350000], rate=61583.58/min [360000], rate=61189.80/min [370000], rate=60821.92/min [380000], rate=60638.30/min [390000], rate=60465.12/min [400000], rate=60759.49/min [410000], rate=61042.18/min [420000], rate=61165.05/min [430000], rate=60280.37/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir --filt_file /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.ZNEdBQDLuY/./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... 4800000.00 reads per min processed... 3750000.00 reads per min processed... 3600000.00 reads per min processed... 3500000.00 reads per min processed... 3428571.43 reads per min processed... 3857142.86 reads per min processed... 4000000.00 reads per min processed... 4125000.00 reads per min processed... 4000000.00 reads per min processed... 3900000.00 reads per min processed... 3818181.82 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.ZNEdBQDLuY/aih-tih-sc-0754d2-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.ZNEdBQDLuY/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -83145.535877 EM: Round [1] log likelihood: -83064.273820 EM: Round [2] log likelihood: -83029.282866 EM: Round [3] log likelihood: -83011.890089 EM: Round [4] log likelihood: -83002.645708 EM: Round [5] log likelihood: -82997.504989 EM: Round [6] log likelihood: -82994.519424 EM: Round [7] log likelihood: -82992.703701 EM: Round [8] log likelihood: -82991.546813 EM: Round [9] log likelihood: -82990.776768 EM: Round [10] log likelihood: -82990.243960 EM: Round [11] log likelihood: -82989.862898 EM: Round [12] log likelihood: -82989.582711 EM: Round [13] log likelihood: -82989.371899 EM: Round [14] log likelihood: -82989.210218 EM: Round [15] log likelihood: -82989.084210 EM: Round [16] log likelihood: -82988.984663 EM: Round [17] log likelihood: -82988.905102 EM: Round [18] log likelihood: -82988.840875 EM: Round [19] log likelihood: -82988.788574 EM: Round [20] log likelihood: -82988.745658 EM: Round [21] log likelihood: -82988.710206 EM: Round [22] log likelihood: -82988.680743 EM: Round [23] log likelihood: -82988.656127 EM: Round [24] log likelihood: -82988.635459 EM: Round [25] log likelihood: -82988.618030 EM: Round [26] log likelihood: -82988.603273 EM: Round [27] log likelihood: -82988.590731 EM: Round [28] log likelihood: -82988.580032 EM: Round [29] log likelihood: -82988.570877 EM: Round [30] log likelihood: -82988.563015 EM: Round [31] log likelihood: -82988.556244 EM: Round [32] log likelihood: -82988.550394 EM: Round [33] log likelihood: -82988.545324 EM: Round [34] log likelihood: -82988.540917 EM: Round [35] log likelihood: -82988.537074 EM: Round [36] log likelihood: -82988.533712 EM: Round [37] log likelihood: -82988.530762 EM: Round [38] log likelihood: -82988.528165 EM: Round [39] log likelihood: -82988.525870 EM: Round [40] log likelihood: -82988.523837 EM: Round [41] log likelihood: -82988.522028 EM: Round [42] log likelihood: -82988.520414 EM: Round [43] log likelihood: -82988.518967 EM: Round [44] log likelihood: -82988.517666 EM: Round [45] log likelihood: -82988.516491 EM: Round [46] log likelihood: -82988.515426 EM: Round [47] log likelihood: -82988.514458 EM: Round [48] log likelihood: -82988.513573 EM: Round [49] log likelihood: -82988.512761 EM: Round [50] log likelihood: -82988.512014 EM: Round [51] log likelihood: -82988.511324 EM: Round [52] log likelihood: -82988.510684 EM: Round [53] log likelihood: -82988.510088 EM: Round [54] log likelihood: -82988.509532 EM: Round [55] log likelihood: -82988.509010 EM: Round [56] log likelihood: -82988.508519 EM: Round [57] log likelihood: -82988.508056 EM: Round [58] log likelihood: -82988.507618 EM: Round [59] log likelihood: -82988.507202 EM: Round [60] log likelihood: -82988.506807 EM: Round [61] log likelihood: -82988.506430 EM: Round [62] log likelihood: -82988.506069 EM: Round [63] log likelihood: -82988.505724 EM: Round [64] log likelihood: -82988.505393 EM: Round [65] log likelihood: -82988.505075 EM: Round [66] log likelihood: -82988.504769 EM: Round [67] log likelihood: -82988.504473 EM: Round [68] log likelihood: -82988.504188 EM: Round [69] log likelihood: -82988.503912 EM: Round [70] log likelihood: -82988.503645 EM: Round [71] log likelihood: -82988.503387 EM: Round [72] log likelihood: -82988.503136 EM: Round [73] log likelihood: -82988.502893 EM: Round [74] log likelihood: -82988.502657 EM: Round [75] log likelihood: -82988.502428 EM: Round [76] log likelihood: -82988.502205 EM: Round [77] log likelihood: -82988.501988 EM: Round [78] log likelihood: -82988.501777 EM: Round [79] log likelihood: -82988.501572 EM: Round [80] log likelihood: -82988.501372 EM: Round [81] log likelihood: -82988.501177 EM: Round [82] log likelihood: -82988.500987 EM: Round [83] log likelihood: -82988.500802 EM: Round [84] log likelihood: -82988.500622 EM: Round [85] log likelihood: -82988.500446 EM: Round [86] log likelihood: -82988.500275 EM: Round [87] log likelihood: -82988.500108 EM: Round [88] log likelihood: -82988.499946 EM: Round [89] log likelihood: -82988.499787 EM: Round [90] log likelihood: -82988.499632 EM: Round [91] log likelihood: -82988.499481 EM: Round [92] log likelihood: -82988.499334 EM: Round [93] log likelihood: -82988.499190 EM: Round [94] log likelihood: -82988.499050 EM: Round [95] log likelihood: -82988.498914 EM: Round [96] log likelihood: -82988.498780 EM: Round [97] log likelihood: -82988.498651 EM: Round [98] log likelihood: -82988.498524 EM: Round [99] log likelihood: -82988.498400 EM: Round [100] log likelihood: -82988.498280 EM: Round [101] log likelihood: -82988.498163 EM: Round [102] log likelihood: -82988.498048 EM: Round [103] log likelihood: -82988.497936 EM: Round [104] log likelihood: -82988.497828 EM: Round [105] log likelihood: -82988.497721 EM: Round [106] log likelihood: -82988.497618 EM: Round [107] log likelihood: -82988.497517 EM: Round [108] log likelihood: -82988.497419 EM: Stopping iterations at round 108 due to insufficient improvement in likelihood. EM: Starting log likelihood: -83095.255537 EM: Round [1] log likelihood: -83026.373424 EM: Round [2] log likelihood: -82998.595011 EM: Round [3] log likelihood: -82985.347006 EM: Round [4] log likelihood: -82978.468763 EM: Round [5] log likelihood: -82974.692800 EM: Round [6] log likelihood: -82972.518142 EM: Round [7] log likelihood: -82971.205611 EM: Round [8] log likelihood: -82970.376096 EM: Round [9] log likelihood: -82969.828468 EM: Round [10] log likelihood: -82969.452284 EM: Round [11] log likelihood: -82969.184673 EM: Round [12] log likelihood: -82968.988504 EM: Round [13] log likelihood: -82968.841027 EM: Round [14] log likelihood: -82968.727804 EM: Round [15] log likelihood: -82968.639354 EM: Round [16] log likelihood: -82968.569255 EM: Round [17] log likelihood: -82968.513032 EM: Round [18] log likelihood: -82968.467488 EM: Round [19] log likelihood: -82968.430283 EM: Round [20] log likelihood: -82968.399674 EM: Round [21] log likelihood: -82968.374338 EM: Round [22] log likelihood: -82968.353255 EM: Round [23] log likelihood: -82968.335629 EM: Round [24] log likelihood: -82968.320831 EM: Round [25] log likelihood: -82968.308362 EM: Round [26] log likelihood: -82968.297817 EM: Round [27] log likelihood: -82968.288872 EM: Round [28] log likelihood: -82968.281259 EM: Round [29] log likelihood: -82968.274761 EM: Round [30] log likelihood: -82968.269198 EM: Round [31] log likelihood: -82968.264422 EM: Round [32] log likelihood: -82968.260310 EM: Round [33] log likelihood: -82968.256759 EM: Round [34] log likelihood: -82968.253683 EM: Round [35] log likelihood: -82968.251010 EM: Round [36] log likelihood: -82968.248680 EM: Round [37] log likelihood: -82968.246643 EM: Round [38] log likelihood: -82968.244855 EM: Round [39] log likelihood: -82968.243280 EM: Round [40] log likelihood: -82968.241888 EM: Round [41] log likelihood: -82968.240653 EM: Round [42] log likelihood: -82968.239553 EM: Round [43] log likelihood: -82968.238569 EM: Round [44] log likelihood: -82968.237685 EM: Round [45] log likelihood: -82968.236888 EM: Round [46] log likelihood: -82968.236167 EM: Round [47] log likelihood: -82968.235510 EM: Round [48] log likelihood: -82968.234910 EM: Round [49] log likelihood: -82968.234360 EM: Round [50] log likelihood: -82968.233853 EM: Round [51] log likelihood: -82968.233384 EM: Round [52] log likelihood: -82968.232948 EM: Round [53] log likelihood: -82968.232542 EM: Round [54] log likelihood: -82968.232162 EM: Round [55] log likelihood: -82968.231805 EM: Round [56] log likelihood: -82968.231469 EM: Round [57] log likelihood: -82968.231151 EM: Round [58] log likelihood: -82968.230849 EM: Round [59] log likelihood: -82968.230563 EM: Round [60] log likelihood: -82968.230289 EM: Round [61] log likelihood: -82968.230028 EM: Round [62] log likelihood: -82968.229779 EM: Round [63] log likelihood: -82968.229539 EM: Round [64] log likelihood: -82968.229308 EM: Round [65] log likelihood: -82968.229087 EM: Round [66] log likelihood: -82968.228873 EM: Round [67] log likelihood: -82968.228666 EM: Round [68] log likelihood: -82968.228467 EM: Round [69] log likelihood: -82968.228274 EM: Round [70] log likelihood: -82968.228087 EM: Round [71] log likelihood: -82968.227906 EM: Round [72] log likelihood: -82968.227730 EM: Round [73] log likelihood: -82968.227560 EM: Round [74] log likelihood: -82968.227394 EM: Round [75] log likelihood: -82968.227233 EM: Round [76] log likelihood: -82968.227077 EM: Round [77] log likelihood: -82968.226925 EM: Round [78] log likelihood: -82968.226777 EM: Round [79] log likelihood: -82968.226633 EM: Round [80] log likelihood: -82968.226493 EM: Round [81] log likelihood: -82968.226357 EM: Round [82] log likelihood: -82968.226224 EM: Round [83] log likelihood: -82968.226095 EM: Round [84] log likelihood: -82968.225969 EM: Round [85] log likelihood: -82968.225846 EM: Round [86] log likelihood: -82968.225727 EM: Round [87] log likelihood: -82968.225611 EM: Round [88] log likelihood: -82968.225497 EM: Round [89] log likelihood: -82968.225387 EM: Round [90] log likelihood: -82968.225279 EM: Round [91] log likelihood: -82968.225175 EM: Round [92] log likelihood: -82968.225073 EM: Round [93] log likelihood: -82968.224973 EM: Stopping iterations at round 93 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.ZNEdBQDLuY/./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.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.ZNEdBQDLuY/./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.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 29706015 > /tmp/nxf.ZNEdBQDLuY/./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.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir > /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir --annotate /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.ZNEdBQDLuY/./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.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir -done, see /tmp/nxf.ZNEdBQDLuY/./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.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.ZNEdBQDLuY/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 835, filtered: 4508) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.ZNEdBQDLuY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.ZNEdBQDLuY/./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.ZNEdBQDLuY/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000287121.1] WARNING, no entry stored in dbm for [ENSG00000254275.6] WARNING, no entry stored in dbm for [ENSG00000187600.14] WARNING, no entry stored in dbm for [ENSG00000260464.