-ctat genome lib [/tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.m5bFFMSaGF/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary
-sample contains 246686357 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir  -J /tmp/nxf.m5bFFMSaGF/BVT_FFPE_TRNA_stm_06_A23WKFTLT4_2.Chimeric.out.junction  -O /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.m5bFFMSaGF/BVT_FFPE_TRNA_stm_06_A23WKFTLT4_2.Chimeric.out.junction
-building interval tree based on /tmp/nxf.m5bFFMSaGF/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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-building interval tree based on /tmp/nxf.m5bFFMSaGF/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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[2770000], rate=42495.53/min -building interval tree based on /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=21428.57/min 
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[2730000], rate=39233.53/min 
[2740000], rate=39236.28/min 
[2750000], rate=39267.02/min -building interval tree based on /tmp/nxf.m5bFFMSaGF/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 
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[2760000], rate=34673.37/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 6000000.00 reads per min processed...  
 12000000.00 reads per min processed...  
 18000000.00 reads per min processed...  
 12000000.00 reads per min processed...  
 7500000.00 reads per min processed...  
 7200000.00 reads per min processed...  
 7000000.00 reads per min processed...  
 6857142.86 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 5571428.57 reads per min processed...  
 5600000.00 reads per min processed...  
 5625000.00 reads per min processed...  
 5333333.33 reads per min processed...  
 5368421.05 reads per min processed...  
 5400000.00 reads per min processed...  
 5428571.43 reads per min processed...  
 5217391.30 reads per min processed...  
 5250000.00 reads per min processed...  
 5280000.00 reads per min processed...  
 5307692.31 reads per min processed...  
 5333333.33 reads per min processed...  
 5172413.79 reads per min processed...  
 5200000.00 reads per min processed...  
 5062500.00 reads per min processed...  
 4941176.47 reads per min processed...  
 4971428.57 reads per min processed...  
 4864864.86 reads per min processed...  
 4894736.84 reads per min processed...  
 4923076.92 reads per min processed...  
 4829268.29 reads per min processed...  
 4857142.86 reads per min processed...  
 4772727.27 reads per min processed...  
 4800000.00 reads per min processed...  
 4826086.96 reads per min processed...  
 4750000.00 reads per min processed...  
 4775510.20 reads per min processed...  
 4800000.00 reads per min processed...  
 4823529.41 reads per min processed...  
 4846153.85 reads per min processed...  
 4867924.53 reads per min processed...  
 4800000.00 reads per min processed...  
 4821428.57 reads per min processed...  
 4842105.26 reads per min processed...  
 4862068.97 reads per min processed...  
 4881355.93 reads per min processed...  
 4900000.00 reads per min processed...  
 4838709.68 reads per min processed...  
 4857142.86 reads per min processed...  
 4875000.00 reads per min processed...  
 4892307.69 reads per min processed...  
 4909090.91 reads per min processed...  
 4925373.13 reads per min processed...  
 5014925.37 reads per min processed...  
 5029411.76 reads per min processed...  
 5043478.26 reads per min processed...  
 5057142.86 reads per min processed...  
 5070422.54 reads per min processed...  
 5083333.33 reads per min processed...  
 5095890.41 reads per min processed...  
 5040000.00 reads per min processed...  
 5052631.58 reads per min processed...  
 5064935.06 reads per min processed...  
 5076923.08 reads per min processed...  
 5088607.59 reads per min processed...  
 5100000.00 reads per min processed...  
 5048780.49 reads per min processed...  
 5060240.96 reads per min processed...  
 5071428.57 reads per min processed...  
 5082352.94 reads per min processed...  
 5093023.26 reads per min processed...  
 5045454.55 reads per min processed...  
 5056179.78 reads per min processed...  
 5066666.67 reads per min processed...  
 5076923.08 reads per min processed...  
 5032258.06 reads per min processed...  
 5042553.19 reads per min processed...  
 5052631.58 reads per min processed...  
 5062500.00 reads per min processed...  
 5072164.95 reads per min processed...  
 5030303.03 reads per min processed...  
 5040000.00 reads per min processed...  
 5049504.95 reads per min processed...  
 5058823.53 reads per min processed...  
 5067961.17 reads per min processed...  
