Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1b/ca2312c61c97a282e311f44ef05719/ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1_2.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/1b/ca2312c61c97a282e311f44ef05719/ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/377527b6189682012486af906b1c01/ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.Chimeric.out.junction Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/50fb651eea01a96f33dac49f242b41/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/50fb651eea01a96f33dac49f242b41/.command.run ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.miIACfCJB2/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.miIACfCJB2/./star-fusion.preliminary -sample contains 36146178 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir -J /tmp/nxf.miIACfCJB2/ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.miIACfCJB2/ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=28571.43/min [20000], rate=30000.00/min [30000], rate=32727.27/min [40000], rate=36363.64/min [50000], rate=38461.54/min [60000], rate=29508.20/min [70000], rate=26582.28/min [80000], rate=24742.27/min [90000], rate=22784.81/min [100000], rate=22058.82/min [110000], rate=22222.22/min [120000], rate=22222.22/min [130000], rate=23076.92/min [140000], rate=23268.70/min [150000], rate=23809.52/min [160000], rate=24552.43/min [170000], rate=25247.52/min [180000], rate=25531.91/min [190000], rate=25850.34/min [200000], rate=26315.79/min [210000], rate=26923.08/min [220000], rate=27385.89/min [230000], rate=27991.89/min [240000], rate=28742.51/min [250000], rate=29126.21/min [260000], rate=29323.31/min [270000], rate=29616.09/min [280000], rate=30107.53/min [290000], rate=30472.85/min [300000], rate=31034.48/min [310000], rate=31525.42/min [320000], rate=32323.23/min [330000], rate=32727.27/min [340000], rate=33170.73/min [350000], rate=33762.06/min [360000], rate=34177.22/min [370000], rate=34418.60/min [380000], rate=34756.10/min [390000], rate=35294.12/min [400000], rate=35982.01/min [410000], rate=36498.52/min [420000], rate=36788.32/min [430000], rate=37337.19/min [440000], rate=37606.84/min [450000], rate=38135.59/min [460000], rate=38655.46/min [470000], rate=39166.67/min [480000], rate=39669.42/min [490000], rate=40273.97/min [500000], rate=40816.33/min [510000], rate=41239.89/min [520000], rate=41767.07/min [530000], rate=42231.08/min [540000], rate=42687.75/min [550000], rate=43080.94/min [560000], rate=43298.97/min [570000], rate=43622.45/min [580000], rate=43994.94/min [590000], rate=44416.56/min [600000], rate=43902.44/min [610000], rate=43262.41/min [620000], rate=43005.78/min [630000], rate=42760.18/min [640000], rate=42857.14/min [650000], rate=42810.10/min [660000], rate=42996.74/min [670000], rate=43318.97/min [680000], rate=43496.80/min [690000], rate=43670.89/min [700000], rate=43750.00/min [710000], rate=43737.17/min [720000], rate=43813.39/min [730000], rate=44108.76/min [740000], rate=44533.60/min [750000], rate=44642.86/min [760000], rate=44749.75/min [770000], rate=44941.63/min [780000], rate=45217.39/min -building interval tree based on /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=27272.73/min [20000], rate=31578.95/min [30000], rate=33962.26/min [40000], rate=37500.00/min [50000], rate=41095.89/min [60000], rate=40000.00/min [70000], rate=35000.00/min [80000], rate=34285.71/min [90000], rate=33128.83/min [100000], rate=32608.70/min [110000], rate=32512.32/min [120000], rate=32579.19/min [130000], rate=32635.98/min [140000], rate=32684.82/min [150000], rate=33962.26/min [160000], rate=34532.37/min [170000], rate=35540.07/min [180000], rate=36120.40/min [190000], rate=36190.48/min [200000], rate=35928.14/min [210000], rate=35195.53/min [220000], rate=34196.89/min [230000], rate=34158.42/min [240000], rate=34449.76/min [250000], rate=34642.03/min [260000], rate=34666.67/min [270000], rate=34913.79/min [280000], rate=35220.13/min [290000], rate=36099.59/min [300000], rate=36511.16/min [310000], rate=36831.68/min [320000], rate=37354.09/min [330000], rate=36598.89/min [340000], rate=36106.19/min [350000], rate=35897.44/min [360000], rate=36000.00/min [370000], rate=36393.44/min [380000], rate=36538.46/min [390000], rate=36734.69/min [400000], rate=36979.97/min [410000], rate=36936.94/min [420000], rate=37113.40/min [430000], rate=37445.57/min [440000], rate=37714.29/min [450000], rate=37974.68/min [460000], rate=38440.11/min [470000], rate=38896.55/min [480000], rate=39237.06/min [490000], rate=39304.81/min [500000], rate=39473.68/min [510000], rate=39586.03/min [520000], rate=39745.22/min [530000], rate=39899.62/min [540000], rate=40148.70/min [550000], rate=40441.18/min [560000], rate=40677.97/min [570000], rate=40762.81/min [580000], rate=40797.19/min [590000], rate=40830.45/min [600000], rate=40862.66/min [610000], rate=40848.21/min [620000], rate=40924.09/min [630000], rate=41042.35/min [640000], rate=41468.68/min [650000], rate=41755.89/min [660000], rate=41993.64/min [670000], rate=42138.36/min [680000], rate=42148.76/min [690000], rate=42244.90/min [700000], rate=42338.71/min [710000], rate=42430.28/min [720000], rate=42561.58/min [730000], rate=42731.71/min [740000], rate=42981.61/min [750000], rate=43310.88/min [760000], rate=43762.00/min [770000], rate=44126.07/min [780000], rate=44486.69/min -building interval tree based on /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=40000.00/min [20000], rate=36363.64/min [30000], rate=36734.69/min [40000], rate=36363.64/min [50000], rate=37974.68/min [60000], rate=40449.44/min [70000], rate=40000.00/min [80000], rate=41025.64/min [90000], rate=43548.39/min [100000], rate=45112.78/min [110000], rate=43137.25/min [120000], rate=41860.47/min [130000], rate=41489.36/min [140000], rate=40579.71/min [150000], rate=40358.74/min [160000], rate=40167.36/min [170000], rate=40316.21/min [180000], rate=40601.50/min [190000], rate=41007.19/min [200000], rate=39867.11/min [210000], rate=39375.00/min [220000], rate=39759.04/min [230000], rate=39541.55/min [240000], rate=39130.43/min [250000], rate=39473.68/min [260000], rate=40102.83/min [270000], rate=41221.37/min [280000], rate=42317.38/min [290000], rate=42962.96/min [300000], rate=42352.94/min [310000], rate=41517.86/min [320000], rate=41201.72/min [330000], rate=40824.74/min [340000], rate=40637.45/min [350000], rate=40776.70/min [360000], rate=40677.97/min [370000], rate=40510.95/min [380000], rate=40140.85/min [390000], rate=39527.03/min [400000], rate=39473.68/min [410000], rate=39360.00/min [420000], rate=39498.43/min [430000], rate=39692.31/min [440000], rate=39639.64/min [450000], rate=39823.01/min [460000], rate=40291.97/min [470000], rate=40692.64/min [480000], rate=41260.74/min [490000], rate=41176.47/min [500000], rate=40160.64/min [510000], rate=39740.26/min [520000], rate=39443.74/min [530000], rate=39503.11/min [540000], rate=39272.73/min [550000], rate=39239.00/min [560000], rate=39344.26/min [570000], rate=39629.20/min [580000], rate=39954.08/min [590000], rate=40181.61/min [600000], rate=40313.55/min [610000], rate=40576.50/min [620000], rate=40969.16/min [630000], rate=41356.67/min [640000], rate=41693.81/min [650000], rate=42207.79/min [660000], rate=42352.94/min [670000], rate=42584.75/min [680000], rate=42812.17/min [690000], rate=42680.41/min [700000], rate=42596.35/min [710000], rate=42261.90/min [720000], rate=42105.26/min [730000], rate=41954.02/min [740000], rate=41886.79/min [750000], rate=41938.49/min [760000], rate=42183.16/min [770000], rate=42424.24/min [780000], rate=42700.73/min -building interval tree based on /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=100000.00/min [20000], rate=70588.24/min [30000], rate=52941.18/min [40000], rate=58536.59/min [50000], rate=55555.56/min [60000], rate=62068.97/min [70000], rate=62686.57/min [80000], rate=62337.66/min [90000], rate=60000.00/min [100000], rate=61855.67/min [110000], rate=62264.15/min [120000], rate=62608.70/min [130000], rate=61904.76/min [140000], rate=62222.22/min [150000], rate=63380.28/min [160000], rate=64864.86/min [170000], rate=64150.94/min [180000], rate=63529.41/min [190000], rate=63687.15/min [200000], rate=61855.67/min [210000], rate=61764.71/min [220000], rate=61682.24/min [230000], rate=52671.76/min [240000], rate=44582.04/min [250000], rate=39267.02/min [260000], rate=35056.18/min [270000], rate=33128.83/min [280000], rate=31578.95/min [290000], rate=30905.86/min [300000], rate=30201.34/min [310000], rate=30097.09/min [320000], rate=30283.91/min [330000], rate=30091.19/min [340000], rate=29955.95/min [350000], rate=30000.00/min [360000], rate=30294.53/min [370000], rate=30578.51/min [380000], rate=30400.00/min [390000], rate=30588.24/min [400000], rate=30848.33/min [410000], rate=31139.24/min [420000], rate=31539.42/min [430000], rate=31851.85/min [440000], rate=32234.43/min [450000], rate=32412.97/min [460000], rate=32470.59/min [470000], rate=32752.61/min [480000], rate=33103.45/min [490000], rate=33295.58/min [500000], rate=33557.05/min [510000], rate=33812.15/min [520000], rate=34173.06/min [530000], rate=34640.52/min [540000], rate=35102.93/min [550000], rate=35483.87/min [560000], rate=35220.13/min [570000], rate=35477.18/min [580000], rate=35365.85/min [590000], rate=35470.94/min [600000], rate=35678.89/min [610000], rate=35637.78/min [620000], rate=35632.18/min [630000], rate=35694.05/min [640000], rate=35955.06/min [650000], rate=36245.35/min [660000], rate=36598.89/min [670000], rate=36880.73/min [680000], rate=37124.66/min [690000], rate=37432.19/min [700000], rate=37668.16/min [710000], rate=37799.47/min [720000], rate=37994.72/min [730000], rate=38186.57/min [740000], rate=38441.56/min [750000], rate=38659.79/min [760000], rate=38874.68/min [770000], rate=39119.39/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir --filt_file /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.miIACfCJB2/./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... 3428571.43 reads per min processed... 3333333.33 reads per min processed... 3272727.27 reads per min processed... 3230769.23 reads per min processed... 3200000.00 reads per min processed... 3176470.59 reads per min processed... 2857142.86 reads per min processed... 2869565.22 reads per min processed... 2880000.00 reads per min processed... 2888888.89 reads per min processed... 2896551.72 reads per min processed... 3000000.00 reads per min processed... 3096774.19 reads per min processed... 3187500.00 reads per min processed... 3272727.27 reads per min processed... 3352941.18 reads per min processed... 3428571.43 reads per min processed... 3500000.00 reads per min processed... 3473684.21 reads per min processed... 3538461.54 reads per min processed... 3512195.12 reads per min processed... 3488372.09 reads per min processed... 3466666.67 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.miIACfCJB2/ColoN_FFPE_L07_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.miIACfCJB2/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -39353.731836 EM: Round [1] log likelihood: -39292.386365 EM: Round [2] log likelihood: -39266.850467 EM: Round [3] log likelihood: -39254.071362 EM: Round [4] log likelihood: -39247.091559 EM: Round [5] log likelihood: -39243.059322 EM: Round [6] log likelihood: -39240.612009 EM: Round [7] log likelihood: -39239.055325 EM: Round [8] log likelihood: -39238.021286 EM: Round [9] log likelihood: -39237.307504 EM: Round [10] log likelihood: -39236.798248 EM: Round [11] log likelihood: -39236.424654 EM: Round [12] log likelihood: -39236.144129 EM: Round [13] log likelihood: -39235.929348 EM: Round [14] log likelihood: -39235.762191 EM: Round [15] log likelihood: -39235.630278 EM: Round [16] log likelihood: -39235.524926 EM: Round [17] log likelihood: -39235.439908 EM: Round [18] log likelihood: -39235.370668 EM: Round [19] log likelihood: -39235.313815 EM: Round [20] log likelihood: -39235.266791 EM: Round [21] log likelihood: -39235.227637 EM: Round [22] log likelihood: -39235.194839 EM: Round [23] log likelihood: -39235.167214 EM: Round [24] log likelihood: -39235.143827 EM: Round [25] log likelihood: -39235.123934 EM: Round [26] log likelihood: -39235.106941 EM: Round [27] log likelihood: -39235.092366 EM: Round [28] log likelihood: -39235.079818 EM: Round [29] log likelihood: -39235.068977 EM: Round [30] log likelihood: -39235.059581 EM: Round [31] log