-ctat genome lib [/tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.ELc5WhXX7r/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary
-sample contains 294508217 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir  -J /tmp/nxf.ELc5WhXX7r/659_cB6-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction  -O /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.ELc5WhXX7r/659_cB6-T1-TRNA-1_B23MHV2LT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

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[3090000], rate=71804.80/min -building interval tree based on /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[2440000], rate=43819.22/min 
[2450000], rate=43919.93/min 
[2460000], rate=44007.16/min 
[2470000], rate=44080.90/min 
[2480000], rate=44167.41/min 
[2490000], rate=44253.55/min 
[2500000], rate=44326.24/min 
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[2530000], rate=44347.06/min 
[2540000], rate=44366.81/min 
[2550000], rate=44386.42/min 
[2560000], rate=44405.90/min 
[2570000], rate=44438.04/min 
[2580000], rate=44482.76/min 
[2590000], rate=44527.22/min 
[2600000], rate=44571.43/min 
[2610000], rate=44628.10/min 
[2620000], rate=44671.78/min 
[2630000], rate=44740.57/min 
[2640000], rate=44796.38/min 
[2650000], rate=44864.56/min 
[2660000], rate=44932.43/min 
[2670000], rate=45000.00/min 
[2680000], rate=45067.26/min 
[2690000], rate=45134.23/min 
[2700000], rate=45213.51/min 
[2710000], rate=45292.48/min 
-building interval tree based on /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=50000.00/min 
[20000], rate=50000.00/min 
[30000], rate=51428.57/min 
[40000], rate=47058.82/min 
[50000], rate=44117.65/min 
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[70000], rate=46666.67/min 
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[1760000], rate=40882.69/min 
[1770000], rate=41003.86/min 
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[2810000], rate=46166.48/min 
[2820000], rate=46254.78/min 
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[2840000], rate=46455.83/min 
[2850000], rate=46492.66/min 
[2860000], rate=46516.67/min 
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[2880000], rate=46564.27/min 
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[2930000], rate=46792.65/min 
[2940000], rate=46852.59/min 
[2950000], rate=46912.27/min 
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[3030000], rate=47566.72/min 
[3040000], rate=47648.90/min 
[3050000], rate=47730.83/min 
[3060000], rate=47812.50/min -building interval tree based on /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=100000.00/min 
[30000], rate=105882.35/min 
[40000], rate=96000.00/min 
[50000], rate=93750.00/min 
[60000], rate=112500.00/min 
[70000], rate=123529.41/min 
[80000], rate=141176.47/min 
[90000], rate=158823.53/min 
[100000], rate=171428.57/min 
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[1460000], rate=34085.60/min 
[1470000], rate=33975.35/min 
[1480000], rate=33906.07/min 
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[1500000], rate=33745.78/min 
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[1650000], rate=33880.90/min 
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[1670000], rate=34012.22/min 
[1680000], rate=34031.06/min 
[1690000], rate=34061.14/min 
[1700000], rate=34068.14/min 
[1710000], rate=34086.38/min 
[1720000], rate=34070.65/min 
[1730000], rate=34043.95/min 
[1740000], rate=34073.11/min 
[1750000], rate=34135.24/min 
[1760000], rate=34207.97/min 
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[1830000], rate=34812.94/min 
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[1870000], rate=35216.57/min 
[1880000], rate=35327.28/min 
[1890000], rate=35437.50/min 
[1900000], rate=35547.24/min 
[1910000], rate=35645.41/min 
[1920000], rate=35754.19/min 
[1930000], rate=35862.50/min 
[1940000], rate=35992.58/min 
[1950000], rate=36066.58/min 
[1960000], rate=36095.76/min 
[1970000], rate=36124.69/min 
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[1990000], rate=36214.74/min 
[2000000], rate=36253.78/min 
[2010000], rate=36292.51/min 
[2020000], rate=36352.73/min 
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[2050000], rate=36541.89/min 