 5076923.08 reads per min processed...  
 5037735.85 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.m5bFFMSaGF/BVT_FFPE_TRNA_stm_06_A23WKFTLT4_2.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.m5bFFMSaGF/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -311573.343292
EM: Round [1] log likelihood: -311381.400772
EM: Round [2] log likelihood: -311308.816301
EM: Round [3] log likelihood: -311273.157113
EM: Round [4] log likelihood: -311253.788447
EM: Round [5] log likelihood: -311242.697614
EM: Round [6] log likelihood: -311236.103141
EM: Round [7] log likelihood: -311232.038444
EM: Round [8] log likelihood: -311229.436703
EM: Round [9] log likelihood: -311227.706190
EM: Round [10] log likelihood: -311226.511837
EM: Round [11] log likelihood: -311225.659131
EM: Round [12] log likelihood: -311225.031824
EM: Round [13] log likelihood: -311224.558213
EM: Round [14] log likelihood: -311224.192617
EM: Round [15] log likelihood: -311223.904990
EM: Round [16] log likelihood: -311223.674976
EM: Round [17] log likelihood: -311223.488392
EM: Round [18] log likelihood: -311223.335120
EM: Round [19] log likelihood: -311223.207778
EM: Round [20] log likelihood: -311223.100888
EM: Round [21] log likelihood: -311223.010310
EM: Round [22] log likelihood: -311222.932882
EM: Round [23] log likelihood: -311222.866151
EM: Round [24] log likelihood: -311222.808199
EM: Round [25] log likelihood: -311222.757512
EM: Round [26] log likelihood: -311222.712882
EM: Round [27] log likelihood: -311222.673339
EM: Round [28] log likelihood: -311222.638100
EM: Round [29] log likelihood: -311222.606526
EM: Round [30] log likelihood: -311222.578095
EM: Round [31] log likelihood: -311222.552374
EM: Round [32] log likelihood: -311222.529006
EM: Round [33] log likelihood: -311222.507691
EM: Round [34] log likelihood: -311222.488179
EM: Round [35] log likelihood: -311222.470258
EM: Round [36] log likelihood: -311222.453748
EM: Round [37] log likelihood: -311222.438495
EM: Round [38] log likelihood: -311222.424369
EM: Round [39] log likelihood: -311222.411254
EM: Round [40] log likelihood: -311222.399054
EM: Round [41] log likelihood: -311222.387682
EM: Round [42] log likelihood: -311222.377062
EM: Round [43] log likelihood: -311222.367129
EM: Round [44] log likelihood: -311222.357825
EM: Round [45] log likelihood: -311222.349097
EM: Round [46] log likelihood: -311222.340899
EM: Round [47] log likelihood: -311222.333191
EM: Round [48] log likelihood: -311222.325934
EM: Round [49] log likelihood: -311222.319096
EM: Round [50] log likelihood: -311222.312647
EM: Round [51] log likelihood: -311222.306559
EM: Round [52] log likelihood: -311222.300808
EM: Round [53] log likelihood: -311222.295369
EM: Round [54] log likelihood: -311222.290224
EM: Round [55] log likelihood: -311222.285353
EM: Round [56] log likelihood: -311222.280738
EM: Round [57] log likelihood: -311222.276364
EM: Round [58] log likelihood: -311222.272215
EM: Round [59] log likelihood: -311222.268278
EM: Round [60] log likelihood: -311222.264541
EM: Round [61] log likelihood: -311222.260991
EM: Round [62] log likelihood: -311222.257618
EM: Round [63] log likelihood: -311222.254411
EM: Round [64] log likelihood: -311222.251362
EM: Round [65] log likelihood: -311222.248461
EM: Round [66] log likelihood: -311222.245700
EM: Round [67] log likelihood: -311222.243071
EM: Round [68] log likelihood: -311222.240567
EM: Round [69] log likelihood: -311222.238183
EM: Round [70] log likelihood: -311222.235910
EM: Round [71] log likelihood: -311222.233744
EM: Round [72] log likelihood: -311222.231678
EM: Round [73] log likelihood: -311222.229708
EM: Round [74] log likelihood: -311222.227828
EM: Round [75] log likelihood: -311222.226035
EM: Round [76] log likelihood: -311222.224323
EM: Round [77] log likelihood: -311222.222689
EM: Round [78] log likelihood: -311222.221129
