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/88/6606ea5a2a8fc038b8b36ff231f058/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/b7d694903039d315ce6c9b69a22a4b/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/ea8be5b9c57cb128d61e43fba51e3b/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/b7d694903039d315ce6c9b69a22a4b/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/6606ea5a2a8fc038b8b36ff231f058/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.NlSgB6SoGa/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary -sample contains 16435072 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir -J /tmp/nxf.NlSgB6SoGa/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.NlSgB6SoGa/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=92307.69/min [30000], rate=94736.84/min [40000], rate=75000.00/min [50000], rate=61224.49/min [60000], rate=62068.97/min [70000], rate=63636.36/min [80000], rate=66666.67/min [90000], rate=68354.43/min [100000], rate=69767.44/min [110000], rate=72527.47/min [120000], rate=75000.00/min [130000], rate=77227.72/min [140000], rate=78504.67/min [150000], rate=80357.14/min [160000], rate=82051.28/min [170000], rate=83606.56/min [180000], rate=87804.88/min [190000], rate=91935.48/min [200000], rate=93750.00/min [210000], rate=94029.85/min [220000], rate=95652.17/min [230000], rate=97183.10/min [240000], rate=97959.18/min [250000], rate=99337.75/min [260000], rate=99363.06/min [270000], rate=98780.49/min [280000], rate=100000.00/min [290000], rate=102958.58/min [300000], rate=105882.35/min [310000], rate=106896.55/min [320000], rate=106077.35/min [330000], rate=107608.70/min [340000], rate=108510.64/min [350000], rate=108808.29/min [360000], rate=110204.08/min [370000], rate=110447.76/min [380000], rate=110144.93/min [390000], rate=110900.47/min [400000], rate=111111.11/min [410000], rate=111312.22/min [420000], rate=111013.22/min [430000], rate=110256.41/min [440000], rate=109090.91/min [450000], rate=104247.10/min [460000], rate=102602.23/min [470000], rate=99646.64/min [480000], rate=98630.14/min [490000], rate=97674.42/min -building interval tree based on /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.07 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=100000.00/min [30000], rate=112500.00/min [40000], rate=120000.00/min [50000], rate=125000.00/min [60000], rate=128571.43/min [70000], rate=127272.73/min [80000], rate=104347.83/min [90000], rate=100000.00/min [100000], rate=90909.09/min [110000], rate=92957.75/min [120000], rate=94736.84/min [130000], rate=93975.90/min [140000], rate=92307.69/min [150000], rate=90909.09/min [160000], rate=89719.63/min [170000], rate=90265.49/min [180000], rate=91525.42/min [190000], rate=89062.50/min [200000], rate=88235.29/min [210000], rate=88111.89/min [220000], rate=88590.60/min [230000], rate=87898.09/min [240000], rate=87272.73/min [250000], rate=88757.40/min [260000], rate=89655.17/min [270000], rate=90502.79/min [280000], rate=88421.05/min [290000], rate=87878.79/min [300000], rate=87804.88/min [310000], rate=87323.94/min [320000], rate=87272.73/min [330000], rate=87610.62/min [340000], rate=88311.69/min [350000], rate=87136.93/min [360000], rate=87096.77/min [370000], rate=86381.32/min [380000], rate=86692.02/min [390000], rate=86029.41/min [400000], rate=84805.65/min [410000], rate=84246.58/min [420000], rate=84563.76/min [430000], rate=85148.51/min [440000], rate=84345.05/min [450000], rate=84112.15/min [460000], rate=84403.67/min [470000], rate=84939.76/min [480000], rate=85459.94/min [490000], rate=85217.39/min -building interval tree based on /tmp/nxf.NlSgB6SoGa/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=171428.57/min [30000], rate=150000.00/min [40000], rate=141176.47/min [50000], rate=157894.74/min [60000], rate=144000.00/min [70000], rate=144827.59/min [80000], rate=141176.47/min [90000], rate=145945.95/min [100000], rate=142857.14/min [110000], rate=140425.53/min [120000], rate=138461.54/min [130000], rate=139285.71/min [140000], rate=137704.92/min [150000], rate=140625.00/min [160000], rate=141176.47/min [170000], rate=139726.03/min [180000], rate=142105.26/min [190000], rate=140740.74/min [200000], rate=141176.47/min [210000], rate=143181.82/min [220000], rate=140425.53/min [230000], rate=138000.00/min [240000], rate=139805.83/min [250000], rate=129310.34/min [260000], rate=107586.21/min [270000], rate=96428.57/min [280000], rate=88421.05/min [290000], rate=84466.02/min [300000], rate=82949.31/min [310000], rate=81222.71/min [320000], rate=80000.00/min [330000], rate=78884.46/min [340000], rate=78160.92/min [350000], rate=77490.77/min [360000], rate=76868.33/min [370000], rate=75510.20/min [380000], rate=74025.97/min [390000], rate=73354.23/min [400000], rate=73394.50/min [410000], rate=71511.63/min [420000], rate=69613.26/min [430000], rate=69729.73/min [440000], rate=70026.53/min [450000], rate=69408.74/min [460000], rate=68656.72/min [470000], rate=68446.60/min [480000], rate=68408.55/min [490000], rate=68852.46/min -building interval tree based on /tmp/nxf.NlSgB6SoGa/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=60000.00/min [30000], rate=58064.52/min [40000], rate=52173.91/min [50000], rate=54545.45/min [60000], rate=58064.52/min [70000], rate=61764.71/min [80000], rate=62337.66/min [90000], rate=64285.71/min [100000], rate=67415.73/min [110000], rate=70212.77/min [120000], rate=65454.55/min [130000], rate=65000.00/min [140000], rate=64122.14/min [150000], rate=63829.79/min [160000], rate=64429.53/min [170000], rate=65806.45/min [180000], rate=67080.75/min [190000], rate=68263.47/min [200000], rate=69364.16/min [210000], rate=69613.26/min [220000], rate=69473.68/min [230000], rate=70769.23/min [240000], rate=72000.00/min [250000], rate=72115.38/min [260000], rate=73584.91/min [270000], rate=74311.93/min [280000], rate=75000.00/min [290000], rate=75982.53/min [300000], rate=75000.00/min [310000], rate=73517.79/min [320000], rate=73282.44/min [330000], rate=72794.12/min [340000], rate=72597.86/min [350000], rate=72916.67/min [360000], rate=71287.13/min [370000], rate=69811.32/min [380000], rate=69300.91/min [390000], rate=68621.70/min [400000], rate=66298.34/min [410000], rate=65425.53/min [420000], rate=65284.97/min [430000], rate=65151.52/min [440000], rate=65024.63/min [450000], rate=65533.98/min [460000], rate=65248.23/min [470000], rate=63800.90/min [480000], rate=63157.89/min [490000], rate=62553.19/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir --filt_file /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.NlSgB6SoGa/./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... 4500000.00 reads per min processed... 4000000.00 reads per min processed... 3333333.33 reads per min processed... 3272727.27 reads per min processed... 3230769.23 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3000000.00 reads per min processed... 3142857.14 reads per min processed... 3272727.27 reads per min processed... 3391304.35 reads per min processed... 3230769.23 reads per min processed... 3214285.71 reads per min processed... 3200000.00 reads per min processed... 3290322.58 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.NlSgB6SoGa/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction --tmpdir /tmp --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --max_promiscuity 10 --min_pct_dom_promiscuity 20 --min_novel_junction_support 1 --min_alt_pct_junction 10 --aggregate_novel_junction_dist 5 --min_spanning_frags_only 1 --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -27857.159511 EM: Round [1] log likelihood: -27792.352912 EM: Round [2] log likelihood: -27764.188172 EM: Round [3] log likelihood: -27749.535879 EM: Round [4] log likelihood: -27741.282262 EM: Round [5] log likelihood: -27736.493021 EM: Round [6] log likelihood: -27733.670168 EM: Round [7] log likelihood: -27731.973654 EM: Round [8] log likelihood: -27730.925200 EM: Round [9] log likelihood: -27730.254914 EM: Round [10] log likelihood: -27729.810826 EM: Round [11] log likelihood: -27729.506356 EM: Round [12] log likelihood: -27729.291039 EM: Round [13] log likelihood: -27729.134582 EM: Round [14] log likelihood: -27729.018206 EM: Round [15] log likelihood: -27728.929891 EM: Round [16] log likelihood: -27728.861701 