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[2080000], rate=36781.61/min 
[2090000], rate=36860.67/min 
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[2110000], rate=37006.72/min 
[2120000], rate=37095.36/min 
[2130000], rate=37194.41/min 
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[2150000], rate=37358.82/min 
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[2180000], rate=37629.46/min 
[2190000], rate=37726.10/min 
[2200000], rate=37833.19/min 
[2210000], rate=37939.91/min 
[2220000], rate=38035.41/min 
[2230000], rate=38152.27/min 
[2240000], rate=38247.01/min 
[2250000], rate=38189.53/min 
[2260000], rate=38143.46/min 
[2270000], rate=38119.23/min 
[2280000], rate=38074.03/min 
[2290000], rate=38018.82/min 
[2300000], rate=38006.06/min 
[2310000], rate=37993.42/min 
[2320000], rate=37929.16/min 
[2330000], rate=37845.15/min 
[2340000], rate=37782.56/min 
[2350000], rate=37801.61/min 
[2360000], rate=37830.62/min 
[2370000], rate=37869.51/min 
[2380000], rate=37908.15/min 
[2390000], rate=37946.55/min 
[2400000], rate=37984.70/min 
[2410000], rate=38022.61/min 
[2420000], rate=38030.38/min 
[2430000], rate=38028.17/min 
[2440000], rate=38045.74/min 
[2450000], rate=38082.90/min 
[2460000], rate=38129.68/min 
[2470000], rate=38156.54/min 
[2480000], rate=38193.02/min 
[2490000], rate=38239.06/min 
[2500000], rate=38275.07/min 
[2510000], rate=38320.61/min 
[2520000], rate=38346.44/min 
[2530000], rate=38372.09/min 
[2540000], rate=38407.26/min 
[2550000], rate=38442.21/min 
[2560000], rate=38486.59/min 
[2570000], rate=38530.73/min 
[2580000], rate=38574.63/min 
[2590000], rate=38618.29/min 
[2600000], rate=38652.13/min 
[2610000], rate=38676.22/min 
[2620000], rate=38719.21/min 
[2630000], rate=38761.97/min 
[2640000], rate=38804.51/min 
[2650000], rate=38846.81/min 
[2660000], rate=38888.89/min 
[2670000], rate=38930.74/min 
[2680000], ra[2720000], rate=42947.37/min 
[2730000], rate=42924.53/min 
[2740000], rate=42890.69/min 
[2750000], rate=42868.28/min 
[2760000], rate=42857.14/min 
[2770000], rate=42846.09/min 
[2780000], rate=42835.13/min 
[2790000], rate=42802.35/min 
[2800000], rate=42791.65/min 
[2810000], rate=42759.32/min 
[2820000], rate=42748.86/min 
[2830000], rate=42760.01/min 
[2840000], rate=42792.57/min 
[2850000], rate=42824.94/min 
[2860000], rate=42857.14/min 
[2870000], rate=42857.14/min 
[2880000], rate=42867.77/min 
[2890000], rate=42899.55/min 
[2900000], rate=42920.57/min 
[2910000], rate=42952.03/min 
[2920000], rate=42972.77/min 
[2930000], rate=42993.40/min 
[2940000], rate=43013.90/min 
[2950000], rate=43044.75/min 
[2960000], rate=43064.99/min 
[2970000], rate=43095.53/min 
[2980000], rate=43125.90/min 
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[3000000], rate=43206.91/min 
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[3020000], rate=43318.19/min 
[3030000], rate=43357.98/min 
[3040000], rate=43397.57/min 
[3050000], rate=43447.29/min te=38972.37/min 
[2690000], rate=39004.35/min 
[2700000], rate=39036.14/min 
[2710000], rate=39067.76/min 
[2720000], rate=39108.55/min 
[2730000], rate=39158.50/min 
[2740000], rate=39198.86/min 
[2750000], rate=39239.00/min 
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[2800000], rate=39243.17/min 
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[2900000], rate=39500.57/min 
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[2940000], rate=39640.45/min 
[2950000], rate=39686.10/min 
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[2970000], rate=39794.55/min 
[2980000], rate=39848.45/min 
[2990000], rate=39884.39/min 
[3000000], rate=39920.16/min 
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[3020000], rate=40000.00/min 
[3030000], rate=40035.23/min 
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[3050000], rate=40122.78/min 
[3060000], rate=40157.48/min 
[3070000], rate=40200.79/min 
[3080000], rate=40235.14/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 0.00 reads per min processed...  
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 6580645.16 reads per min processed...  
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 6333333.33 reads per min processed...  
 6329670.33 reads per min processed...  