EM: Round [79] log likelihood: -311222.219638
EM: Round [80] log likelihood: -311222.218214
EM: Round [81] log likelihood: -311222.216854
EM: Round [82] log likelihood: -311222.215554
EM: Round [83] log likelihood: -311222.214311
EM: Round [84] log likelihood: -311222.213123
EM: Round [85] log likelihood: -311222.211986
EM: Round [86] log likelihood: -311222.210900
EM: Round [87] log likelihood: -311222.209860
EM: Round [88] log likelihood: -311222.208865
EM: Round [89] log likelihood: -311222.207914
EM: Round [90] log likelihood: -311222.207003
EM: Round [91] log likelihood: -311222.206131
EM: Round [92] log likelihood: -311222.205296
EM: Round [93] log likelihood: -311222.204497
EM: Round [94] log likelihood: -311222.203732
EM: Round [95] log likelihood: -311222.202999
EM: Round [96] log likelihood: -311222.202296
EM: Round [97] log likelihood: -311222.201624
EM: Round [98] log likelihood: -311222.200979
EM: Round [99] log likelihood: -311222.200361
EM: Round [100] log likelihood: -311222.199769
EM: Round [101] log likelihood: -311222.199201
EM: Round [102] log likelihood: -311222.198657
EM: Round [103] log likelihood: -311222.198136
EM: Round [104] log likelihood: -311222.197635
EM: Round [105] log likelihood: -311222.197155
EM: Round [106] log likelihood: -311222.196695
EM: Round [107] log likelihood: -311222.196254
EM: Round [108] log likelihood: -311222.195830
EM: Round [109] log likelihood: -311222.195424
EM: Round [110] log likelihood: -311222.195034
EM: Round [111] log likelihood: -311222.194660
EM: Round [112] log likelihood: -311222.194300
EM: Round [113] log likelihood: -311222.193955
EM: Round [114] log likelihood: -311222.193624
EM: Round [115] log likelihood: -311222.193307
EM: Round [116] log likelihood: -311222.193001
EM: Round [117] log likelihood: -311222.192708
EM: Round [118] log likelihood: -311222.192427
EM: Round [119] log likelihood: -311222.192156
EM: Round [120] log likelihood: -311222.191897
EM: Round [121] log likelihood: -311222.191647
EM: Round [122] log likelihood: -311222.191407
EM: Round [123] log likelihood: -311222.191177
EM: Round [124] log likelihood: -311222.190955
EM: Round [125] log likelihood: -311222.190742
EM: Round [126] log likelihood: -311222.190538
EM: Round [127] log likelihood: -311222.190341
EM: Round [128] log likelihood: -311222.190152
EM: Round [129] log likelihood: -311222.189970
EM: Round [130] log likelihood: -311222.189795
EM: Round [131] log likelihood: -311222.189627
EM: Round [132] log likelihood: -311222.189466
EM: Round [133] log likelihood: -311222.189310
EM: Round [134] log likelihood: -311222.189160
EM: Round [135] log likelihood: -311222.189016
EM: Round [136] log likelihood: -311222.188878
EM: Round [137] log likelihood: -311222.188745
EM: Round [138] log likelihood: -311222.188616
EM: Round [139] log likelihood: -311222.188493
EM: Round [140] log likelihood: -311222.188374
EM: Round [141] log likelihood: -311222.188260
EM: Round [142] log likelihood: -311222.188150
EM: Round [143] log likelihood: -311222.188044
EM: Round [144] log likelihood: -311222.187942
EM: Round [145] log likelihood: -311222.187843
EM: Stopping iterations at round 145 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -311006.533096
EM: Round [1] log likelihood: -310853.524531
EM: Round [2] log likelihood: -310797.606622
EM: Round [3] log likelihood: -310770.872910
EM: Round [4] log likelihood: -310756.679246
EM: Round [5] log likelihood: -310748.709356
EM: Round [6] log likelihood: -310744.049958
EM: Round [7] log likelihood: -310741.219754
EM: Round [8] log likelihood: -310739.430471
EM: Round [9] log likelihood: -310738.251966
EM: Round [10] log likelihood: -310737.444243
EM: Round [11] log likelihood: -310736.869907
EM: Round [12] log likelihood: -310736.447939
EM: Round [13] log likelihood: -310736.128996
EM: Round [14] log likelihood: -310735.882010
