-ctat genome lib [/tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir] validates. CMD: mkdir -p /tmp/nxf.x9YT2HSNW6/./_starF_checkpoints CMD: mkdir -p /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary -sample contains 115055067 rnaseq fragments * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir -J /tmp/nxf.x9YT2HSNW6/dna_s775.Chimeric.out.junction -O /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 -parsing fusion evidence: /tmp/nxf.x9YT2HSNW6/dna_s775.Chimeric.out.junction -building interval tree based on /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=46153.85/min [20000], rate=46153.85/min [30000], rate=43902.44/min [40000], rate=43636.36/min [50000], rate=45454.55/min [60000], rate=47368.42/min [70000], rate=50000.00/min [80000], rate=51612.90/min [90000], rate=52427.18/min [100000], rate=52631.58/min [110000], rate=53225.81/min [120000], rate=54135.34/min [130000], rate=55319.15/min [140000], rate=56756.76/min [150000], rate=59602.65/min [160000], rate=62745.10/min [170000], rate=63750.00/min [180000], rate=63905.33/min [190000], rate=64406.78/min [200000], rate=64516.13/min [210000], rate=64615.38/min [220000], rate=65024.63/min [230000], rate=65094.34/min [240000], rate=64864.86/min [250000], rate=64655.17/min [260000], rate=64730.29/min [270000], rate=63035.02/min [280000], rate=61992.62/min [290000], rate=61052.63/min [300000], rate=59800.66/min [310000], rate=59047.62/min [320000], rate=58715.60/min [330000], rate=58235.29/min [340000], rate=57790.37/min [350000], rate=57377.05/min [360000], rate=57142.86/min [370000], rate=57216.49/min [380000], rate=57286.43/min [390000], rate=57352.94/min [400000], rate=57831.33/min [410000], rate=57746.48/min [420000], rate=56884.88/min [430000], rate=56209.15/min [440000], rate=55696.20/min [450000], rate=55327.87/min [460000], rate=55200.00/min [470000], rate=55185.91/min [480000], rate=55066.92/min [490000], rate=55159.47/min [500000], rate=55147.06/min [510000], rate=55334.54/min [520000], rate=55516.01/min [530000], rate=55789.47/min [540000], rate=55670.10/min [550000], rate=55276.38/min [560000], rate=54991.82/min [570000], rate=54720.00/min [580000], rate=54460.09/min [590000], rate=54211.33/min [600000], rate=54054.05/min [610000], rate=54062.04/min [620000], rate=54069.77/min [630000], rate=54077.25/min [640000], rate=54160.79/min -building interval tree based on /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=66666.67/min [20000], rate=50000.00/min [30000], rate=45000.00/min [40000], rate=43636.36/min [50000], rate=43478.26/min [60000], rate=43902.44/min [70000], rate=44680.85/min [80000], rate=45283.02/min [90000], rate=46551.72/min [100000], rate=47244.09/min [110000], rate=48529.41/min [120000], rate=49655.17/min [130000], rate=50649.35/min [140000], rate=50299.40/min [150000], rate=49450.55/min [160000], rate=48730.96/min [170000], rate=48341.23/min [180000], rate=48214.29/min [190000], rate=48101.27/min [200000], rate=48192.77/min [210000], rate=48275.86/min [220000], rate=48351.65/min [230000], rate=48763.25/min [240000], rate=49146.76/min [250000], rate=49668.87/min [260000], rate=50322.58/min [270000], rate=50943.40/min [280000], rate=50755.29/min [290000], rate=50289.02/min [300000], rate=50139.28/min [310000], rate=49865.95/min [320000], rate=49870.13/min [330000], rate=49874.06/min [340000], rate=49877.75/min [350000], rate=50000.00/min [360000], rate=50000.00/min [370000], rate=50000.00/min [380000], rate=50220.26/min [390000], rate=50539.96/min [400000], rate=50314.47/min [410000], rate=50101.83/min [420000], rate=50199.20/min [430000], rate=50292.40/min [440000], rate=50381.68/min [450000], rate=50373.13/min [460000], rate=50457.04/min [470000], rate=50537.63/min [480000], rate=50704.23/min [490000], rate=50953.21/min [500000], rate=51107.33/min [510000], rate=51515.15/min [520000], rate=51655.63/min [530000], rate=51623.38/min [540000], rate=51510.33/min [550000], rate=51643.19/min [560000], rate=51692.31/min [570000], rate=51896.81/min [580000], rate=51940.30/min [590000], rate=51982.38/min [600000], rate=52249.64/min [610000], rate=52360.52/min [620000], rate=52616.69/min [630000], rate=52867.13/min [640000], rate=53038.67/min -building interval tree based on /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=85714.29/min [20000], rate=92307.69/min [30000], rate=78260.87/min [40000], rate=70588.24/min [50000], rate=66666.67/min [60000], rate=62068.97/min [70000], rate=61764.71/min [80000], rate=62337.66/min [90000], rate=62068.97/min [100000], rate=59405.94/min [110000], rate=58928.57/min [120000], rate=58064.52/min [130000], rate=58208.96/min [140000], rate=58333.33/min [150000], rate=59210.53/min [160000], rate=60000.00/min [170000], rate=60714.29/min [180000], rate=61714.29/min [190000], rate=61290.32/min [200000], rate=60301.51/min [210000], rate=59433.96/min [220000], rate=58928.57/min [230000], rate=58474.58/min [240000], rate=59016.39/min [250000], rate=59055.12/min [260000], rate=59315.59/min [270000], rate=59778.60/min [280000], rate=60649.82/min [290000], rate=59385.67/min [300000], rate=58631.92/min [310000], rate=57943.93/min [320000], rate=57485.03/min [330000], rate=57225.43/min [340000], rate=56983.24/min [350000], rate=56603.77/min [360000], rate=56396.87/min [370000], rate=56345.18/min [380000], rate=56296.30/min [390000], rate=56521.74/min [400000], rate=56603.77/min [410000], rate=56551.72/min [420000], rate=56502.24/min [430000], rate=56703.30/min [440000], rate=56896.55/min [450000], rate=56367.43/min [460000], rate=55645.16/min [470000], rate=55078.12/min [480000], rate=54752.85/min [490000], rate=54343.81/min [500000], rate=54151.62/min [510000], rate=54159.29/min [520000], rate=54355.40/min [530000], rate=54545.45/min [540000], rate=54545.45/min [550000], rate=53921.57/min [560000], rate=53588.52/min [570000], rate=53354.13/min [580000], rate=53129.77/min [590000], rate=52757.08/min [600000], rate=52478.13/min [610000], rate=52285.71/min [620000], rate=52027.97/min [630000], rate=51994.50/min [640000], rate=51962.11/min -building interval tree based on /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu -done building interval tree (0.08 min). -mapping reads to genes [10000], rate=120000.00/min [20000], rate=109090.91/min [30000], rate=94736.84/min [40000], rate=109090.91/min [50000], rate=83333.33/min [60000], rate=62068.97/min [70000], rate=52500.00/min [80000], rate=48484.85/min [90000], rate=45378.15/min [100000], rate=43795.62/min [110000], rate=42580.65/min [120000], rate=41618.50/min [130000], rate=41269.84/min [140000], rate=40975.61/min [150000], rate=40909.09/min [160000], rate=41379.31/min [170000], rate=41463.41/min [180000], rate=41860.47/min [190000], rate=41911.76/min [200000], rate=42105.26/min [210000], rate=42567.57/min [220000], rate=42996.74/min [230000], rate=43396.23/min [240000], rate=43902.44/min [250000], rate=44247.79/min [260000], rate=44827.59/min [270000], rate=45505.62/min [280000], rate=45405.41/min [290000], rate=45549.74/min [300000], rate=45918.37/min [310000], rate=46153.85/min [320000], rate=46376.81/min [330000], rate=46478.87/min [340000], rate=46575.34/min [350000], rate=46666.67/min [360000], rate=46956.52/min [370000], rate=47639.48/min [380000], rate=48000.00/min [390000], rate=47368.42/min [400000], rate=47151.28/min [410000], rate=47126.44/min [420000], rate=47014.93/min [430000], rate=46823.96/min [440000], rate=46808.51/min [450000], rate=46875.00/min [460000], rate=47018.74/min [470000], rate=47236.18/min [480000], rate=47682.12/min [490000], rate=47960.85/min [500000], rate=47694.75/min [510000], rate=47441.86/min [520000], rate=47344.46/min [530000], rate=47041.42/min [540000], rate=46888.57/min [550000], rate=46808.51/min [560000], rate=46796.66/min [570000], rate=46849.32/min [580000], rate=47090.66/min [590000], rate=47263.02/min [600000], rate=47493.40/min [610000], rate=47843.14/min [620000], rate=48124.19/min [630000], rate=48337.60/min [640000], rate=48669.20/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir --filt_file /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -parsing /tmp/nxf.x9YT2HSNW6/./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... 