 6326086.96 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.ELc5WhXX7r/659_cB6-T1-TRNA-1_B23MHV2LT4_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.ELc5WhXX7r/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -184591.238917
EM: Round [1] log likelihood: -184484.077635
EM: Round [2] log likelihood: -184444.274573
EM: Round [3] log likelihood: -184425.486470
EM: Round [4] log likelihood: -184415.584179
EM: Round [5] log likelihood: -184409.982730
EM: Round [6] log likelihood: -184406.619165
EM: Round [7] log likelihood: -184404.483143
EM: Round [8] log likelihood: -184403.054550
EM: Round [9] log likelihood: -184402.054249
EM: Round [10] log likelihood: -184401.326018
EM: Round [11] log likelihood: -184400.778541
EM: Round [12] log likelihood: -184400.356057
EM: Round [13] log likelihood: -184400.023044
EM: Round [14] log likelihood: -184399.755968
EM: Round [15] log likelihood: -184399.538671
EM: Round [16] log likelihood: -184399.359719
EM: Round [17] log likelihood: -184399.210802
EM: Round [18] log likelihood: -184399.085745
EM: Round [19] log likelihood: -184398.979873
EM: Round [20] log likelihood: -184398.889589
EM: Round [21] log likelihood: -184398.812090
EM: Round [22] log likelihood: -184398.745160
EM: Round [23] log likelihood: -184398.687036
EM: Round [24] log likelihood: -184398.636296
EM: Round [25] log likelihood: -184398.591786
EM: Round [26] log likelihood: -184398.552565
EM: Round [27] log likelihood: -184398.517855
EM: Round [28] log likelihood: -184398.487012
EM: Round [29] log likelihood: -184398.459500
EM: Round [30] log likelihood: -184398.434869
EM: Round [31] log likelihood: -184398.412740
EM: Round [32] log likelihood: -184398.392793
EM: Round [33] log likelihood: -184398.374755
EM: Round [34] log likelihood: -184398.358393
EM: Round [35] log likelihood: -184398.343509
EM: Round [36] log likelihood: -184398.329930
EM: Round [37] log likelihood: -184398.317508
EM: Round [38] log likelihood: -184398.306117
EM: Round [39] log likelihood: -184398.295644
EM: Round [40] log likelihood: -184398.285992
EM: Round [41] log likelihood: -184398.277078
EM: Round [42] log likelihood: -184398.268827
EM: Round [43] log likelihood: -184398.261173
EM: Round [44] log likelihood: -184398.254060
EM: Round [45] log likelihood: -184398.247437
EM: Round [46] log likelihood: -184398.241259
EM: Round [47] log likelihood: -184398.235487
EM: Round [48] log likelihood: -184398.230084
EM: Round [49] log likelihood: -184398.225020
EM: Round [50] log likelihood: -184398.220266
EM: Round [51] log likelihood: -184398.215797
EM: Round [52] log likelihood: -184398.211591
EM: Round [53] log likelihood: -184398.207627
EM: Round [54] log likelihood: -184398.203886
EM: Round [55] log likelihood: -184398.200353
EM: Round [56] log likelihood: -184398.197012
EM: Round [57] log likelihood: -184398.193850
EM: Round [58] log likelihood: -184398.190854
EM: Round [59] log likelihood: -184398.188012
EM: Round [60] log likelihood: -184398.185316
EM: Round [61] log likelihood: -184398.182755
EM: Round [62] log likelihood: -184398.180321
EM: Round [63] log likelihood: -184398.178005
EM: Round [64] log likelihood: -184398.175801
EM: Round [65] log likelihood: -184398.173702
EM: Round [66] log likelihood: -184398.171702
EM: Round [67] log likelihood: -184398.169795
EM: Round [68] log likelihood: -184398.167976
EM: Round [69] log likelihood: -184398.166239
EM: Round [70] log likelihood: -184398.164581
EM: Round [71] log likelihood: -184398.162997
EM: Round [72] log likelihood: -184398.161483
EM: Round [73] log likelihood: -184398.160036
EM: Round [74] log likelihood: -184398.158652
EM: Round [75] log likelihood: -184398.157328
EM: Round [76] log likelihood: -184398.156061
EM: Round [77] log likelihood: -184398.154847
EM: Round [78] log likelihood: -184398.153686
EM: Round [79] log likelihood: -184398.152573
EM: Round [80] log likelihood: -184398.151507
EM: Round [81] log likelihood: -184398.150485
EM: Round [82] log likelihood: -184398.149506
EM: Round [83] log likelihood: -184398.148567
EM: Round [84] log likelihood: -184398.147667
EM: Round [85] log likelihood: -184398.146803
EM: Round [86] log likelihood: -184398.145975
