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/0f/b121c22649d3ac1bf77f68733e3c98/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/8f067a3232b25971915d5e58659dcb/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/b121c22649d3ac1bf77f68733e3c98/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/8f067a3232b25971915d5e58659dcb/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/369a4c1784fa5c8c1eb6124589dba9/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction ==> STAGING COMPLETE (6 inputs) -ctat genome lib [/tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.x3pRS9bmiL/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary -sample contains 33064515 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir -J /tmp/nxf.x3pRS9bmiL/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.x3pRS9bmiL/BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -building interval tree based on /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=35294.12/min [20000], rate=37500.00/min [30000], rate=39130.43/min [40000], rate=42105.26/min [50000], rate=41095.89/min [60000], rate=42352.94/min [70000], rate=40000.00/min [80000], rate=40336.13/min [90000], rate=39416.06/min [100000], rate=33707.87/min [110000], rate=30841.12/min [120000], rate=30000.00/min [130000], rate=30115.83/min [140000], rate=30324.91/min [150000], rate=30303.03/min [160000], rate=29906.54/min [170000], rate=30000.00/min [180000], rate=30508.47/min [190000], rate=30238.73/min [200000], rate=30379.75/min [210000], rate=31034.48/min [220000], rate=31730.77/min [230000], rate=32547.17/min [240000], rate=33103.45/min [250000], rate=33936.65/min [260000], rate=34977.58/min [270000], rate=35217.39/min [280000], rate=35000.00/min [290000], rate=34730.54/min [300000], rate=34026.47/min [310000], rate=34380.78/min [320000], rate=34782.61/min [330000], rate=35168.74/min [340000], rate=35478.26/min [350000], rate=36144.58/min [360000], rate=36241.61/min [370000], rate=36694.21/min [380000], rate=37438.42/min [390000], rate=37440.00/min [400000], rate=37676.61/min [410000], rate=37788.02/min [420000], rate=38356.16/min [430000], rate=38738.74/min [440000], rate=39227.34/min [450000], rate=39531.48/min [460000], rate=39884.39/min [470000], rate=40285.71/min [480000], rate=40563.38/min [490000], rate=41061.45/min [500000], rate=41782.73/min [510000], rate=41860.47/min [520000], rate=41991.92/min [530000], rate=42343.54/min [540000], rate=42800.53/min [550000], rate=42635.66/min [560000], rate=43187.66/min [570000], rate=43401.02/min [580000], rate=43283.58/min [590000], rate=43435.58/min [600000], rate=43269.23/min [610000], rate=43364.93/min [620000], rate=43713.28/min [630000], rate=43699.42/min [640000], rate=43636.36/min [650000], rate=43771.04/min [660000], rate=43951.17/min [670000], rate=44321.94/min [680000], rate=44492.91/min [690000], rate=44420.60/min [700000], rate=44444.44/min [710000], rate=44607.33/min [720000], rate=43857.87/min [730000], rate=43280.63/min [740000], rate=42898.55/min [750000], rate=42412.82/min [760000], rate=41911.76/min [770000], rate=42000.00/min [780000], rate=42048.52/min [790000], rate=42170.82/min -building interval tree based on /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.10 min). -mapping reads to genes [10000], rate=60000.00/min [20000], rate=63157.89/min [30000], rate=64285.71/min [40000], rate=66666.67/min [50000], rate=51724.14/min [60000], rate=50704.23/min [70000], rate=51219.51/min [80000], rate=42105.26/min [90000], rate=40298.51/min [100000], rate=39215.69/min [110000], rate=40000.00/min [120000], rate=40449.44/min [130000], rate=40000.00/min [140000], rate=40975.61/min [150000], rate=42056.07/min [160000], rate=43243.24/min [170000], rate=43776.82/min [180000], rate=42187.50/min [190000], rate=40860.22/min [200000], rate=39867.11/min [210000], rate=40000.00/min [220000], rate=40366.97/min [230000], rate=40588.24/min [240000], rate=40449.44/min [250000], rate=40431.27/min [260000], rate=41160.95/min [270000], rate=40601.50/min [280000], rate=39344.26/min [290000], rate=38580.93/min [300000], rate=38297.87/min [310000], rate=38036.81/min [320000], rate=37721.02/min [330000], rate=37500.00/min [340000], rate=37500.00/min [350000], rate=38112.52/min [360000], rate=38434.16/min [370000], rate=38675.96/min [380000], rate=38907.85/min [390000], rate=39065.11/min [400000], rate=38709.68/min [410000], rate=38258.16/min [420000], rate=37724.55/min [430000], rate=37609.33/min [440000], rate=37288.14/min [450000], rate=36986.30/min [460000], rate=36849.13/min [470000], rate=37203.17/min [480000], rate=37548.89/min [490000], rate=37886.60/min [500000], rate=38216.56/min [510000], rate=38442.21/min [520000], rate=38329.24/min [530000], rate=38359.47/min [540000], rate=38297.87/min [550000], rate=38461.54/min [560000], rate=38799.08/min [570000], rate=38996.58/min [580000], rate=39500.57/min [590000], rate=39686.10/min [600000], rate=39560.44/min [610000], rate=39439.66/min [620000], rate=39658.85/min [630000], rate=39915.52/min [640000], rate=39916.84/min [650000], rate=40414.51/min [660000], rate=40740.74/min [670000], rate=40688.26/min [680000], rate=40759.24/min [690000], rate=40667.98/min [700000], rate=40697.67/min [710000], rate=40687.68/min [720000], rate=40639.70/min [730000], rate=40630.80/min [740000], rate=40771.35/min [750000], rate=40909.09/min [760000], rate=41304.35/min [770000], rate=41734.42/min [780000], rate=41785.71/min -building interval tree based on /tmp/nxf.x3pRS9bmiL/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=109090.91/min [30000], rate=112500.00/min [40000], rate=120000.00/min [50000], rate=120000.00/min [60000], rate=128571.43/min [70000], rate=120000.00/min [80000], rate=126315.79/min [90000], rate=135000.00/min [100000], rate=130434.78/min [110000], rate=120000.00/min [120000], rate=109090.91/min [130000], rate=105405.41/min [140000], rate=102439.02/min [150000], rate=101123.60/min [160000], rate=95049.50/min [170000], rate=95327.10/min [180000], rate=99082.57/min [190000], rate=93442.62/min [200000], rate=90909.09/min [210000], rate=90647.48/min [220000], rate=91666.67/min [230000], rate=92617.45/min [240000], rate=94117.65/min [250000], rate=92592.59/min [260000], rate=91764.71/min [270000], rate=90502.79/min [280000], rate=89839.57/min [290000], rate=88324.87/min [300000], rate=86956.52/min [310000], rate=87735.85/min [320000], rate=87671.23/min [330000], rate=86086.96/min [340000], rate=71578.95/min [350000], rate=59659.09/min [360000], rate=53333.33/min [370000], rate=48684.21/min [380000], rate=45059.29/min [390000], rate=41860.47/min [400000], rate=40268.46/min [410000], rate=39613.53/min [420000], rate=39313.57/min [430000], rate=38738.74/min [440000], rate=37714.29/min [450000], rate=37396.12/min [460000], rate=37146.70/min [470000], rate=36293.44/min [480000], rate=35955.06/min [490000], rate=35679.61/min [500000], rate=35587.19/min [510000], rate=35457.71/min [520000], rate=35494.88/min [530000], rate=35730.34/min [540000], rate=36040.04/min [550000], rate=36383.68/min [560000], rate=36129.03/min [570000], rate=36267.23/min [580000], rate=36439.79/min [590000], rate=36683.94/min [600000], rate=36960.99/min [610000], rate=37270.88/min [620000], rate=37575.76/min [630000], rate=37951.81/min [640000], rate=38133.07/min [650000], rate=38160.47/min [660000], rate=37786.26/min [670000], rate=37640.45/min [680000], rate=37673.13/min [690000], rate=37670.61/min [700000], rate=37668.16/min [710000], rate=37665.78/min [720000], rate=37663.47/min [730000], rate=37693.63/min [740000], rate=37659.03/min [750000], rate=37593.98/min [760000], rate=37592.75/min [770000], rate=37591.54/min [780000], rate=37410.07/min -building interval tree based on /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.12 min). -mapping reads to genes [10000], rate=37500.00/min [20000], rate=30769.23/min [30000], rate=30000.00/min [40000], rate=28235.29/min [50000], rate=29702.97/min [60000], rate=31858.41/min [70000], rate=33333.33/min [80000], rate=33566.43/min [90000], rate=32926.83/min [100000], rate=29411.76/min [110000], rate=28695.65/min [120000], rate=28800.00/min [130000], rate=29545.45/min [140000], rate=28378.38/min [150000], rate=28753.99/min [160000], rate=28571.43/min [170000], rate=28412.26/min [180000], rate=27906.98/min [190000], rate=28078.82/min [200000], rate=27842.23/min [210000], rate=27571.12/min [220000], rate=27672.96/min [230000], rate=28105.91/min [240000], rate=28571.43/min [250000], rate=29126.21/min [260000], rate=29714.29/min [270000], rate=30167.60/min [280000], rate=30490.02/min [290000], rate=31071.43/min [300000], rate=30981.07/min [310000], rate=31208.05/min [320000], rate=31372.55/min [330000], rate=31680.00/min [340000], rate=32278.48/min [350000], rate=32915.36/min [360000], rate=33384.85/min [370000], rate=33893.13/min [380000], rate=34650.46/min [390000], rate=34821.43/min [400000], rate=35036.50/min [410000], rate=35860.06/min [420000], rate=36416.18/min [430000], rate=36492.22/min [440000], rate=36464.09/min [450000], rate=36784.74/min [460000], rate=36800.00/min [470000], rate=37007.87/min [480000], rate=37209.30/min [490000], rate=37357.05/min [500000], rate=37128.71/min [510000], rate=37592.14/min [520000], rate=37187.13/min [530000], rate=36848.20/min [540000], rate=36734.69/min [550000], rate=36666.67/min [560000], rate=36561.48/min [570000], rate=36695.28/min [580000], rate=36670.18/min [590000], rate=36570.25/min [600000], rate=36585.37/min [610000], rate=36820.93/min [620000], rate=37162.84/min [630000], rate=36699.03/min [640000], rate=35820.90/min [650000], rate=35454.55/min [660000], rate=35357.14/min [670000], rate=35170.60/min [680000], rate=35142.12/min [690000], rate=35114.50/min [700000], rate=35353.54/min [710000], rate=35529.61/min [720000], rate=35673.00/min [730000], rate=35931.09/min [740000], rate=36363.64/min [750000], rate=36704.73/min [760000], rate=37012.99/min [770000], rate=37258.06/min [780000], rate=37172.36/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir --filt_file /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.x3pRS9bmiL/./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... 9000000.00 reads per min processed... 6000000.00 reads per min processed... 5000000.00 reads per min processed... 4000000.00 reads per min processed... 3818181.82 reads per min processed... 3692307.69 reads per min processed... 3600000.00 reads per min processed... 3529411.76 reads per min processed... 3300000.00 reads per min processed... 3272727.27 reads per min processed... 3250000.00 reads per min processed... 3230769.23 reads per min processed... 3214285.71 reads per min processed... 3200000.00 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... 3567567.57 reads per min processed... 3631578.95 reads per min processed... 3600000.00 reads per min processed... 3658536.59 reads per min processed... 