EM: Round [15] log likelihood: -310735.686756
EM: Round [16] log likelihood: -310735.529647
EM: Round [17] log likelihood: -310735.401280
EM: Round [18] log likelihood: -310735.294976
EM: Round [19] log likelihood: -310735.205879
EM: Round [20] log likelihood: -310735.130389
EM: Round [21] log likelihood: -310735.065788
EM: Round [22] log likelihood: -310735.009997
EM: Round [23] log likelihood: -310734.961404
EM: Round [24] log likelihood: -310734.918744
EM: Round [25] log likelihood: -310734.881019
EM: Round [26] log likelihood: -310734.847429
EM: Round [27] log likelihood: -310734.817334
EM: Round [28] log likelihood: -310734.790212
EM: Round [29] log likelihood: -310734.765639
EM: Round [30] log likelihood: -310734.743266
EM: Round [31] log likelihood: -310734.722805
EM: Round [32] log likelihood: -310734.704018
EM: Round [33] log likelihood: -310734.686702
EM: Round [34] log likelihood: -310734.670691
EM: Round [35] log likelihood: -310734.655840
EM: Round [36] log likelihood: -310734.642029
EM: Round [37] log likelihood: -310734.629154
EM: Round [38] log likelihood: -310734.617124
EM: Round [39] log likelihood: -310734.605862
EM: Round [40] log likelihood: -310734.595301
EM: Round [41] log likelihood: -310734.585382
EM: Round [42] log likelihood: -310734.576051
EM: Round [43] log likelihood: -310734.567264
EM: Round [44] log likelihood: -310734.558978
EM: Round [45] log likelihood: -310734.551158
EM: Round [46] log likelihood: -310734.543769
EM: Round [47] log likelihood: -310734.536783
EM: Round [48] log likelihood: -310734.530172
EM: Round [49] log likelihood: -310734.523911
EM: Round [50] log likelihood: -310734.517979
EM: Round [51] log likelihood: -310734.512355
EM: Round [52] log likelihood: -310734.507020
EM: Round [53] log likelihood: -310734.501956
EM: Round [54] log likelihood: -310734.497147
EM: Round [55] log likelihood: -310734.492580
EM: Round [56] log likelihood: -310734.488239
EM: Round [57] log likelihood: -310734.484112
EM: Round [58] log likelihood: -310734.480187
EM: Round [59] log likelihood: -310734.476453
EM: Round [60] log likelihood: -310734.472900
EM: Round [61] log likelihood: -310734.469517
EM: Round [62] log likelihood: -310734.466296
EM: Round [63] log likelihood: -310734.463228
EM: Round [64] log likelihood: -310734.460305
EM: Round [65] log likelihood: -310734.457519
EM: Round [66] log likelihood: -310734.454864
EM: Round [67] log likelihood: -310734.452332
EM: Round [68] log likelihood: -310734.449918
EM: Round [69] log likelihood: -310734.447615
EM: Round [70] log likelihood: -310734.445418
EM: Round [71] log likelihood: -310734.443321
EM: Round [72] log likelihood: -310734.441320
EM: Round [73] log likelihood: -310734.439410
EM: Round [74] log likelihood: -310734.437586
EM: Round [75] log likelihood: -310734.435844
EM: Round [76] log likelihood: -310734.434180
EM: Round [77] log likelihood: -310734.432590
EM: Round [78] log likelihood: -310734.431071
EM: Round [79] log likelihood: -310734.429619
EM: Round [80] log likelihood: -310734.428232
EM: Round [81] log likelihood: -310734.426905
EM: Round [82] log likelihood: -310734.425637
EM: Round [83] log likelihood: -310734.424424
EM: Round [84] log likelihood: -310734.423264
EM: Round [85] log likelihood: -310734.422154
EM: Round [86] log likelihood: -310734.421092
EM: Round [87] log likelihood: -310734.420076
EM: Round [88] log likelihood: -310734.419104
EM: Round [89] log likelihood: -310734.418173
EM: Round [90] log likelihood: -310734.417282
EM: Round [91] log likelihood: -310734.416429
EM: Round [92] log likelihood: -310734.415612
EM: Round [93] log likelihood: -310734.414829
EM: Round [94] log likelihood: -310734.414080
EM: Round [95] log likelihood: -310734.413362
EM: Round [96] log likelihood: -310734.412674
EM: Round [97] log likelihood: -310734.412015