4800000.00 reads per min processed... 5000000.00 reads per min processed... 5142857.14 reads per min processed... 5250000.00 reads per min processed... 4800000.00 reads per min processed... 4909090.91 reads per min processed... 5000000.00 reads per min processed... 5076923.08 reads per min processed... 5142857.14 reads per min processed... 5200000.00 reads per min processed... 5250000.00 reads per min processed... 5294117.65 reads per min processed... 5052631.58 reads per min processed... 5100000.00 reads per min processed... 5142857.14 reads per min processed... done. * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion -parsing fusion evidence: /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -outputting fusion candidates to file: /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.x9YT2HSNW6/dna_s775.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.x9YT2HSNW6/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion CMD: mkdir -p /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir EM: Starting log likelihood: -137736.395448 EM: Round [1] log likelihood: -137640.456875 EM: Round [2] log likelihood: -137614.759908 EM: Round [3] log likelihood: -137604.260315 EM: Round [4] log likelihood: -137598.813363 EM: Round [5] log likelihood: -137595.575318 EM: Round [6] log likelihood: -137593.475834 EM: Round [7] log likelihood: -137592.028128 EM: Round [8] log likelihood: -137590.981728 EM: Round [9] log likelihood: -137590.196278 EM: Round [10] log likelihood: -137589.588019 EM: Round [11] log likelihood: -137589.104476 EM: Round [12] log likelihood: -137588.711475 EM: Round [13] log likelihood: -137588.386032 EM: Round [14] log likelihood: -137588.112251 EM: Round [15] log likelihood: -137587.878860 EM: Round [16] log likelihood: -137587.677679 EM: Round [17] log likelihood: -137587.502644 EM: Round [18] log likelihood: -137587.349169 EM: Round [19] log likelihood: -137587.213720 EM: Round [20] log likelihood: -137587.093525 EM: Round [21] log likelihood: -137586.986375 EM: Round [22] log likelihood: -137586.890483 EM: Round [23] log likelihood: -137586.804383 EM: Round [24] log likelihood: -137586.726858 EM: Round [25] log likelihood: -137586.656888 EM: Round [26] log likelihood: -137586.593606 EM: Round [27] log likelihood: -137586.536270 EM: Round [28] log likelihood: -137586.484242 EM: Round [29] log likelihood: -137586.436967 EM: Round [30] log likelihood: -137586.393959 EM: Round [31] log likelihood: -137586.354792 EM: Round [32] log likelihood: -137586.319090 EM: Round [33] log likelihood: -137586.286520 EM: Round [34] log likelihood: -137586.256784 EM: Round [35] log likelihood: -137586.229619 EM: Round [36] log likelihood: -137586.204785 EM: Round [37] log likelihood: -137586.182071 EM: Round [38] log likelihood: -137586.161286 EM: Round [39] log likelihood: -137586.142255 EM: Round [40] log likelihood: -137586.124825 EM: Round [41] log likelihood: -137586.108853 EM: Round [42] log likelihood: -137586.094211 EM: Round [43] log likelihood: -137586.080786 EM: Round [44] log likelihood: -137586.068470 EM: Round [45] log likelihood: -137586.057169 EM: Round [46] log likelihood: -137586.046796 EM: Round [47] log likelihood: -137586.037272 EM: Round [48] log likelihood: -137586.028525 EM: Round [49] log likelihood: -137586.020490 EM: Round [50] log likelihood: -137586.013106 EM: Round [51] log likelihood: -137586.006320 EM: Round [52] log likelihood: -137586.000081 EM: Round [53] log likelihood: -137585.994343 EM: Round [54] log likelihood: -137585.989066 EM: Round [55] log likelihood: -137585.984211 EM: Round [56] log likelihood: -137585.979743 EM: Round [57] log likelihood: -137585.975631 EM: Round [58] log likelihood: -137585.971845 EM: Round [59] log likelihood: -137585.968359 EM: Round [60] log likelihood: -137585.965149 EM: Round [61] log likelihood: -137585.962192 EM: Round [62] log likelihood: -137585.959467 EM: Round [63] log likelihood: -137585.956956 EM: Round [64] log likelihood: -137585.954641 EM: Round [65] log likelihood: -137585.952508 EM: Round [66] log likelihood: -137585.950540 EM: Round [67] log likelihood: -137585.948726 EM: Round [68] log likelihood: -137585.947052 EM: Round [69] log likelihood: -137585.945508 EM: Round [70] log likelihood: -137585.944082 EM: Round [71] log likelihood: -137585.942767 EM: Round [72] log likelihood: -137585.941553 EM: Round [73] log likelihood: -137585.940432 EM: Round [74] log likelihood: -137585.939397 EM: Round [75] log likelihood: -137585.938441 EM: Round [76] log likelihood: -137585.937558 EM: Round [77] log likelihood: -137585.936742 EM: Round [78] log likelihood: -137585.935988 EM: Round [79] log likelihood: -137585.935291 EM: Round [80] log likelihood: -137585.934646 EM: Round [81] log likelihood: -137585.934050 EM: Round [82] log likelihood: -137585.933500 EM: Round [83] log likelihood: -137585.932990 EM: Round [84] log likelihood: -137585.932519 EM: Round [85] log likelihood: -137585.932083 EM: Round [86] log likelihood: -137585.931679 EM: Round [87] log likelihood: -137585.931306 EM: Round [88] log likelihood: -137585.930960 EM: Round [89] log likelihood: -137585.930640 EM: Round [90] log likelihood: -137585.930343 EM: Round [91] log likelihood: -137585.930069 EM: Round [92] log likelihood: -137585.929815 EM: Round [93] log likelihood: -137585.929579 EM: Round [94] log likelihood: -137585.929361 EM: Round [95] log likelihood: -137585.929159 EM: Round [96] log likelihood: -137585.928971 EM: Round [97] log likelihood: -137585.928798 EM: Round [98] log likelihood: -137585.928636 EM: Round [99] log likelihood: -137585.928487 EM: Round [100] log likelihood: -137585.928348 EM: Round [101] log likelihood: -137585.928220 EM: Round [102] log likelihood: -137585.928101 EM: Round [103] log likelihood: -137585.927990 EM: Round [104] log likelihood: -137585.927887 EM: Round [105] log likelihood: -137585.927792 EM: Stopping iterations at round 105 due to insufficient improvement in likelihood. EM: Starting log likelihood: -137724.333486 EM: Round [1] log likelihood: -137632.596921 EM: Round [2] log likelihood: -137608.934558 EM: Round [3] log likelihood: -137599.689298 EM: Round [4] log likelihood: -137595.119238 EM: Round [5] log likelihood: -137592.523843 EM: Round [6] log likelihood: -137590.906781 EM: Round [7] log likelihood: -137589.828345 EM: Round [8] log likelihood: -137589.070141 EM: Round [9] log likelihood: -137588.514141 EM: Round [10] log likelihood: -137588.092298 EM: Round [11] log likelihood: -137587.763263 EM: Round [12] log likelihood: -137587.500763 EM: Round [13] log likelihood: -137587.287439 EM: Round [14] log likelihood: -137587.111414 EM: Round [15] log likelihood: -137586.964313 EM: Round [16] log likelihood: -137586.840067 EM: Round [17] log likelihood: -137586.734174 EM: Round [18] log likelihood: -137586.643225 EM: Round [19] log likelihood: -137586.564589 EM: Round [20] log likelihood: -137586.496206 EM: Round [21] log likelihood: -137586.436439 EM: Round [22] log likelihood: -137586.383971 EM: Round [23] log likelihood: -137586.337728 EM: Round [24] log likelihood: -137586.296832 EM: Round [25] log likelihood: -137586.260551 EM: Round [26] log likelihood: -137586.228275 EM: Round [27] log likelihood: -137586.199491 EM: Round [28] log likelihood: -137586.173763 EM: Round [29] log likelihood: -137586.150720 EM: Round [30] log likelihood: -137586.130044 EM: Round [31] log likelihood: -137586.111459 EM: Round [32] log likelihood: -137586.094730 EM: Round [33] log likelihood: -137586.079649 EM: Round [34] log likelihood: -137586.066036 EM: Round [35] log likelihood: -137586.053734 EM: Round [36] log likelihood: -137586.042603 EM: Round [37] log likelihood: -137586.032522 EM: Round [38] log likelihood: -137586.023383 EM: Round [39] log likelihood: -137586.015091 EM: Round [40] log likelihood: -137586.007559 EM: Round [41] log likelihood: -137586.000714 EM: Round [42] log likelihood: -137585.994487 EM: Round [43] log likelihood: -137585.988819 EM: Round [44] log likelihood: -137585.983655 EM: Round [45] log likelihood: -137585.978948 EM: Round [46] log likelihood: -137585.974654 EM: Round [47] log likelihood: -137585.970735 EM: Round [48] log likelihood: -137585.967156 EM: Round [49] log likelihood: -137585.963885 EM: Round [50] log likelihood: -137585.960895 EM: Round [51] log likelihood: -137585.958159 EM: Round [52] log likelihood: -137585.955654 EM: Round [53] log likelihood: -137585.953360 EM: Round [54] log likelihood: -137585.951258 EM: Round [55] log likelihood: -137585.949331 EM: Round [56] log likelihood: -137585.947564 EM: Round [57] log likelihood: -137585.945942 EM: Round [58] log likelihood: -137585.944452 EM: Round [59] log likelihood: -137585.943084 EM: Round [60] log likelihood: -137585.941827 EM: Round [61] log likelihood: -137585.940671 EM: Round [62] log likelihood: -137585.939607 EM: Round [63] log likelihood: -137585.938628 EM: Round [64] log likelihood: -137585.937727 EM: Round [65] log likelihood: -137585.936897 EM: Round [66] log likelihood: -137585.936132 EM: Round [67] log likelihood: -137585.935427 EM: Round [68] log likelihood: -137585.934777 EM: Round [69] log likelihood: -137585.934176 EM: Round [70] log likelihood: -137585.933622 EM: Round [71] log likelihood: -137585.933111 EM: Round [72] log likelihood: -137585.932638 EM: Round [73] log likelihood: -137585.932201 EM: Round [74] log likelihood: -137585.931798 EM: Round [75] log likelihood: -137585.931424 EM: Round [76] log likelihood: -137585.931078 EM: Round [77] log likelihood: -137585.930758 EM: Round [78] log likelihood: -137585.930462 EM: Round [79] log likelihood: -137585.930188 EM: Round [80] log likelihood: -137585.929934 EM: Round [81] log likelihood: -137585.929698 EM: Round [82] log likelihood: -137585.929479 EM: Round [83] log likelihood: -137585.929277 EM: Round [84] log likelihood: -137585.929088 EM: Round [85] log likelihood: -137585.928914 EM: Round [86] log likelihood: -137585.928752 EM: Round [87] log likelihood: -137585.928601 EM: Round [88] log likelihood: -137585.928461 EM: Round [89] log likelihood: -137585.928331 EM: Round [90] log likelihood: -137585.928210 EM: Round [91] log likelihood: -137585.928097 EM: Round [92] log likelihood: -137585.927993 EM: Round [93] log likelihood: -137585.927895 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.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20 CMD: cp /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.x9YT2HSNW6/./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.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged CMD: ln -sf /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.x9YT2HSNW6/./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.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 115055067 > /tmp/nxf.x9YT2HSNW6/./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.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir > /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo * Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir --annotate /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.x9YT2HSNW6/./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.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir -done, see /tmp/nxf.x9YT2HSNW6/./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.