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000213090.2] WARNING, no entry stored in dbm for [ENSG00000218175.2] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000280061.1] WARNING, no entry stored in dbm for [ENSG00000287679.1] WARNING, no entry stored in dbm for [ENSG00000205485.13] WARNING, no entry stored in dbm for [ENSG00000287710.1] WARNING, no entry stored in dbm for [ENSG00000235674.2] WARNING, no entry stored in dbm for [ENSG00000261040.7] WARNING, no entry stored in dbm for [ENSG00000259950.1] WARNING, no entry stored in dbm for [ENSG00000279036.1] WARNING, no entry stored in dbm for [ENSG00000256663.1] WARNING, no entry stored in dbm for [ENSG00000234964.4] WARNING, no entry stored in dbm for [ENSG00000235211.4] WARNING, no entry stored in dbm for [ENSG00000260864.1] WARNING, no entry stored in dbm for [ENSG00000242741.2] WARNING, no entry stored in dbm for [ENSG00000259057.1] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000233133.1] WARNING, no entry stored in dbm for [ENSG00000128438.10] WARNING, no entry stored in dbm for [ENSG00000128438.10] WARNING, no entry stored in dbm for [ENSG00000226823.1] WARNING, no entry stored in dbm for [ENSG00000251593.1] WARNING, no entry stored in dbm for [ENSG00000271643.2] WARNING, no entry stored in dbm for [ENSG00000261192.1] WARNING, no entry stored in dbm for [ENSG00000225511.7] WARNING, no entry stored in dbm for [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000228374.1] WARNING, no entry stored in dbm for [ENSG00000213935.3] WARNING, no entry stored in dbm for [ENSG00000241129.3] WARNING, no entry stored in dbm for [ENSG00000180764.13] WARNING, no entry stored in dbm for [ENSG00000238825.1] WARNING, no entry stored in dbm for [ENSG00000207205.1] WARNING, no entry stored in dbm for [ENSG00000199197.1] WARNING, no entry stored in dbm for [ENSG00000222448.1] WARNING, no entry stored in dbm for [ENSG00000271161.1] WARNING, no entry stored in dbm for [ENSG00000235908.1] WARNING, no entry stored in dbm for [ENSG00000255410.2] WARNING, no entry stored in dbm for [ENSG00000205534.6] WARNING, no entry stored in dbm for [ENSG00000270938.1] WARNING, no entry stored in dbm for [ENSG00000249007.1] WARNING, no entry stored in dbm for [ENSG00000259241.1] WARNING, no entry stored in dbm for [ENSG00000240211.1] WARNING, no entry stored in dbm for [ENSG00000239556.4] WARNING, no entry stored in dbm for [ENSG00000254681.6] WARNING, no entry stored in dbm for [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000218426.5] WARNING, no entry stored in dbm for [ENSG00000223705.9] WARNING, no entry stored in dbm for [ENSG00000187812.12] WARNING, no entry stored in dbm for [ENSG00000228818.1] WARNING, no entry stored in dbm for [ENSG00000228526.7] WARNING, no entry stored in dbm for [ENSG00000270069.1] WARNING, no entry stored in dbm for [ENSG00000196312.15] WARNING, no entry stored in dbm for [ENSG00000237729.2] WARNING, no entry stored in dbm for [ENSG00000251562.8] WARNING, no entry stored in dbm for [ENSG00000275716.1] WARNING, no entry stored in dbm for [ENSG00000257139.1] WARNING, no entry stored in dbm for [ENSG00000255008.3] WARNING, no entry stored in dbm for [ENSG00000231566.2] WARNING, no entry stored in dbm for [ENSG00000250358.6] WARNING, no entry stored in dbm for [ENSG00000263146.2] WARNING, no entry stored in dbm for [ENSG00000237491.10] WARNING, no entry stored in dbm for [ENSG00000237491.10] WARNING, no entry stored in dbm for [ENSG00000244578.1] WARNING, no entry stored in dbm for [ENSG00000204054.14] WARNING, no entry stored in dbm for [ENSG00000215483.11] WARNING, no entry stored in dbm for [ENSG00000225511.7] WARNING, no entry stored in dbm for [ENSG00000236871.7] WARNING, no entry stored in dbm for [ENSG00000224468.3] 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 [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000224129.1] WARNING, no entry stored in dbm for [ENSG00000225851.1] WARNING, no entry stored in dbm for [ENSG00000225465.10] WARNING, no entry stored in dbm for [ENSG00000258667.2] WARNING, no entry stored in dbm for [ENSG00000248932.6] WARNING, no entry