EM: Round [98] log likelihood: -310734.411383
EM: Round [99] log likelihood: -310734.410778
EM: Round [100] log likelihood: -310734.410198
EM: Round [101] log likelihood: -310734.409641
EM: Round [102] log likelihood: -310734.409108
EM: Round [103] log likelihood: -310734.408596
EM: Round [104] log likelihood: -310734.408106
EM: Round [105] log likelihood: -310734.407635
EM: Round [106] log likelihood: -310734.407184
EM: Round [107] log likelihood: -310734.406751
EM: Round [108] log likelihood: -310734.406335
EM: Round [109] log likelihood: -310734.405937
EM: Round [110] log likelihood: -310734.405554
EM: Round [111] log likelihood: -310734.405187
EM: Round [112] log likelihood: -310734.404834
EM: Round [113] log likelihood: -310734.404496
EM: Round [114] log likelihood: -310734.404171
EM: Round [115] log likelihood: -310734.403859
EM: Round [116] log likelihood: -310734.403559
EM: Round [117] log likelihood: -310734.403272
EM: Round [118] log likelihood: -310734.402995
EM: Round [119] log likelihood: -310734.402730
EM: Round [120] log likelihood: -310734.402475
EM: Round [121] log likelihood: -310734.402230
EM: Round [122] log likelihood: -310734.401994
EM: Round [123] log likelihood: -310734.401768
EM: Round [124] log likelihood: -310734.401550
EM: Round [125] log likelihood: -310734.401341
EM: Round [126] log likelihood: -310734.401140
EM: Round [127] log likelihood: -310734.400947
EM: Round [128] log likelihood: -310734.400761
EM: Round [129] log likelihood: -310734.400583
EM: Round [130] log likelihood: -310734.400411
EM: Round [131] log likelihood: -310734.400246
EM: Round [132] log likelihood: -310734.400087
EM: Round [133] log likelihood: -310734.399934
EM: Round [134] log likelihood: -310734.399787
EM: Round [135] log likelihood: -310734.399646
EM: Round [136] log likelihood: -310734.399509
EM: Round [137] log likelihood: -310734.399378
EM: Round [138] log likelihood: -310734.399252
EM: Round [139] log likelihood: -310734.399131
EM: Round [140] log likelihood: -310734.399014
EM: Round [141] log likelihood: -310734.398902
EM: Round [142] log likelihood: -310734.398793
EM: Round [143] log likelihood: -310734.398689
EM: Round [144] log likelihood: -310734.398589
EM: Round [145] log likelihood: -310734.398492
EM: Stopping iterations at round 145 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.m5bFFMSaGF/./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.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.m5bFFMSaGF/./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.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 246686357 > /tmp/nxf.m5bFFMSaGF/./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.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir > /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir --annotate /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.m5bFFMSaGF/./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.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir
-done, see /tmp/nxf.m5bFFMSaGF/./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.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.m5bFFMSaGF/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1373, filtered: 12150)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.m5bFFMSaGF/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.m5bFFMSaGF/./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.m5bFFMSaGF/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH.g@-ext]
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WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000244257.5]
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WARNING, no entry stored in dbm for [ENSG00000259485.2]
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WARNING, no entry stored in dbm for [ENSG00000232023.3]
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WARNING, no entry stored in dbm for [ENSG00000198685.4]