3627906.98 reads per min processed... 3600000.00 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.x3pRS9bmiL/BreastNP_FFPE_L03_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.x3pRS9bmiL/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -48868.252451 EM: Round [1] log likelihood: -48750.890590 EM: Round [2] log likelihood: -48699.826139 EM: Round [3] log likelihood: -48673.305331 EM: Round [4] log likelihood: -48658.545335 EM: Round [5] log likelihood: -48650.071203 EM: Round [6] log likelihood: -48645.079511 EM: Round [7] log likelihood: -48642.048251 EM: Round [8] log likelihood: -48640.141512 EM: Round [9] log likelihood: -48638.897228 EM: Round [10] log likelihood: -48638.055979 EM: Round [11] log likelihood: -48637.468464 EM: Round [12] log likelihood: -48637.046126 EM: Round [13] log likelihood: -48636.734725 EM: Round [14] log likelihood: -48636.499967 EM: Round [15] log likelihood: -48636.319508 EM: Round [16] log likelihood: -48636.178382 EM: Round [17] log likelihood: -48636.066315 EM: Round [18] log likelihood: -48635.976095 EM: Round [19] log likelihood: -48635.902562 EM: Round [20] log likelihood: -48635.841960 EM: Round [21] log likelihood: -48635.791509 EM: Round [22] log likelihood: -48635.749127 EM: Round [23] log likelihood: -48635.713231 EM: Round [24] log likelihood: -48635.682603 EM: Round [25] log likelihood: -48635.656298 EM: Round [26] log likelihood: -48635.633569 EM: Round [27] log likelihood: -48635.613826 EM: Round [28] log likelihood: -48635.596593 EM: Round [29] log likelihood: -48635.581487 EM: Round [30] log likelihood: -48635.568193 EM: Round [31] log likelihood: -48635.556453 EM: Round [32] log likelihood: -48635.546051 EM: Round [33] log likelihood: -48635.536809 EM: Round [34] log likelihood: -48635.528575 EM: Round [35] log likelihood: -48635.521221 EM: Round [36] log likelihood: -48635.514638 EM: Round [37] log likelihood: -48635.508733 EM: Round [38] log likelihood: -48635.503425 EM: Round [39] log likelihood: -48635.498646 EM: Round [40] log likelihood: -48635.494335 EM: Round [41] log likelihood: -48635.490439 EM: Round [42] log likelihood: -48635.486914 EM: Round [43] log likelihood: -48635.483719 EM: Round [44] log likelihood: -48635.480818 EM: Round [45] log likelihood: -48635.478182 EM: Round [46] log likelihood: -48635.475782 EM: Round [47] log likelihood: -48635.473594 EM: Round [48] log likelihood: -48635.471598 EM: Round [49] log likelihood: -48635.469773 EM: Round [50] log likelihood: -48635.468104 EM: Round [51] log likelihood: -48635.466574 EM: Round [52] log likelihood: -48635.465171 EM: Round [53] log likelihood: -48635.463882 EM: Round [54] log likelihood: -48635.462698 EM: Round [55] log likelihood: -48635.461607 EM: Round [56] log likelihood: -48635.460602 EM: Round [57] log likelihood: -48635.459674 EM: Round [58] log likelihood: -48635.458817 EM: Round [59] log likelihood: -48635.458024 EM: Round [60] log likelihood: -48635.457291 EM: Round [61] log likelihood: -48635.456611 EM: Round [62] log likelihood: -48635.455979 EM: Round [63] log likelihood: -48635.455393 EM: Round [64] log likelihood: -48635.454848 EM: Round [65] log likelihood: -48635.454340 EM: Round [66] log likelihood: -48635.453867 EM: Round [67] log likelihood: -48635.453426 EM: Round [68] log likelihood: -48635.453014 EM: Round [69] log likelihood: -48635.452629 EM: Round [70] log likelihood: -48635.452269 EM: Round [71] log likelihood: -48635.451931 EM: Round [72] log likelihood: -48635.451615 EM: Round [73] log likelihood: -48635.451318 EM: Round [74] log likelihood: -48635.451039 EM: Round [75] log likelihood: -48635.450776 EM: Round [76] log likelihood: -48635.450530 EM: Round [77] log likelihood: -48635.450297 EM: Round [78] log likelihood: -48635.450078 EM: Round [79] log likelihood: -48635.449871 EM: Round [80] log likelihood: -48635.449676 EM: Round [81] log likelihood: -48635.449492 EM: Round [82] log likelihood: -48635.449317 EM: Round [83] log likelihood: -48635.449152 EM: Round [84] log likelihood: -48635.448995 EM: Round [85] log likelihood: -48635.448847 EM: Round [86] log likelihood: -48635.448706 EM: Round [87] log likelihood: -48635.448573 EM: Round [88] log likelihood: -48635.448446 EM: Round [89] log likelihood: -48635.448325 EM: Round [90] log likelihood: -48635.448211 EM: Round [91] log likelihood: -48635.448101 EM: Round [92] log likelihood: -48635.447997 EM: Round [93] log likelihood: -48635.447898 EM: Stopping iterations at round 93 due to insufficient improvement in likelihood. EM: Starting log likelihood: -48804.140024 EM: Round [1] log likelihood: -48702.492977 EM: Round [2] log likelihood: -48659.365448 EM: Round [3] log likelihood: -48637.220038 EM: Round [4] log likelihood: -48625.006033 EM: Round [5] log likelihood: -48618.065163 EM: Round [6] log likelihood: -48614.023392 EM: Round [7] log likelihood: -48611.597652 EM: Round [8] log likelihood: -48610.088035 EM: Round [9] log likelihood: -48609.111259 EM: Round [10] log likelihood: -48608.454637 EM: Round [11] log likelihood: -48607.997377 EM: Round [12] log likelihood: -48607.668796 EM: Round [13] log likelihood: -48607.426137 EM: Round [14] log likelihood: -48607.242650 EM: Round [15] log likelihood: -48607.101042 EM: Round [16] log likelihood: -48606.989796 EM: Round [17] log likelihood: -48606.901031 EM: Round [18] log likelihood: -48606.829222 EM: Round [19] log likelihood: -48606.770415 EM: Round [20] log likelihood: -48606.721726 EM: Round [21] log likelihood: -48606.681018 EM: Round [22] log likelihood: -48606.646684 EM: Round [23] log likelihood: -48606.617497 EM: Round [24] log likelihood: -48606.592510 EM: Round [25] log likelihood: -48606.570983 EM: Round [26] log likelihood: -48606.552333 EM: Round [27] log likelihood: -48606.536091 EM: Round [28] log likelihood: -48606.521883 EM: Round [29] log likelihood: -48606.509403 EM: Round [30] log likelihood: -48606.498398 EM: Round [31] log likelihood: -48606.488663 EM: Round [32] log likelihood: -48606.480023 EM: Round [33] log likelihood: -48606.472333 EM: Round [34] log likelihood: -48606.465472 EM: Round [35] log likelihood: -48606.459334 EM: Round [36] log likelihood: -48606.453832 EM: Round [37] log likelihood: -48606.448888 EM: Round [38] log likelihood: -48606.444438 EM: Round [39] log likelihood: -48606.440424 EM: Round [40] log likelihood: -48606.436797 EM: Round [41] log likelihood: -48606.433514 EM: Round [42] log likelihood: -48606.430537 EM: Round [43] log likelihood: -48606.427834 EM: Round [44] log likelihood: -48606.425375 EM: Round [45] log likelihood: -48606.423136 EM: Round [46] log likelihood: -48606.421093 EM: Round [47] log likelihood: -48606.419226 EM: Round [48] log likelihood: -48606.417519 EM: Round [49] log likelihood: -48606.415954 EM: Round [50] log likelihood: -48606.414519 EM: Round [51] log likelihood: -48606.413201 EM: Round [52] log likelihood: -48606.411988 EM: Round [53] log likelihood: -48606.410871 EM: Round [54] log likelihood: -48606.409842 EM: Round [55] log likelihood: -48606.408891 EM: Round [56] log likelihood: -48606.408012 EM: Round [57] log likelihood: -48606.407198 EM: Round [58] log likelihood: -48606.406444 EM: Round [59] log likelihood: -48606.405745 EM: Round [60] log likelihood: -48606.405095 