likelihood: -39235.051412 EM: Round [32] log likelihood: -39235.044289 EM: Round [33] log likelihood: -39235.038062 EM: Round [34] log likelihood: -39235.032604 EM: Round [35] log likelihood: -39235.027809 EM: Round [36] log likelihood: -39235.023587 EM: Round [37] log likelihood: -39235.019862 EM: Round [38] log likelihood: -39235.016568 EM: Round [39] log likelihood: -39235.013651 EM: Round [40] log likelihood: -39235.011062 EM: Round [41] log likelihood: -39235.008760 EM: Round [42] log likelihood: -39235.006712 EM: Round [43] log likelihood: -39235.004885 EM: Round [44] log likelihood: -39235.003253 EM: Round [45] log likelihood: -39235.001795 EM: Round [46] log likelihood: -39235.000489 EM: Round [47] log likelihood: -39234.999319 EM: Round [48] log likelihood: -39234.998268 EM: Round [49] log likelihood: -39234.997324 EM: Round [50] log likelihood: -39234.996475 EM: Round [51] log likelihood: -39234.995711 EM: Round [52] log likelihood: -39234.995022 EM: Round [53] log likelihood: -39234.994401 EM: Round [54] log likelihood: -39234.993840 EM: Round [55] log likelihood: -39234.993333 EM: Round [56] log likelihood: -39234.992874 EM: Round [57] log likelihood: -39234.992459 EM: Round [58] log likelihood: -39234.992083 EM: Round [59] log likelihood: -39234.991742 EM: Round [60] log likelihood: -39234.991433 EM: Round [61] log likelihood: -39234.991152 EM: Round [62] log likelihood: -39234.990897 EM: Round [63] log likelihood: -39234.990665 EM: Round [64] log likelihood: -39234.990454 EM: Round [65] log likelihood: -39234.990262 EM: Round [66] log likelihood: -39234.990087 EM: Round [67] log likelihood: -39234.989927 EM: Round [68] log likelihood: -39234.989782 EM: Round [69] log likelihood: -39234.989649 EM: Round [70] log likelihood: -39234.989527 EM: Round [71] log likelihood: -39234.989416 EM: Round [72] log likelihood: -39234.989315 EM: Round [73] log likelihood: -39234.989222 EM: Stopping iterations at round 73 due to insufficient improvement in likelihood. EM: Starting log likelihood: -39343.133834 EM: Round [1] log likelihood: -39285.451452 EM: Round [2] log likelihood: -39262.185038 EM: Round [3] log likelihood: -39250.887531 EM: Round [4] log likelihood: -39244.872207 EM: Round [5] log likelihood: -39241.479201 EM: Round [6] log likelihood: -39239.467413 EM: Round [7] log likelihood: -39238.215012 EM: Round [8] log likelihood: -39237.397700 EM: Round [9] log likelihood: -39236.840505 EM: Round [10] log likelihood: -39236.445642 EM: Round [11] log likelihood: -39236.156388 EM: Round [12] log likelihood: -39235.938553 EM: Round [13] log likelihood: -39235.770723 EM: Round [14] log likelihood: -39235.638982 EM: Round [15] log likelihood: -39235.533967 EM: Round [16] log likelihood: -39235.449184 EM: Round [17] log likelihood: -39235.379995 EM: Round [18] log likelihood: -39235.323014 EM: Round [19] log likelihood: -39235.275715 EM: Round [20] log likelihood: -39235.236180 EM: Round [21] log likelihood: -39235.202931 EM: Round [22] log likelihood: -39235.174813 EM: Round [23] log likelihood: -39235.150917 EM: Round [24] log likelihood: -39235.130517 EM: Round [25] log likelihood: -39235.113027 EM: Round [26] log likelihood: -39235.097976 EM: Round [27] log likelihood: -39235.084977 EM: Round [28] log likelihood: -39235.073713 EM: Round [29] log likelihood: -39235.063922 EM: Round [30] log likelihood: -39235.055386 EM: Round [31] log likelihood: -39235.047926 EM: Round [32] log likelihood: -39235.041387 EM: Round [33] log likelihood: -39235.035644 EM: Round [34] log likelihood: -39235.030586 EM: Round [35] log likelihood: -39235.026124 EM: Round [36] log likelihood: -39235.022179 EM: Round [37] log likelihood: -39235.018685 EM: Round [38] log likelihood: -39235.015583 EM: Round [39] log likelihood: -39235.012826 EM: Round [40] log likelihood: -39235.010372 EM: Round [41] log likelihood: -39235.008183 EM: Round [42] log likelihood: -39235.006228 EM: Round [43] log likelihood: -39235.004480 EM: Round [44] log likelihood: -39235.002915 EM: Round [45] log likelihood: -39235.001511 EM: Round [46] log likelihood: -39235.000252 EM: Round [47] log likelihood: -39234.999120 