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WARNING, no entry stored in dbm for [ENSG00000261455.1]
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WARNING, no entry stored in dbm for [ENSG00000258279.4]
WARNING, no entry stored in dbm for [ENSG00000205837.7]
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WARNING, no entry stored in dbm for [ENSG00000206623.1]
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WARNING, no entry stored in dbm for [ENSG00000207204.1]
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WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000187952.9]
WARNING, no entry stored in dbm for [ENSG00000222004.7]
WARNING, no entry stored in dbm for [ENSG00000255920.3]
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WARNING, no entry stored in dbm for [ENSG00000236539.3]
WARNING, no entry stored in dbm for [ENSG00000215283.3]
WARNING, no entry stored in dbm for [ENSG00000255391.1]
WARNING, no entry stored in dbm for [ENSG00000223656.1]
WARNING, no entry stored in dbm for [ENSG00000124097.7]
WARNING, no entry stored in dbm for [ENSG00000228078.1]
WARNING, no entry stored in dbm for [ENSG00000248785.1]
WARNING, no entry stored in dbm for [ENSG00000233299.1]
WARNING, no entry stored in dbm for [ENSG00000286250.1]
WARNING, no entry stored in dbm for [ENSG00000233836.7]
WARNING, no entry stored in dbm for [ENSG00000233930.4]
WARNING, no entry stored in dbm for [ENSG00000223896.2]
WARNING, no entry stored in dbm for [ENSG00000234948.2]
WARNING, no entry stored in dbm for [ENSG00000226472.8]
WARNING, no entry stored in dbm for [ENSG00000226747.6]
WARNING, no entry stored in dbm for [ENSG00000273382.1]
WARNING, no entry stored in dbm for [ENSG00000198468.9]
WARNING, no entry stored in dbm for [ENSG00000241860.7]
WARNING, no entry stored in dbm for [ENSG00000231431.7]
WARNING, no entry stored in dbm for [ENSG00000274177.1]
WARNING, no entry stored in dbm for [ENSG00000278895.1]
WARNING, no entry stored in dbm for [ENSG00000231528.3]
WARNING, no entry stored in dbm for [ENSG00000243562.3]
WARNING, no entry stored in dbm for [ENSG00000225393.1]
WARNING, no entry stored in dbm for [ENSG00000271335.6]
WARNING, no entry stored in dbm for [ENSG00000271118.1]
WARNING, no entry stored in dbm for [ENSG00000245205.3]
WARNING, no entry stored in dbm for [ENSG00000249859.12]
WARNING, no entry stored in dbm for [ENSG00000185904.12]
WARNING, no entry stored in dbm for [ENSG00000224897.8]
WARNING, no entry stored in dbm for [ENSG00000229358.3]
WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [ENSG00000271086.7]
WARNING, no entry stored in dbm for [ENSG00000176584.18]
WARNING, no entry stored in dbm for [ENSG00000261520.5]
WARNING, no entry stored in dbm for [ENSG00000229231.1]
WARNING, no entry stored in dbm for [ENSG00000254275.6]
WARNING, no entry stored in dbm for [ENSG00000215030.5]
WARNING, no entry stored in dbm for [ENSG00000273297.2]
WARNING, no entry stored in dbm for [ENSG00000222041.11]
WARNING, no entry stored in dbm for [ENSG00000237036.5]
WARNING, no entry stored in dbm for [ENSG00000286458.1]
WARNING, no entry stored in dbm for [ENSG00000226752.9]
WARNING, no entry stored in dbm for [ENSG00000226752.9]
WARNING, no entry stored in dbm for [ENSG00000278903.3]
WARNING, no entry stored in dbm for [ENSG00000265728.1]
WARNING, no entry stored in dbm for [ENSG00000233025.1]
WARNING, no entry stored in dbm for [ENSG00000080947.15]
WARNING, no entry stored in dbm for [ENSG00000237773.7]
WARNING, no entry stored in dbm for [ENSG00000241818.1]
WARNING, no entry stored in dbm for [ENSG00000227201.2]
WARNING, no entry stored in dbm for [ENSG00000225005.1]
WARNING, no entry stored in dbm for [ENSG00000260896.6]
WARNING, no entry stored in dbm for [ENSG00000232553.3]
WARNING, no entry stored in dbm for [ENSG00000254851.1]