EM: Round [61] log likelihood: -48606.404491 EM: Round [62] log likelihood: -48606.403928 EM: Round [63] log likelihood: -48606.403404 EM: Round [64] log likelihood: -48606.402915 EM: Round [65] log likelihood: -48606.402458 EM: Round [66] log likelihood: -48606.402031 EM: Round [67] log likelihood: -48606.401631 EM: Round [68] log likelihood: -48606.401256 EM: Round [69] log likelihood: -48606.400905 EM: Round [70] log likelihood: -48606.400575 EM: Round [71] log likelihood: -48606.400265 EM: Round [72] log likelihood: -48606.399973 EM: Round [73] log likelihood: -48606.399699 EM: Round [74] log likelihood: -48606.399440 EM: Round [75] log likelihood: -48606.399197 EM: Round [76] log likelihood: -48606.398966 EM: Round [77] log likelihood: -48606.398749 EM: Round [78] log likelihood: -48606.398543 EM: Round [79] log likelihood: -48606.398349 EM: Round [80] log likelihood: -48606.398165 EM: Round [81] log likelihood: -48606.397990 EM: Round [82] log likelihood: -48606.397825 EM: Round [83] log likelihood: -48606.397668 EM: Round [84] log likelihood: -48606.397518 EM: Round [85] log likelihood: -48606.397377 EM: Round [86] log likelihood: -48606.397242 EM: Round [87] log likelihood: -48606.397114 EM: Round [88] log likelihood: -48606.396992 EM: Round [89] log likelihood: -48606.396875 EM: Round [90] log likelihood: -48606.396765 EM: Round [91] log likelihood: -48606.396659 EM: Round [92] log likelihood: -48606.396558 EM: Round [93] log likelihood: -48606.396462 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.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.x3pRS9bmiL/./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.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.x3pRS9bmiL/./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.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 33064515 > /tmp/nxf.x3pRS9bmiL/./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.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir > /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir --annotate /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.x3pRS9bmiL/./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.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir -done, see /tmp/nxf.x3pRS9bmiL/./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.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.x3pRS9bmiL/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 199, filtered: 2689) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.x3pRS9bmiL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.x3pRS9bmiL/./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.x3pRS9bmiL/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [ENSG00000246067.8] WARNING, no entry stored in dbm for [ENSG00000214433.4] WARNING, no entry stored in dbm for [ENSG00000287991.1] WARNING, no entry stored in dbm for [ENSG00000248830.1] WARNING, no entry stored in dbm for [ENSG00000248830.1] WARNING, no entry stored in dbm for [ENSG00000248830.1] WARNING, no entry stored in dbm for [ENSG00000248830.1] WARNING, no entry stored in dbm for [ENSG00000248830.1] WARNING, no entry stored in dbm for [ENSG00000232732.11] WARNING, no entry stored in dbm for [ENSG00000274376.4] WARNING, no entry stored in dbm for [ENSG00000226049.3] WARNING, no entry stored in dbm for [ENSG00000260404.3] WARNING, no entry stored in dbm for [ENSG00000240549.2] WARNING, no entry stored in dbm for [ENSG00000240549.2] WARNING, no entry stored in dbm for [ENSG00000270964.1] WARNING, no entry stored in dbm for [ENSG00000235919.4] WARNING, no entry stored in dbm for [ENSG00000248956.1] WARNING, no