EM: Round [48] log likelihood: -39234.998102 EM: Round [49] log likelihood: -39234.997185 EM: Round [50] log likelihood: -39234.996358 EM: Round [51] log likelihood: -39234.995613 EM: Round [52] log likelihood: -39234.994940 EM: Round [53] log likelihood: -39234.994331 EM: Round [54] log likelihood: -39234.993781 EM: Round [55] log likelihood: -39234.993283 EM: Round [56] log likelihood: -39234.992832 EM: Round [57] log likelihood: -39234.992423 EM: Round [58] log likelihood: -39234.992052 EM: Round [59] log likelihood: -39234.991715 EM: Round [60] log likelihood: -39234.991409 EM: Round [61] log likelihood: -39234.991131 EM: Round [62] log likelihood: -39234.990879 EM: Round [63] log likelihood: -39234.990648 EM: Round [64] log likelihood: -39234.990439 EM: Round [65] log likelihood: -39234.990248 EM: Round [66] log likelihood: -39234.990074 EM: Round [67] log likelihood: -39234.989915 EM: Round [68] log likelihood: -39234.989770 EM: Round [69] log likelihood: -39234.989637 EM: Round [70] log likelihood: -39234.989516 EM: Round [71] log likelihood: -39234.989406 EM: Round [72] log likelihood: -39234.989304 EM: Round [73] log likelihood: -39234.989212 EM: Stopping iterations at round 73 due to insufficient improvement in likelihood. CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.miIACfCJB2/./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.miIACfCJB2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.miIACfCJB2/./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.miIACfCJB2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 36146178 > /tmp/nxf.miIACfCJB2/./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.miIACfCJB2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir > /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir --annotate /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.miIACfCJB2/./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.miIACfCJB2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir -done, see /tmp/nxf.miIACfCJB2/./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.miIACfCJB2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.miIACfCJB2/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 277, filtered: 3454) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.miIACfCJB2/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.miIACfCJB2/./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.miIACfCJB2/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000229739.4] WARNING, no entry stored in dbm for [ENSG00000264538.6] WARNING, no entry stored in dbm for [ENSG00000232732.11] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000283696.1] WARNING, no entry stored in dbm for [ENSG00000180747.15] WARNING, no entry stored in dbm for [ENSG00000261702.2] WARNING, no entry stored in dbm for [ENSG00000214535.3] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000279217.1] WARNING, no entry stored in dbm for [ENSG00000230666.5] WARNING, no entry stored in dbm for [ENSG00000212694.8] WARNING, no entry stored in dbm for [ENSG00000240549.2] WARNING, no entry stored in dbm for [ENSG00000229180.7] WARNING, no entry stored in dbm for [ENSG00000158482.10] WARNING, no entry stored in dbm for [ENSG00000277458.1] WARNING, no entry stored in dbm for [ENSG00000277142.1] WARNING, no entry stored in dbm for [ENSG00000224209.8] WARNING, no entry stored in dbm for [ENSG00000223508.5] WARNING, no entry stored in dbm for [ENSG00000254762.1] WARNING, no entry stored in dbm for [ENSG00000265735.2] WARNING, no entry stored in dbm for [ENSG00000240116.3] WARNING, no entry stored in dbm for [ENSG00000276168.1] WARNING, no entry stored in dbm for [ENSG00000240116.3] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000200708.1] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000200794.1] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000202406.1] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000201287.1] WARNING, no entry stored in dbm for [ENSG00000202415.1] WARNING, no entry stored in dbm for [ENSG00000200488.1] 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 [ENSG00000248764.1] WARNING, no entry stored