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.x9YT2HSNW6/ctat_genome_lib_build_dir -filter_likely_RT_artifacts: (pass: 278, filtered: 10827) * Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.x9YT2HSNW6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001 * Running CMD: cp /tmp/nxf.x9YT2HSNW6/./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.x9YT2HSNW6/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv WARNING, no entry stored in dbm for [IGH.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 [ENSG00000266904.6] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGL-.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000234405.2] WARNING, no entry stored in dbm for [ENSG00000213205.3] WARNING, no entry stored in dbm for [ENSG00000270788.1] WARNING, no entry stored in dbm for [ENSG00000249274.1] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000230023.2] WARNING, no entry stored in dbm for [ENSG00000250822.1] 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 [ENSG00000213280.2] WARNING, no entry stored in dbm for [ENSG00000267408.1] WARNING, no entry stored in dbm for [ENSG00000111788.10] WARNING, no entry stored in dbm for [ENSG00000257612.2] WARNING, no entry stored in dbm for [ENSG00000286271.2] WARNING, no entry stored in dbm for [ENSG00000260528.5] WARNING, no entry stored in dbm for [ENSG00000285803.1] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000215386.13] 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 [IGH.g@-ext] WARNING, no entry stored in dbm for [IGL.g@-ext] WARNING, no entry stored in dbm for [ENSG00000233747.1] WARNING, no entry stored in dbm for [ENSG00000231427.6] WARNING, no entry stored in dbm for [ENSG00000219665.8] WARNING, no entry stored in dbm for [ENSG00000280383.1] WARNING, no entry stored in dbm for [ENSG00000197558.13] WARNING, no entry stored in dbm for [ENSG00000249073.1] WARNING, no entry stored in dbm for [ENSG00000260776.6] WARNING, no entry stored in dbm for [ENSG00000257052.1] WARNING, no entry stored in dbm for [ENSG00000213411.2] WARNING, no entry stored in dbm for [ENSG00000242435.1] WARNING, no entry stored in dbm for [ENSG00000248671.8] WARNING, no entry stored in dbm for [ENSG00000200432.1] WARNING, no entry stored in dbm for [ENSG00000233017.3] WARNING, no entry stored in dbm for [ENSG00000285935.1] WARNING, no entry stored in dbm for [ENSG00000286147.1] WARNING, no entry stored in dbm for [ENSG00000234405.2] WARNING, no entry stored in dbm for [ENSG00000231527.7] WARNING, no entry stored in dbm for [ENSG00000240023.1] WARNING, no entry stored in dbm for [ENSG00000256686.1] WARNING, no entry stored in dbm for [ENSG00000225259.4] WARNING, no entry stored in dbm for [ENSG00000237689.1] WARNING, no entry stored in dbm for [ENSG00000222042.2] WARNING, no entry stored in dbm for [ENSG00000158482.10] WARNING, no entry stored in dbm for [ENSG00000279190.1] WARNING, no entry stored in dbm for [ENSG00000161103.11] WARNING, no entry stored in dbm for [ENSG00000235885.8] WARNING, no entry stored in dbm for [ENSG00000234981.1] WARNING, no entry stored in dbm for [ENSG00000280042.1] WARNING, no entry stored in dbm for [ENSG00000213655.4] WARNING, no entry stored in dbm for [ENSG00000267322.2] WARNING, no entry stored in dbm for [ENSG00000243323.7] WARNING, no entry stored in dbm for [ENSG00000215867.4] WARNING, no entry stored in dbm for [ENSG00000255440.2] WARNING, no entry stored in dbm for [ENSG00000234696.1] WARNING, no entry stored in dbm for [ENSG00000287289.1] WARNING, no entry stored in dbm for [ENSG00000203560.3] WARNING, no entry stored in dbm for [ENSG00000176748.6] WARNING, no entry stored in dbm for [ENSG00000232907.8] WARNING, no entry stored in dbm for [ENSG00000257137.7] WARNING, no entry stored in dbm for [ENSG00000212100.2] WARNING, no entry stored in dbm for [ENSG00000258128.2] WARNING, no entry stored in dbm for [ENSG00000249816.7] WARNING, no entry stored in dbm for [ENSG00000248281.1] WARNING, no entry stored in dbm for [ENSG00000228882.1] WARNING, no entry stored in dbm for [ENSG00000226450.2] WARNING, no entry stored in