EM: Round [87] log likelihood: -184398.145180
EM: Round [88] log likelihood: -184398.144418
EM: Round [89] log likelihood: -184398.143686
EM: Round [90] log likelihood: -184398.142983
EM: Round [91] log likelihood: -184398.142309
EM: Round [92] log likelihood: -184398.141661
EM: Round [93] log likelihood: -184398.141040
EM: Round [94] log likelihood: -184398.140443
EM: Round [95] log likelihood: -184398.139869
EM: Round [96] log likelihood: -184398.139318
EM: Round [97] log likelihood: -184398.138789
EM: Round [98] log likelihood: -184398.138281
EM: Round [99] log likelihood: -184398.137793
EM: Round [100] log likelihood: -184398.137323
EM: Round [101] log likelihood: -184398.136873
EM: Round [102] log likelihood: -184398.136439
EM: Round [103] log likelihood: -184398.136023
EM: Round [104] log likelihood: -184398.135622
EM: Round [105] log likelihood: -184398.135238
EM: Round [106] log likelihood: -184398.134868
EM: Round [107] log likelihood: -184398.134512
EM: Round [108] log likelihood: -184398.134170
EM: Round [109] log likelihood: -184398.133842
EM: Round [110] log likelihood: -184398.133526
EM: Round [111] log likelihood: -184398.133222
EM: Round [112] log likelihood: -184398.132930
EM: Round [113] log likelihood: -184398.132649
EM: Round [114] log likelihood: -184398.132379
EM: Round [115] log likelihood: -184398.132119
EM: Round [116] log likelihood: -184398.131869
EM: Round [117] log likelihood: -184398.131629
EM: Round [118] log likelihood: -184398.131398
EM: Round [119] log likelihood: -184398.131176
EM: Round [120] log likelihood: -184398.130962
EM: Round [121] log likelihood: -184398.130757
EM: Round [122] log likelihood: -184398.130559
EM: Round [123] log likelihood: -184398.130369
EM: Round [124] log likelihood: -184398.130186
EM: Round [125] log likelihood: -184398.130010
EM: Round [126] log likelihood: -184398.129840
EM: Round [127] log likelihood: -184398.129678
EM: Round [128] log likelihood: -184398.129521
EM: Round [129] log likelihood: -184398.129370
EM: Round [130] log likelihood: -184398.129225
EM: Round [131] log likelihood: -184398.129086
EM: Round [132] log likelihood: -184398.128952
EM: Round [133] log likelihood: -184398.128822
EM: Round [134] log likelihood: -184398.128698
EM: Round [135] log likelihood: -184398.128579
EM: Round [136] log likelihood: -184398.128464
EM: Round [137] log likelihood: -184398.128353
EM: Round [138] log likelihood: -184398.128247
EM: Round [139] log likelihood: -184398.128144
EM: Round [140] log likelihood: -184398.128046
EM: Stopping iterations at round 140 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -184506.174273
EM: Round [1] log likelihood: -184409.012967
EM: Round [2] log likelihood: -184373.655373
EM: Round [3] log likelihood: -184357.306951
EM: Round [4] log likelihood: -184348.826148
EM: Round [5] log likelihood: -184344.072744
EM: Round [6] log likelihood: -184341.230104
EM: Round [7] log likelihood: -184339.427021
EM: Round [8] log likelihood: -184338.220826
EM: Round [9] log likelihood: -184337.375617
EM: Round [10] log likelihood: -184336.759844
EM: Round [11] log likelihood: -184336.296764
EM: Round [12] log likelihood: -184335.939557
EM: Round [13] log likelihood: -184335.658392
EM: Round [14] log likelihood: -184335.433480
EM: Round [15] log likelihood: -184335.251207
EM: Round [16] log likelihood: -184335.101902
EM: Round [17] log likelihood: -184334.978506
EM: Round [18] log likelihood: -184334.875749
EM: Round [19] log likelihood: -184334.789618
EM: Round [20] log likelihood: -184334.717010
EM: Round [21] log likelihood: -184334.655493
EM: Round [22] log likelihood: -184334.603136
EM: Round [23] log likelihood: -184334.558394
EM: Round [24] log likelihood: -184334.520017
EM: Round [25] log likelihood: -184334.486990
EM: Round [26] log likelihood: -184334.458477
EM: Round [27] log likelihood: -184334.433790
EM: Round [28] log likelihood: -184334.412360
EM: Round [29] log likelihood: -184334.393711
EM: Round [30] log likelihood: -184334.377443
EM: Round [31] log likelihood: -184334.363222
EM: Round [32] log likelihood: -184334.350763
EM: Round [33] log likelihood: -184334.339829