stored in dbm for [ENSG00000262202.4] WARNING, no entry stored in dbm for [ENSG00000206417.8] WARNING, no entry stored in dbm for [ENSG00000265863.1] WARNING, no entry stored in dbm for [ENSG00000241621.1] WARNING, no entry stored in dbm for [ENSG00000259394.2] WARNING, no entry stored in dbm for [ENSG00000233485.1] WARNING, no entry stored in dbm for [ENSG00000182057.5] WARNING, no entry stored in dbm for [ENSG00000196167.10] WARNING, no entry stored in dbm for [ENSG00000271569.1] WARNING, no entry stored in dbm for [ENSG00000225210.10] WARNING, no entry stored in dbm for [ENSG00000231607.13] WARNING, no entry stored in dbm for [ENSG00000176124.15] WARNING, no entry stored in dbm for [ENSG00000235706.8] WARNING, no entry stored in dbm for [ENSG00000232111.2] WARNING, no entry stored in dbm for [ENSG00000258471.2] WARNING, no entry stored in dbm for [ENSG00000270533.2] WARNING, no entry stored in dbm for [ENSG00000261783.1] WARNING, no entry stored in dbm for [ENSG00000249839.1] WARNING, no entry stored in dbm for [ENSG00000259577.2] WARNING, no entry stored in dbm for [ENSG00000261499.2] WARNING, no entry stored in dbm for [ENSG00000235574.1] WARNING, no entry stored in dbm for [ENSG00000205534.6] WARNING, no entry stored in dbm for [ENSG00000222826.1] WARNING, no entry stored in dbm for [ENSG00000260372.7] WARNING, no entry stored in dbm for [ENSG00000230479.1] WARNING, no entry stored in dbm for [ENSG00000213365.3] WARNING, no entry stored in dbm for [ENSG00000283064.1] 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 [ENSG00000286108.1] WARNING, no entry stored in dbm for [ENSG00000258656.1] WARNING, no entry stored in dbm for [ENSG00000271335.6] WARNING, no entry stored in dbm for [ENSG00000285646.2] WARNING, no entry stored in dbm for [ENSG00000229425.3] WARNING, no entry stored in dbm for [ENSG00000230869.1] WARNING, no entry stored in dbm for [ENSG00000265069.1] WARNING, no entry stored in dbm for [ENSG00000237250.3] WARNING, no entry stored in dbm for [ENSG00000274265.5] WARNING, no entry stored in dbm for [ENSG00000277125.1] WARNING, no entry stored in dbm for [ENSG00000239969.5] WARNING, no entry stored in dbm for [ENSG00000242073.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000229930.1] WARNING, no entry stored in dbm for [ENSG00000260670.1] WARNING, no entry stored in dbm for [ENSG00000198555.7] WARNING, no entry stored in dbm for [ENSG00000214135.8] WARNING, no entry stored in dbm for [ENSG00000243929.1] WARNING, no entry stored in dbm for [ENSG00000237666.2] WARNING, no entry stored in dbm for [ENSG00000237666.2] WARNING, no entry stored in dbm for [ENSG00000204745.4] WARNING, no entry stored in dbm for [ENSG00000239969.5] WARNING, no entry stored in dbm for [ENSG00000253107.1] WARNING, no entry stored in dbm for [ENSG00000253107.1] WARNING, no entry stored in dbm for [ENSG00000253107.1] WARNING, no entry stored in dbm for [ENSG00000272693.4] WARNING, no entry stored in dbm for [ENSG00000229212.8] WARNING, no entry stored in dbm for [ENSG00000242327.1] WARNING, no entry stored in dbm for [ENSG00000226659.1] WARNING, no entry stored in dbm for [ENSG00000234624.2] WARNING, no entry stored in dbm for [ENSG00000261329.6] WARNING, no entry stored in dbm for [ENSG00000267605.7] WARNING, no entry stored in dbm for [ENSG00000255106.1] WARNING, no entry stored in dbm for [ENSG00000241741.1] WARNING, no entry stored in dbm for [ENSG00000254887.1] WARNING, no entry stored in dbm for [ENSG00000253297.1] WARNING, no entry stored in dbm for [ENSG00000224415.1] WARNING, no entry stored in dbm for [ENSG00000185641.6] WARNING, no entry stored in dbm for [ENSG00000214243.3] WARNING, no entry stored in dbm for [ENSG00000205485.13] WARNING, no entry stored in dbm for [ENSG00000228204.2] WARNING, no entry stored in dbm for [ENSG00000235776.2] * STAR-Fusion complete. See output: /tmp/nxf.ZNEdBQDLuY/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)