in dbm for [ENSG00000230305.2] WARNING, no entry stored in dbm for [ENSG00000273129.2] WARNING, no entry stored in dbm for [ENSG00000261046.1] WARNING, no entry stored in dbm for [ENSG00000267107.8] WARNING, no entry stored in dbm for [ENSG00000225072.1] WARNING, no entry stored in dbm for [ENSG00000224367.6] WARNING, no entry stored in dbm for [ENSG00000266916.7] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000198496.12] WARNING, no entry stored in dbm for [ENSG00000262879.6] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000215386.13] WARNING, no entry stored in dbm for [ENSG00000283774.1] WARNING, no entry stored in dbm for [ENSG00000221063.3] WARNING, no entry stored in dbm for [ENSG00000244171.4] WARNING, no entry stored in dbm for [ENSG00000229382.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000213247.3] WARNING, no entry stored in dbm for [ENSG00000237929.1] WARNING, no entry stored in dbm for [ENSG00000254401.2] WARNING, no entry stored in dbm for [ENSG00000231566.2] WARNING, no entry stored in dbm for [ENSG00000281721.1] WARNING, no entry stored in dbm for [ENSG00000229433.2] WARNING, no entry stored in dbm for [ENSG00000261008.7] WARNING, no entry stored in dbm for [ENSG00000281912.1] WARNING, no entry stored in dbm for [ENSG00000249069.8] WARNING, no entry stored in dbm for [ENSG00000235703.6] WARNING, no entry stored in dbm for [ENSG00000241769.7] WARNING, no entry stored in dbm for [ENSG00000259905.7] WARNING, no entry stored in dbm for [ENSG00000225718.2] 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 [ENSG00000279128.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000231074.9] WARNING, no entry stored in dbm for [ENSG00000166104.15] WARNING, no entry stored in dbm for [ENSG00000166104.15] WARNING, no entry stored in dbm for [ENSG00000124835.2] WARNING, no entry stored in dbm for [ENSG00000124835.2] WARNING, no entry stored in dbm for [ENSG00000124835.2] WARNING, no entry stored in dbm for [ENSG00000255410.2] WARNING, no entry stored in dbm for [ENSG00000283103.3] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000262870.1] WARNING, no entry stored in dbm for [ENSG00000229212.8] WARNING, no entry stored in dbm for [ENSG00000236204.6] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [ENSG00000272578.5] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000279484.2] WARNING, no entry stored in dbm for [ENSG00000285799.1] WARNING, no entry stored in dbm for [ENSG00000254741.1] WARNING, no entry stored in dbm for [ENSG00000282885.2] WARNING, no entry stored in dbm for [ENSG00000244236.3] WARNING, no entry stored in dbm for [ENSG00000287356.1] WARNING, no entry stored in dbm for [ENSG00000225032.5] WARNING, no entry stored in dbm for [ENSG00000236740.6] WARNING, no entry stored in dbm for [ENSG00000286073.1] WARNING, no entry stored in dbm for [ENSG00000226499.1] WARNING, no entry stored in dbm for [ENSG00000239670.1] WARNING, no entry stored in dbm for [ENSG00000258875.6] WARNING, no entry stored in dbm for [ENSG00000244237.1] WARNING, no entry stored in dbm for [ENSG00000181524.6] WARNING, no entry stored in dbm for [ENSG00000259121.2] WARNING, no entry stored in dbm for [ENSG00000274717.1] WARNING, no entry stored in dbm for [ENSG00000279738.1] WARNING, no entry stored in dbm for [ENSG00000259456.4] WARNING, no entry stored in dbm for [ENSG00000285492.1] WARNING, no entry stored in dbm for [ENSG00000227242.4] WARNING, no entry stored in dbm for [ENSG00000282375.1] WARNING, no entry stored in dbm for [ENSG00000260236.1] WARNING, no entry stored in dbm for [ENSG00000269001.2] WARNING, no entry stored in dbm for [ENSG00000258320.1] WARNING, no entry stored in dbm for [ENSG00000264151.6] WARNING, no entry stored in dbm for [ENSG00000222043.2] WARNING, no entry stored in dbm for [ENSG00000273765.1] WARNING, no entry stored in dbm for [ENSG00000205682.2] WARNING, no entry stored in dbm for [ENSG00000213963.6] WARNING, no entry stored in dbm for [ENSG00000230073.1] WARNING, no entry stored in dbm for [ENSG00000249631.6] * STAR-Fusion complete. See output: /tmp/nxf.miIACfCJB2/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)