EM: Round [34] log likelihood: -184334.330213
EM: Round [35] log likelihood: -184334.321742
EM: Round [36] log likelihood: -184334.314267
EM: Round [37] log likelihood: -184334.307660
EM: Round [38] log likelihood: -184334.301811
EM: Round [39] log likelihood: -184334.296625
EM: Round [40] log likelihood: -184334.292020
EM: Round [41] log likelihood: -184334.287925
EM: Round [42] log likelihood: -184334.284279
EM: Round [43] log likelihood: -184334.281027
EM: Round [44] log likelihood: -184334.278124
EM: Round [45] log likelihood: -184334.275528
EM: Round [46] log likelihood: -184334.273204
EM: Round [47] log likelihood: -184334.271120
EM: Round [48] log likelihood: -184334.269250
EM: Round [49] log likelihood: -184334.267569
EM: Round [50] log likelihood: -184334.266057
EM: Round [51] log likelihood: -184334.264694
EM: Round [52] log likelihood: -184334.263464
EM: Round [53] log likelihood: -184334.262353
EM: Round [54] log likelihood: -184334.261348
EM: Round [55] log likelihood: -184334.260439
EM: Round [56] log likelihood: -184334.259614
EM: Round [57] log likelihood: -184334.258864
EM: Round [58] log likelihood: -184334.258183
EM: Round [59] log likelihood: -184334.257563
EM: Round [60] log likelihood: -184334.256998
EM: Round [61] log likelihood: -184334.256483
EM: Round [62] log likelihood: -184334.256011
EM: Round [63] log likelihood: -184334.255580
EM: Round [64] log likelihood: -184334.255185
EM: Round [65] log likelihood: -184334.254823
EM: Round [66] log likelihood: -184334.254490
EM: Round [67] log likelihood: -184334.254183
EM: Round [68] log likelihood: -184334.253901
EM: Round [69] log likelihood: -184334.253641
EM: Round [70] log likelihood: -184334.253400
EM: Round [71] log likelihood: -184334.253178
EM: Round [72] log likelihood: -184334.252972
EM: Round [73] log likelihood: -184334.252781
EM: Round [74] log likelihood: -184334.252604
EM: Round [75] log likelihood: -184334.252440
EM: Round [76] log likelihood: -184334.252286
EM: Round [77] log likelihood: -184334.252143
EM: Round [78] log likelihood: -184334.252010
EM: Round [79] log likelihood: -184334.251886
EM: Round [80] log likelihood: -184334.251769
EM: Round [81] log likelihood: -184334.251660
EM: Round [82] log likelihood: -184334.251558
EM: Round [83] log likelihood: -184334.251462
EM: Stopping iterations at round 83 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.ELc5WhXX7r/./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.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.ELc5WhXX7r/./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.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 294508217 > /tmp/nxf.ELc5WhXX7r/./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.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir > /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir --annotate /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.ELc5WhXX7r/./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.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir
-done, see /tmp/nxf.ELc5WhXX7r/./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.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.ELc5WhXX7r/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1937, filtered: 8931)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.ELc5WhXX7r/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.ELc5WhXX7r/./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.ELc5WhXX7r/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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WARNING, no entry stored in dbm for [ENSG00000276758.1]
WARNING, no entry stored in dbm for [ENSG00000241877.1]
WARNING, no entry stored in dbm for [ENSG00000200434.1]
WARNING, no entry stored in dbm for [ENSG00000248231.1]
WARNING, no entry stored in dbm for [ENSG00000217477.2]
WARNING, no entry stored in dbm for [ENSG00000214514.8]
WARNING, no entry stored in dbm for [ENSG00000235716.1]
WARNING, no entry stored in dbm for [ENSG00000260528.5]
WARNING, no entry stored in dbm for [ENSG00000253591.2]
WARNING, no entry stored in dbm for [ENSG00000197536.11]
WARNING, no entry stored in dbm for [ENSG00000254034.2]