WARNING, no entry stored in dbm for [ENSG00000233695.2]
WARNING, no entry stored in dbm for [ENSG00000285051.2]
WARNING, no entry stored in dbm for [ENSG00000235084.3]
WARNING, no entry stored in dbm for [ENSG00000233109.4]
WARNING, no entry stored in dbm for [ENSG00000213753.11]
WARNING, no entry stored in dbm for [ENSG00000225264.3]
WARNING, no entry stored in dbm for [ENSG00000243144.7]
WARNING, no entry stored in dbm for [ENSG00000251264.1]
WARNING, no entry stored in dbm for [ENSG00000256695.2]
WARNING, no entry stored in dbm for [ENSG00000203930.12]
WARNING, no entry stored in dbm for [ENSG00000214064.3]
WARNING, no entry stored in dbm for [ENSG00000279434.1]
WARNING, no entry stored in dbm for [ENSG00000264617.1]
WARNING, no entry stored in dbm for [ENSG00000254166.3]
WARNING, no entry stored in dbm for [ENSG00000270994.1]
WARNING, no entry stored in dbm for [ENSG00000205885.7]
WARNING, no entry stored in dbm for [ENSG00000251629.7]
WARNING, no entry stored in dbm for [ENSG00000215158.9]
WARNING, no entry stored in dbm for [ENSG00000182352.8]
WARNING, no entry stored in dbm for [ENSG00000285756.2]
WARNING, no entry stored in dbm for [ENSG00000254676.1]
WARNING, no entry stored in dbm for [ENSG00000258099.1]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000243289.1]
WARNING, no entry stored in dbm for [ENSG00000285967.1]
WARNING, no entry stored in dbm for [ENSG00000279022.1]
WARNING, no entry stored in dbm for [ENSG00000286444.1]
WARNING, no entry stored in dbm for [ENSG00000286966.1]
WARNING, no entry stored in dbm for [ENSG00000261286.1]
WARNING, no entry stored in dbm for [ENSG00000257252.6]
WARNING, no entry stored in dbm for [ENSG00000213698.2]
WARNING, no entry stored in dbm for [ENSG00000267080.6]
WARNING, no entry stored in dbm for [ENSG00000260896.6]
WARNING, no entry stored in dbm for [ENSG00000271579.1]
WARNING, no entry stored in dbm for [ENSG00000231453.1]
WARNING, no entry stored in dbm for [ENSG00000124224.17]
WARNING, no entry stored in dbm for [ENSG00000284639.1]
WARNING, no entry stored in dbm for [ENSG00000232677.9]
WARNING, no entry stored in dbm for [ENSG00000257038.1]
WARNING, no entry stored in dbm for [ENSG00000266373.1]
WARNING, no entry stored in dbm for [ENSG00000236304.1]
WARNING, no entry stored in dbm for [ENSG00000234509.1]
WARNING, no entry stored in dbm for [ENSG00000236375.3]
WARNING, no entry stored in dbm for [ENSG00000224309.7]
WARNING, no entry stored in dbm for [ENSG00000257331.1]
WARNING, no entry stored in dbm for [ENSG00000223837.2]
WARNING, no entry stored in dbm for [ENSG00000285799.1]
WARNING, no entry stored in dbm for [ENSG00000254741.1]
WARNING, no entry stored in dbm for [ENSG00000225096.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000270066.3]
WARNING, no entry stored in dbm for [ENSG00000236713.1]
WARNING, no entry stored in dbm for [ENSG00000230628.1]
WARNING, no entry stored in dbm for [ENSG00000228436.3]
WARNING, no entry stored in dbm for [ENSG00000233379.2]
WARNING, no entry stored in dbm for [ENSG00000283078.1]
WARNING, no entry stored in dbm for [ENSG00000242888.1]
WARNING, no entry stored in dbm for [ENSG00000279253.1]
WARNING, no entry stored in dbm for [ENSG00000237686.7]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000260464.1]
WARNING, no entry stored in dbm for [ENSG00000226310.1]
WARNING, no entry stored in dbm for [ENSG00000287920.1]
WARNING, no entry stored in dbm for [ENSG00000265018.6]
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 [ENSG00000284620.2]
WARNING, no entry stored in dbm for [ENSG00000230590.11]
WARNING, no entry stored in dbm for [ENSG00000286912.1]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000132204.14]
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000239969.5]
WARNING, no entry stored in dbm for [ENSG00000247130.2]