dbm for [ENSG00000229000.1] WARNING, no entry stored in dbm for [ENSG00000250508.1] WARNING, no entry stored in dbm for [ENSG00000233431.1] WARNING, no entry stored in dbm for [ENSG00000230866.2] WARNING, no entry stored in dbm for [ENSG00000228799.6] WARNING, no entry stored in dbm for [ENSG00000234551.2] WARNING, no entry stored in dbm for [ENSG00000258735.1] WARNING, no entry stored in dbm for [ENSG00000213500.3] WARNING, no entry stored in dbm for [ENSG00000248313.1] WARNING, no entry stored in dbm for [ENSG00000213212.3] WARNING, no entry stored in dbm for [ENSG00000255262.3] WARNING, no entry stored in dbm for [ENSG00000269821.1] WARNING, no entry stored in dbm for [ENSG00000158482.10] WARNING, no entry stored in dbm for [ENSG00000237978.6] WARNING, no entry stored in dbm for [ENSG00000279080.1] WARNING, no entry stored in dbm for [ENSG00000261523.1] WARNING, no entry stored in dbm for [ENSG00000261523.1] WARNING, no entry stored in dbm for [ENSG00000285758.2] WARNING, no entry stored in dbm for [ENSG00000274919.1] WARNING, no entry stored in dbm for [ENSG00000230368.2] WARNING, no entry stored in dbm for [ENSG00000236438.7] WARNING, no entry stored in dbm for [ENSG00000233581.1] WARNING, no entry stored in dbm for [ENSG00000234028.3] WARNING, no entry stored in dbm for [ENSG00000287171.1] WARNING, no entry stored in dbm for [ENSG00000231079.7] WARNING, no entry stored in dbm for [ENSG00000248724.6] WARNING, no entry stored in dbm for [ENSG00000233776.5] WARNING, no entry stored in dbm for [ENSG00000271162.1] WARNING, no entry stored in dbm for [ENSG00000258661.1] WARNING, no entry stored in dbm for [ENSG00000278931.1] WARNING, no entry stored in dbm for [ENSG00000233002.2] WARNING, no entry stored in dbm for [ENSG00000228409.6] WARNING, no entry stored in dbm for [ENSG00000248103.1] WARNING, no entry stored in dbm for [ENSG00000228294.6] WARNING, no entry stored in dbm for [ENSG00000249207.2] WARNING, no entry stored in dbm for [ENSG00000235062.4] WARNING, no entry stored in dbm for [ENSG00000204959.4] WARNING, no entry stored in dbm for [ENSG00000286512.1] WARNING, no entry stored in dbm for [ENSG00000251396.7] WARNING, no entry stored in dbm for [ENSG00000268635.2] WARNING, no entry stored in dbm for [ENSG00000229473.2] WARNING, no entry stored in dbm for [ENSG00000286735.1] WARNING, no entry stored in dbm for [ENSG00000237422.2] WARNING, no entry stored in dbm for [ENSG00000230927.3] WARNING, no entry stored in dbm for [ENSG00000283078.1] WARNING, no entry stored in dbm for [ENSG00000277304.1] WARNING, no entry stored in dbm for [ENSG00000270955.1] WARNING, no entry stored in dbm for [ENSG00000271155.1] WARNING, no entry stored in dbm for [ENSG00000282221.1] WARNING, no entry stored in dbm for [ENSG00000267098.2] WARNING, no entry stored in dbm for [ENSG00000253483.1] WARNING, no entry stored in dbm for [ENSG00000253483.1] WARNING, no entry stored in dbm for [ENSG00000253483.1] WARNING, no entry stored in dbm for [ENSG00000266283.1] WARNING, no entry stored in dbm for [ENSG00000263588.1] WARNING, no entry stored in dbm for [ENSG00000254398.1] WARNING, no entry stored in dbm for [ENSG00000254398.1] WARNING, no entry stored in dbm for [ENSG00000227574.2] WARNING, no entry stored in dbm for [ENSG00000254092.2] WARNING, no entry stored in dbm for [ENSG00000233109.4] WARNING, no entry stored in dbm for [ENSG00000268015.1] WARNING, no entry stored in dbm for [ENSG00000249042.6] WARNING, no entry stored in dbm for [ENSG00000287360.1] WARNING, no entry stored in dbm for [ENSG00000213798.3] WARNING, no entry stored in dbm for [ENSG00000237298.10] WARNING, no entry stored in dbm for [IGH.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 [IGH.g@-ext] WARNING, no entry stored in dbm for [ENSG00000261687.1] WARNING, no entry stored in dbm for [IGL-.g@-ext] * STAR-Fusion complete. See output: /tmp/nxf.x9YT2HSNW6/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)