WARNING, no entry stored in dbm for [ENSG00000236679.2]
WARNING, no entry stored in dbm for [ENSG00000188451.8]
WARNING, no entry stored in dbm for [ENSG00000244627.5]
WARNING, no entry stored in dbm for [ENSG00000165874.13]
WARNING, no entry stored in dbm for [ENSG00000257464.1]
WARNING, no entry stored in dbm for [ENSG00000258556.1]
WARNING, no entry stored in dbm for [ENSG00000280927.1]
WARNING, no entry stored in dbm for [ENSG00000276550.4]
WARNING, no entry stored in dbm for [ENSG00000281344.1]
WARNING, no entry stored in dbm for [ENSG00000214546.4]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000285280.2]
WARNING, no entry stored in dbm for [ENSG00000234945.8]
WARNING, no entry stored in dbm for [ENSG00000234945.8]
WARNING, no entry stored in dbm for [ENSG00000226002.1]
WARNING, no entry stored in dbm for [ENSG00000226400.2]
WARNING, no entry stored in dbm for [ENSG00000259683.1]
WARNING, no entry stored in dbm for [ENSG00000214433.4]
WARNING, no entry stored in dbm for [ENSG00000227893.1]
WARNING, no entry stored in dbm for [ENSG00000232520.2]
WARNING, no entry stored in dbm for [ENSG00000228376.3]
WARNING, no entry stored in dbm for [ENSG00000196295.12]
WARNING, no entry stored in dbm for [ENSG00000216360.1]
WARNING, no entry stored in dbm for [ENSG00000260377.1]
WARNING, no entry stored in dbm for [ENSG00000230590.11]
WARNING, no entry stored in dbm for [ENSG00000282826.2]
WARNING, no entry stored in dbm for [ENSG00000232160.7]
WARNING, no entry stored in dbm for [ENSG00000215483.11]
WARNING, no entry stored in dbm for [ENSG00000215483.11]
WARNING, no entry stored in dbm for [ENSG00000235665.6]
WARNING, no entry stored in dbm for [ENSG00000213211.2]
WARNING, no entry stored in dbm for [ENSG00000275620.1]
WARNING, no entry stored in dbm for [ENSG00000223652.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000255052.5]
WARNING, no entry stored in dbm for [ENSG00000254016.3]
WARNING, no entry stored in dbm for [ENSG00000249631.6]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000251595.7]
WARNING, no entry stored in dbm for [ENSG00000249859.12]
WARNING, no entry stored in dbm for [ENSG00000286863.1]
WARNING, no entry stored in dbm for [ENSG00000234690.7]
WARNING, no entry stored in dbm for [ENSG00000287219.1]
WARNING, no entry stored in dbm for [ENSG00000179523.5]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000251476.2]
WARNING, no entry stored in dbm for [ENSG00000231764.10]
WARNING, no entry stored in dbm for [ENSG00000257222.1]
WARNING, no entry stored in dbm for [ENSG00000227308.2]
WARNING, no entry stored in dbm for [ENSG00000224165.6]
WARNING, no entry stored in dbm for [ENSG00000254633.2]
WARNING, no entry stored in dbm for [ENSG00000261645.7]
WARNING, no entry stored in dbm for [ENSG00000226070.1]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000270533.2]
WARNING, no entry stored in dbm for [ENSG00000225077.3]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000283541.1]
WARNING, no entry stored in dbm for [ENSG00000229214.2]
WARNING, no entry stored in dbm for [ENSG00000278969.1]
WARNING, no entry stored in dbm for [ENSG00000206337.12]
WARNING, no entry stored in dbm for [ENSG00000273145.1]
WARNING, no entry stored in dbm for [ENSG00000255240.6]
WARNING, no entry stored in dbm for [ENSG00000286572.1]
WARNING, no entry stored in dbm for [ENSG00000273599.1]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000256007.1]
WARNING, no entry stored in dbm for [ENSG00000260495.1]
WARNING, no entry stored in dbm for [ENSG00000178722.13]
WARNING, no entry stored in dbm for [ENSG00000197171.6]
WARNING, no entry stored in dbm for [ENSG00000227252.2]
WARNING, no entry stored in dbm for [ENSG00000215146.5]
WARNING, no entry stored in dbm for [ENSG00000231422.2]
WARNING, no entry stored in dbm for [ENSG00000259001.3]
WARNING, no entry stored in dbm for [ENSG00000225206.10]
WARNING, no entry stored in dbm for [ENSG00000257038.1]
WARNING, no entry stored in dbm for [ENSG00000258397.1]
WARNING, no entry stored in dbm for [ENSG00000261618.2]
WARNING, no entry stored in dbm for [ENSG00000283445.1]
WARNING, no entry stored in dbm for [ENSG00000180747.15]
WARNING, no entry stored in dbm for [ENSG00000183199.6]