WARNING, no entry stored in dbm for [ENSG00000180229.12]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000283511.1]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000259704.2]
WARNING, no entry stored in dbm for [ENSG00000278791.1]
WARNING, no entry stored in dbm for [ENSG00000239482.6]
WARNING, no entry stored in dbm for [ENSG00000286182.1]
WARNING, no entry stored in dbm for [ENSG00000251654.2]
WARNING, no entry stored in dbm for [ENSG00000260278.1]
WARNING, no entry stored in dbm for [ENSG00000284648.1]
WARNING, no entry stored in dbm for [ENSG00000242759.8]
WARNING, no entry stored in dbm for [ENSG00000261104.1]
WARNING, no entry stored in dbm for [ENSG00000260805.2]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000251652.1]
WARNING, no entry stored in dbm for [ENSG00000253123.4]
WARNING, no entry stored in dbm for [ENSG00000278863.1]
WARNING, no entry stored in dbm for [ENSG00000266356.1]
WARNING, no entry stored in dbm for [ENSG00000213650.3]
WARNING, no entry stored in dbm for [ENSG00000267737.1]
WARNING, no entry stored in dbm for [ENSG00000266677.1]
WARNING, no entry stored in dbm for [ENSG00000242299.1]
WARNING, no entry stored in dbm for [ENSG00000288663.1]
WARNING, no entry stored in dbm for [ENSG00000288663.1]
WARNING, no entry stored in dbm for [ENSG00000257539.2]
WARNING, no entry stored in dbm for [ENSG00000257337.7]
WARNING, no entry stored in dbm for [ENSG00000254859.1]
WARNING, no entry stored in dbm for [ENSG00000260005.6]
WARNING, no entry stored in dbm for [ENSG00000250140.1]
WARNING, no entry stored in dbm for [ENSG00000254485.5]
WARNING, no entry stored in dbm for [ENSG00000260693.1]
WARNING, no entry stored in dbm for [ENSG00000276272.1]
WARNING, no entry stored in dbm for [ENSG00000273658.1]
WARNING, no entry stored in dbm for [ENSG00000255511.1]
WARNING, no entry stored in dbm for [ENSG00000268747.1]
WARNING, no entry stored in dbm for [ENSG00000268093.1]
WARNING, no entry stored in dbm for [ENSG00000213963.6]
WARNING, no entry stored in dbm for [ENSG00000261329.6]
WARNING, no entry stored in dbm for [ENSG00000261329.6]
WARNING, no entry stored in dbm for [ENSG00000286449.1]
WARNING, no entry stored in dbm for [ENSG00000249406.3]
WARNING, no entry stored in dbm for [ENSG00000265041.1]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000285587.1]
WARNING, no entry stored in dbm for [ENSG00000213777.5]
WARNING, no entry stored in dbm for [ENSG00000286234.1]
WARNING, no entry stored in dbm for [ENSG00000204850.4]
WARNING, no entry stored in dbm for [ENSG00000259933.6]
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 [ENSG00000267727.1]
WARNING, no entry stored in dbm for [ENSG00000267379.1]
WARNING, no entry stored in dbm for [ENSG00000235583.2]
WARNING, no entry stored in dbm for [ENSG00000286739.1]
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 [ENSG00000229365.3]
WARNING, no entry stored in dbm for [ENSG00000268460.2]
WARNING, no entry stored in dbm for [ENSG00000226824.7]
WARNING, no entry stored in dbm for [ENSG00000224365.1]
WARNING, no entry stored in dbm for [ENSG00000267469.1]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000241057.2]
WARNING, no entry stored in dbm for [ENSG00000228434.1]
WARNING, no entry stored in dbm for [ENSG00000127957.18]
WARNING, no entry stored in dbm for [ENSG00000273419.1]
WARNING, no entry stored in dbm for [ENSG00000262678.1]
WARNING, no entry stored in dbm for [ENSG00000227948.4]
WARNING, no entry stored in dbm for [ENSG00000227948.4]
WARNING, no entry stored in dbm for [ENSG00000262265.2]
WARNING, no entry stored in dbm for [ENSG00000238098.9]
WARNING, no entry stored in dbm for [ENSG00000238098.9]
WARNING, no entry stored in dbm for [ENSG00000251595.7]
WARNING, no entry stored in dbm for [ENSG00000239408.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.m5bFFMSaGF/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)