entry stored in dbm for [ENSG00000286288.1] WARNING, no entry stored in dbm for [ENSG00000272668.2] WARNING, no entry stored in dbm for [ENSG00000235065.1] WARNING, no entry stored in dbm for [ENSG00000244237.1] WARNING, no entry stored in dbm for [ENSG00000231322.5] WARNING, no entry stored in dbm for [ENSG00000251889.1] WARNING, no entry stored in dbm for [ENSG00000201806.1] WARNING, no entry stored in dbm for [ENSG00000239742.3] WARNING, no entry stored in dbm for [ENSG00000239437.3] WARNING, no entry stored in dbm for [ENSG00000239742.3] WARNING, no entry stored in dbm for [ENSG00000244642.3] WARNING, no entry stored in dbm for [ENSG00000244642.3] WARNING, no entry stored in dbm for [ENSG00000243541.3] WARNING, no entry stored in dbm for [ENSG00000244642.3] WARNING, no entry stored in dbm for [ENSG00000222259.1] WARNING, no entry stored in dbm for [ENSG00000202058.1] WARNING, no entry stored in dbm for [ENSG00000287218.1] WARNING, no entry stored in dbm for [ENSG00000276255.2] WARNING, no entry stored in dbm for [ENSG00000239883.8] WARNING, no entry stored in dbm for [ENSG00000233997.5] WARNING, no entry stored in dbm for [ENSG00000249673.7] WARNING, no entry stored in dbm for [ENSG00000286641.1] WARNING, no entry stored in dbm for [ENSG00000249072.1] WARNING, no entry stored in dbm for [ENSG00000263146.2] WARNING, no entry stored in dbm for [ENSG00000287356.1] WARNING, no entry stored in dbm for [ENSG00000234199.3] WARNING, no entry stored in dbm for [ENSG00000153363.13] WARNING, no entry stored in dbm for [ENSG00000242628.6] WARNING, no entry stored in dbm for [ENSG00000248890.2] WARNING, no entry stored in dbm for [ENSG00000228876.4] WARNING, no entry stored in dbm for [ENSG00000273420.1] WARNING, no entry stored in dbm for [ENSG00000230335.1] WARNING, no entry stored in dbm for [ENSG00000224415.1] WARNING, no entry stored in dbm for [ENSG00000268812.3] WARNING, no entry stored in dbm for [ENSG00000262966.2] WARNING, no entry stored in dbm for [ENSG00000277047.5] WARNING, no entry stored in dbm for [ENSG00000234715.2] WARNING, no entry stored in dbm for [ENSG00000270780.1] WARNING, no entry stored in dbm for [ENSG00000234589.4] WARNING, no entry stored in dbm for [ENSG00000258561.2] WARNING, no entry stored in dbm for [ENSG00000225032.5] WARNING, no entry stored in dbm for [ENSG00000274993.1] WARNING, no entry stored in dbm for [ENSG00000259692.6] WARNING, no entry stored in dbm for [ENSG00000235908.1] WARNING, no entry stored in dbm for [ENSG00000230869.1] WARNING, no entry stored in dbm for [ENSG00000272140.2] WARNING, no entry stored in dbm for [ENSG00000279057.1] WARNING, no entry stored in dbm for [ENSG00000229930.1] WARNING, no entry stored in dbm for [ENSG00000251314.2] WARNING, no entry stored in dbm for [ENSG00000285108.1] WARNING, no entry stored in dbm for [ENSG00000287007.1] WARNING, no entry stored in dbm for [ENSG00000253973.3] WARNING, no entry stored in dbm for [ENSG00000254741.1] WARNING, no entry stored in dbm for [ENSG00000266830.1] WARNING, no entry stored in dbm for [ENSG00000234773.7] WARNING, no entry stored in dbm for [ENSG00000248830.1] WARNING, no entry stored in dbm for [ENSG00000280007.1] WARNING, no entry stored in dbm for [ENSG00000283041.1] WARNING, no entry stored in dbm for [ENSG00000277458.1] WARNING, no entry stored in dbm for [ENSG00000189149.12] WARNING, no entry stored in dbm for [ENSG00000250614.1] WARNING, no entry stored in dbm for [ENSG00000185684.15] WARNING, no entry stored in dbm for [ENSG00000277283.1] * STAR-Fusion complete. See output: /tmp/nxf.x3pRS9bmiL/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)