EM: Round [17] log likelihood: -27728.808252 EM: Round [18] log likelihood: -27728.765794 EM: Round [19] log likelihood: -27728.731665 EM: Round [20] log likelihood: -27728.703933 EM: Round [21] log likelihood: -27728.681174 EM: Round [22] log likelihood: -27728.662325 EM: Round [23] log likelihood: -27728.646579 EM: Round [24] log likelihood: -27728.633318 EM: Round [25] log likelihood: -27728.622063 EM: Round [26] log likelihood: -27728.612441 EM: Round [27] log likelihood: -27728.604155 EM: Round [28] log likelihood: -27728.596969 EM: Round [29] log likelihood: -27728.590697 EM: Round [30] log likelihood: -27728.585185 EM: Round [31] log likelihood: -27728.580310 EM: Round [32] log likelihood: -27728.575972 EM: Round [33] log likelihood: -27728.572088 EM: Round [34] log likelihood: -27728.568589 EM: Round [35] log likelihood: -27728.565419 EM: Round [36] log likelihood: -27728.562532 EM: Round [37] log likelihood: -27728.559889 EM: Round [38] log likelihood: -27728.557456 EM: Round [39] log likelihood: -27728.555206 EM: Round [40] log likelihood: -27728.553116 EM: Round [41] log likelihood: -27728.551167 EM: Round [42] log likelihood: -27728.549342 EM: Round [43] log likelihood: -27728.547628 EM: Round [44] log likelihood: -27728.546012 EM: Round [45] log likelihood: -27728.544485 EM: Round [46] log likelihood: -27728.543037 EM: Round [47] log likelihood: -27728.541662 EM: Round [48] log likelihood: -27728.540353 EM: Round [49] log likelihood: -27728.539104 EM: Round [50] log likelihood: -27728.537911 EM: Round [51] log likelihood: -27728.536771 EM: Round [52] log likelihood: -27728.535678 EM: Round [53] log likelihood: -27728.534631 EM: Round [54] log likelihood: -27728.533626 EM: Round [55] log likelihood: -27728.532661 EM: Round [56] log likelihood: -27728.531734 EM: Round [57] log likelihood: -27728.530842 EM: Round [58] log likelihood: -27728.529985 EM: Round [59] log likelihood: -27728.529161 EM: Round [60] log likelihood: -27728.528368 EM: Round [61] log likelihood: -27728.527605 EM: Round [62] log likelihood: -27728.526871 EM: Round [63] log likelihood: -27728.526164 EM: Round [64] log likelihood: -27728.525484 EM: Round [65] log likelihood: -27728.524830 EM: Round [66] log likelihood: -27728.524200 EM: Round [67] log likelihood: -27728.523595 EM: Round [68] log likelihood: -27728.523012 EM: Round [69] log likelihood: -27728.522451 EM: Round [70] log likelihood: -27728.521912 EM: Round [71] log likelihood: -27728.521394 EM: Round [72] log likelihood: -27728.520895 EM: Round [73] log likelihood: -27728.520416 EM: Round [74] log likelihood: -27728.519956 EM: Round [75] log likelihood: -27728.519514 EM: Round [76] log likelihood: -27728.519089 EM: Round [77] log likelihood: -27728.518680 EM: Round [78] log likelihood: -27728.518288 EM: Round [79] log likelihood: -27728.517912 EM: Round [80] log likelihood: -27728.517551 EM: Round [81] log likelihood: -27728.517204 EM: Round [82] log likelihood: -27728.516871 EM: Round [83] log likelihood: -27728.516552 EM: Round [84] log likelihood: -27728.516245 EM: Round [85] log likelihood: -27728.515951 EM: Round [86] log likelihood: -27728.515669 EM: Round [87] log likelihood: -27728.515399 EM: Round [88] log likelihood: -27728.515140 EM: Round [89] log likelihood: -27728.514892 EM: Round [90] log likelihood: -27728.514653 EM: Round [91] log likelihood: -27728.514425 EM: Round [92] log likelihood: -27728.514206 EM: Round [93] log likelihood: -27728.513997 EM: Round [94] log likelihood: -27728.513796 EM: Round [95] log likelihood: -27728.513604 EM: Round [96] log likelihood: -27728.513419 EM: Round [97] log likelihood: -27728.513243 EM: Round [98] log likelihood: -27728.513074 EM: Round [99] log likelihood: -27728.512912 EM: Round [100] log likelihood: -27728.512756 EM: Round [101] log likelihood: -27728.512608 EM: Round [102] log likelihood: -27728.512465 EM: Round [103] log likelihood: -27728.512329 EM: Round [104] log likelihood: -27728.512199 EM: Round [105] log likelihood: -27728.512074 EM: Round [106] log likelihood: -27728.511954 EM: Round [107] log likelihood: -27728.511840 EM: Round [108] log likelihood: -27728.511730 EM: Round [109] log likelihood: -27728.511625 EM: Round [110] log likelihood: -27728.511524 EM: Round [111] log likelihood: -27728.511428 EM: Stopping iterations at round 111 due to insufficient improvement in likelihood. EM: Starting log likelihood: -27841.924843 EM: Round [1] log likelihood: -27783.441666 EM: Round [2] log likelihood: -27758.713878 EM: Round [3] log likelihood: -27746.074209 EM: Round [4] log likelihood: -27739.049465 EM: Round [5] log likelihood: -27735.024583 EM: Round [6] log likelihood: -27732.683635 EM: Round [7] log likelihood: -27731.295428 EM: Round [8] log likelihood: -27730.448220 EM: Round [9] log likelihood: -27729.912509 EM: Round [10] log likelihood: -27729.560644 EM: Round [11] log likelihood: -27729.320787 EM: Round [12] log likelihood: -27729.151595 EM: Round [13] log likelihood: -27729.028577 EM: Round [14] log likelihood: -27728.936756 EM: Round [15] log likelihood: -27728.866663 EM: Round [16] log likelihood: -27728.812120 EM: Round [17] log likelihood: -27728.768974 EM: Round [18] log likelihood: -27728.734354 EM: Round [19] log likelihood: -27728.706228 EM: Round [20] log likelihood: -27728.683124 EM: Round [21] log likelihood: -27728.663960 EM: Round [22] log likelihood: -27728.647920 EM: Round [23] log likelihood: -27728.634385 EM: Round [24] log likelihood: -27728.622877 EM: Round [25] log likelihood: -27728.613022 EM: Round [26] log likelihood: -27728.604526 EM: Round [27] log likelihood: -27728.597152 EM: Round [28] log likelihood: -27728.590713 EM: Round [29] log likelihood: -27728.585055 EM: Round [30] log likelihood: -27728.580053 EM: Round [31] log likelihood: -27728.575606 EM: Round [32] log likelihood: -27728.571629 EM: Round [33] log likelihood: -27728.568052 EM: Round [34] log likelihood: -27728.564817 EM: Round [35] log likelihood: -27728.561877 EM: Round [36] log likelihood: -27728.559190 EM: Round [37] log likelihood: -27728.556723 EM: Round [38] log likelihood: -27728.554446 EM: Round [39] log likelihood: -27728.552337 EM: Round [40] log likelihood: -27728.550374 EM: Round [41] log likelihood: -27728.548540 EM: Round [42] log likelihood: -27728.546821 EM: Round [43] log likelihood: -27728.545203 EM: Round [44] log likelihood: -27728.543678 EM: Round [45] log likelihood: -27728.542234 EM: Round [46] log likelihood: -27728.540865 EM: Round [47] log likelihood: -27728.539564 EM: Round [48] log likelihood: -27728.538325 EM: Round [49] log likelihood: -27728.537143 EM: Round [50] log likelihood: -27728.536013 EM: Round [51] log likelihood: -27728.534933 EM: Round [52] log likelihood: -27728.533898 EM: Round [53] log likelihood: -27728.532907 EM: Round [54] log likelihood: -27728.531956 EM: Round [55] log likelihood: -27728.531042 EM: Round [56] log likelihood: -27728.530165 EM: Round [57] log likelihood: -27728.529323 EM: Round [58] log likelihood: -27728.528513 EM: Round [59] log likelihood: -27728.527734 EM: Round [60] log likelihood: -27728.526985 EM: Round [61] log likelihood: -27728.526264 EM: Round [62] log likelihood: -27728.525572 EM: Round [63] log likelihood: -27728.524905 EM: Round [64] log likelihood: -27728.524264 EM: Round [65] log likelihood: -27728.523648 EM: Round [66] log likelihood: -27728.523055 EM: Round [67] log likelihood: -27728.522485 EM: Round [68] log likelihood: -27728.521937 EM: Round [69] log likelihood: -27728.521410 EM: Round [70] log likelihood: -27728.520903 EM: Round [71] log likelihood: -27728.520417 EM: Round [72] log likelihood: -27728.519949 EM: Round [73] log likelihood: -27728.519500 EM: Round [74] log likelihood: -27728.519068 EM: Round [75] log likelihood: -27728.518654 EM: Round [76] log likelihood: -27728.518256 EM: Round [77] log likelihood: -27728.517874 EM: Round [78] log likelihood: -27728.517507 EM: Round [79] log likelihood: -27728.517155 EM: Round [80] log likelihood: -27728.516817 EM: Round [81] log likelihood: -27728.516493 EM: Round [82] log likelihood: -27728.516183 EM: Round [83] log likelihood: -27728.515885 EM: Round [84] log likelihood: -27728.515599 EM: Round [85] log likelihood: -27728.515325 EM: Round [86] log likelihood: -27728.515062 EM: Round [87] log likelihood: -27728.514811 EM: Round [88] log likelihood: -27728.514570 EM: Round [89] log likelihood: -27728.514339 EM: Round [90] log likelihood: -27728.514117 EM: Round [91] log likelihood: -27728.513905 EM: Round [92] log likelihood: -27728.513702 EM: Round [93] log likelihood: -27728.513507 EM: Round [94] log likelihood: -27728.513321 EM: Round [95] log likelihood: -27728.513142 EM: Round [96] log likelihood: -27728.512972 EM: Round [97] log likelihood: -27728.512808 EM: Round [98] log likelihood: -27728.512651 EM: Round [99] log likelihood: -27728.512501 EM: Round [100] log likelihood: -27728.512358 EM: Round [101] log likelihood: -27728.512220 EM: Round [102] log likelihood: -27728.512089 EM: Round [103] log likelihood: -27728.511963 EM: Round [104] log likelihood: -27728.511843 EM: Round [105] log likelihood: -27728.511727 EM: Round [106] log likelihood: -27728.511617 EM: Round [107] log likelihood: -27728.511512 EM: Round [108] log likelihood: -27728.511411 EM: Round [109] log likelihood: -27728.511314 EM: Stopping iterations at round 109 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 16435072 > /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir > /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir --annotate /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir -done, see /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 146, filtered: 2126) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000205634.7] WARNING, no entry stored in dbm for [ENSG00000279910.1] 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 [ENSG00000219491.7] WARNING, no entry stored in dbm for [ENSG00000234782.3] WARNING, no entry stored in dbm for [ENSG00000224271.7] WARNING, no entry stored in dbm for [ENSG00000224437.2] WARNING, no entry stored in dbm for [ENSG00000214559.3] 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 [ENSG00000228948.2] WARNING, no entry stored in dbm for [ENSG00000171101.13] WARNING, no entry stored in dbm for [ENSG00000236190.1] WARNING, no entry stored in dbm for [ENSG00000236047.1] WARNING, no entry stored in dbm for [ENSG00000236047.1] WARNING, no entry stored in dbm for [ENSG00000236047.1] WARNING, no entry stored in dbm for [ENSG00000278771.1] WARNING, no entry stored in dbm for [ENSG00000240877.3] WARNING, no entry stored in dbm for [ENSG00000278771.1] WARNING, no entry stored in dbm for [ENSG00000244112.3] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000221817.10] WARNING, no entry stored in dbm for [ENSG00000261393.1] WARNING, no entry stored in dbm for [ENSG00000230305.2] WARNING, no entry stored in dbm for [ENSG00000231367.6] WARNING, no entry stored in dbm for [ENSG00000204792.2] WARNING, no entry stored in dbm for [ENSG00000260807.7] WARNING, no entry stored in dbm for [ENSG00000270761.1] WARNING, no entry stored in dbm for [ENSG00000230202.1] 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 [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 [ENSG00000233101.10] WARNING, no entry stored in dbm for [ENSG00000231367.6] WARNING, no entry stored in dbm for [ENSG00000260807.7] WARNING, no entry stored in dbm for [ENSG00000250662.1] WARNING, no entry stored in dbm for [ENSG00000237296.9] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000283849.1] WARNING, no entry stored in dbm for [ENSG00000223896.2] WARNING, no entry stored in dbm for [ENSG00000241104.5] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000215559.8] WARNING, no entry stored in dbm for [ENSG00000264958.2] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000287991.1] WARNING, no entry stored in dbm for [ENSG00000211459.2] WARNING, no entry stored in dbm for [ENSG00000276850.5] WARNING, no entry stored in dbm for [ENSG00000246596.7] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000260757.1] WARNING, no entry stored in dbm for [ENSG00000260757.1] WARNING, no entry stored in dbm for [ENSG00000286176.2] WARNING, no entry stored in dbm for [ENSG00000282033.1] WARNING, no entry stored in dbm for [ENSG00000257167.2] * STAR-Fusion complete. See output: /tmp/nxf.NlSgB6SoGa/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)