WARNING, no entry stored in dbm for [ENSG00000256720.1]
WARNING, no entry stored in dbm for [ENSG00000271614.1]
WARNING, no entry stored in dbm for [ENSG00000176124.15]
WARNING, no entry stored in dbm for [ENSG00000235849.1]
WARNING, no entry stored in dbm for [ENSG00000215409.4]
WARNING, no entry stored in dbm for [ENSG00000243069.8]
WARNING, no entry stored in dbm for [ENSG00000265688.2]
WARNING, no entry stored in dbm for [ENSG00000250062.5]
WARNING, no entry stored in dbm for [ENSG00000225264.3]
WARNING, no entry stored in dbm for [ENSG00000250397.2]
WARNING, no entry stored in dbm for [ENSG00000228463.10]
WARNING, no entry stored in dbm for [ENSG00000256591.5]
WARNING, no entry stored in dbm for [ENSG00000279771.1]
WARNING, no entry stored in dbm for [ENSG00000248409.2]
WARNING, no entry stored in dbm for [ENSG00000286643.1]
WARNING, no entry stored in dbm for [ENSG00000287593.1]
WARNING, no entry stored in dbm for [ENSG00000266931.2]
WARNING, no entry stored in dbm for [ENSG00000204455.7]
WARNING, no entry stored in dbm for [ENSG00000255910.2]
WARNING, no entry stored in dbm for [ENSG00000273443.1]
WARNING, no entry stored in dbm for [ENSG00000235121.1]
WARNING, no entry stored in dbm for [ENSG00000238009.6]
WARNING, no entry stored in dbm for [ENSG00000215840.3]
WARNING, no entry stored in dbm for [ENSG00000287356.1]
WARNING, no entry stored in dbm for [ENSG00000285961.1]
WARNING, no entry stored in dbm for [ENSG00000238260.1]
WARNING, no entry stored in dbm for [ENSG00000230638.4]
WARNING, no entry stored in dbm for [ENSG00000225096.3]
WARNING, no entry stored in dbm for [ENSG00000225096.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000275285.1]
WARNING, no entry stored in dbm for [ENSG00000229407.5]
WARNING, no entry stored in dbm for [ENSG00000229407.5]
WARNING, no entry stored in dbm for [ENSG00000233817.1]
WARNING, no entry stored in dbm for [ENSG00000288537.1]
WARNING, no entry stored in dbm for [ENSG00000230537.2]
WARNING, no entry stored in dbm for [ENSG00000276375.1]
WARNING, no entry stored in dbm for [ENSG00000267309.1]
WARNING, no entry stored in dbm for [ENSG00000228436.3]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000288543.1]
WARNING, no entry stored in dbm for [ENSG00000226310.1]
WARNING, no entry stored in dbm for [ENSG00000230912.1]
WARNING, no entry stored in dbm for [ENSG00000234146.1]
WARNING, no entry stored in dbm for [ENSG00000277449.1]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000284620.2]
WARNING, no entry stored in dbm for [ENSG00000258730.1]
WARNING, no entry stored in dbm for [ENSG00000268635.2]
WARNING, no entry stored in dbm for [ENSG00000225879.2]
WARNING, no entry stored in dbm for [ENSG00000236938.1]
WARNING, no entry stored in dbm for [ENSG00000268869.6]
WARNING, no entry stored in dbm for [ENSG00000204745.4]
WARNING, no entry stored in dbm for [ENSG00000212743.2]
WARNING, no entry stored in dbm for [ENSG00000285062.1]
WARNING, no entry stored in dbm for [ENSG00000285062.1]
WARNING, no entry stored in dbm for [ENSG00000276850.5]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000277702.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000261273.1]
WARNING, no entry stored in dbm for [ENSG00000261273.1]
WARNING, no entry stored in dbm for [ENSG00000260413.1]
WARNING, no entry stored in dbm for [ENSG00000287522.1]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000223509.8]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
WARNING, no entry stored in dbm for [ENSG00000262151.1]
WARNING, no entry stored in dbm for [ENSG00000285668.1]
WARNING, no entry stored in dbm for [ENSG00000227479.1]
WARNING, no entry stored in dbm for [ENSG00000229782.1]
WARNING, no entry stored in dbm for [ENSG00000235421.1]
WARNING, no entry stored in dbm for [ENSG00000256612.7]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000282572.2]
WARNING, no entry stored in dbm for [ENSG00000250195.1]
WARNING, no entry stored in dbm for [ENSG00000259867.6]
WARNING, no entry stored in dbm for [ENSG00000254548.1]
WARNING, no entry stored in dbm for [ENSG00000287780.1]
WARNING, no entry stored in dbm for [ENSG00000261710.1]
WARNING, no entry stored in dbm for [ENSG00000254158.1]
WARNING, no entry stored in dbm for [ENSG00000273230.1]
WARNING, no entry stored in dbm for [ENSG00000249001.5]
WARNING, no entry stored in dbm for [ENSG00000273118.1]
WARNING, no entry stored in dbm for [ENSG00000231304.2]
WARNING, no entry stored in dbm for [ENSG00000248787.2]
WARNING, no entry stored in dbm for [ENSG00000236391.3]
WARNING, no entry stored in dbm for [ENSG00000259655.1]
WARNING, no entry stored in dbm for [ENSG00000253888.2]
WARNING, no entry stored in dbm for [ENSG00000254102.2]
WARNING, no entry stored in dbm for [ENSG00000257308.1]
WARNING, no entry stored in dbm for [ENSG00000263164.1]
WARNING, no entry stored in dbm for [ENSG00000249685.1]
WARNING, no entry stored in dbm for [ENSG00000234072.1]
WARNING, no entry stored in dbm for [ENSG00000228010.6]
WARNING, no entry stored in dbm for [ENSG00000239985.2]
WARNING, no entry stored in dbm for [ENSG00000239985.2]
WARNING, no entry stored in dbm for [ENSG00000239985.2]
WARNING, no entry stored in dbm for [ENSG00000232611.1]
WARNING, no entry stored in dbm for [ENSG00000227902.2]
WARNING, no entry stored in dbm for [ENSG00000259433.2]
WARNING, no entry stored in dbm for [ENSG00000229212.8]
WARNING, no entry stored in dbm for [ENSG00000261502.4]
WARNING, no entry stored in dbm for [ENSG00000258345.1]
WARNING, no entry stored in dbm for [ENSG00000235140.2]
WARNING, no entry stored in dbm for [ENSG00000287677.2]
WARNING, no entry stored in dbm for [ENSG00000257454.1]
WARNING, no entry stored in dbm for [ENSG00000259702.3]
WARNING, no entry stored in dbm for [ENSG00000247877.7]
WARNING, no entry stored in dbm for [ENSG00000250636.1]
WARNING, no entry stored in dbm for [ENSG00000213963.6]
WARNING, no entry stored in dbm for [ENSG00000278330.1]
WARNING, no entry stored in dbm for [ENSG00000267605.7]
WARNING, no entry stored in dbm for [ENSG00000267605.7]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000274499.1]
WARNING, no entry stored in dbm for [ENSG00000254254.6]
WARNING, no entry stored in dbm for [ENSG00000197813.6]
WARNING, no entry stored in dbm for [ENSG00000267383.7]
WARNING, no entry stored in dbm for [ENSG00000244151.1]
WARNING, no entry stored in dbm for [ENSG00000259663.2]
WARNING, no entry stored in dbm for [ENSG00000259663.2]
WARNING, no entry stored in dbm for [ENSG00000248664.1]
WARNING, no entry stored in dbm for [ENSG00000267327.2]
WARNING, no entry stored in dbm for [ENSG00000259972.3]
WARNING, no entry stored in dbm for [ENSG00000280334.1]
WARNING, no entry stored in dbm for [ENSG00000257403.2]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000269706.1]
WARNING, no entry stored in dbm for [ENSG00000250258.1]
WARNING, no entry stored in dbm for [ENSG00000250258.1]
WARNING, no entry stored in dbm for [ENSG00000226472.8]
WARNING, no entry stored in dbm for [ENSG00000161132.6]
WARNING, no entry stored in dbm for [ENSG00000236886.2]
WARNING, no entry stored in dbm for [ENSG00000235583.2]
WARNING, no entry stored in dbm for [ENSG00000277458.1]
WARNING, no entry stored in dbm for [ENSG00000263345.1]
WARNING, no entry stored in dbm for [ENSG00000242593.7]
WARNING, no entry stored in dbm for [ENSG00000261786.1]
WARNING, no entry stored in dbm for [ENSG00000262879.6]
WARNING, no entry stored in dbm for [ENSG00000185710.9]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000214243.3]
WARNING, no entry stored in dbm for [ENSG00000214243.3]
WARNING, no entry stored in dbm for [ENSG00000243554.1]
WARNING, no entry stored in dbm for [ENSG00000258423.1]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000261578.1]
WARNING, no entry stored in dbm for [ENSG00000255769.7]
WARNING, no entry stored in dbm for [ENSG00000205754.12]
WARNING, no entry stored in dbm for [ENSG00000251595.7]
WARNING, no entry stored in dbm for [ENSG00000283544.1]
WARNING, no entry stored in dbm for [ENSG00000229153.5]
WARNING, no entry stored in dbm for [ENSG00000229153.5]
WARNING, no entry stored in dbm for [ENSG00000254349.6]
WARNING, no entry stored in dbm for [ENSG00000286797.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.ELc5WhXX7r/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)