-ctat genome lib [/tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.BEWR0nSQG6/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary
-sample contains 292294413 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir  -J /tmp/nxf.BEWR0nSQG6/SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.BEWR0nSQG6/SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.BEWR0nSQG6/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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[2630000-building interval tree based on /tmp/nxf.BEWR0nSQG6/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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[4500000], rate=107142.86/min 
[4510000], rate=107210.78/min 
[4520000], rate=107151.32/min 
[4530000], rate=107176.66/min -building interval tree based on /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=42857.14/min 
[20000], rate=27272.73/min 
[30000], rate=27692.31/min 
[40000], rate=30000.00/min 
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[2570000], rate=59444.87/min 
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[2620000], rate=59545.45/min 
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[2650000], rate=59639.91/min 
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[2680000], rate=59732.54/min 
[2690000], rate=59755.65/min 
[2700000], rate=59800.66/min 
[2710000], rate=59889.50/min 
-building interval tree based on /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=85714.29/min 
[20000], rate=85714.29/min 
[30000], rate=81818.18/min 
[40000], rate=88888.89/min 
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[100000], rate=85714.29/min 
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[1110000], rate=51990.63/min 
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[1210000], rate=52608.70/min 
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[1230000], rate=52941.18/min 
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[3400000], rate=58219.18/min 
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[3420000], rate=58295.45/min 
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[3580000], rate=58800.99/min 
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[3600000], rate=58887.68/min 
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[4450000], rate=61776.96/min 
[4460000], rate=61758.60/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

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done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.BEWR0nSQG6/SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  --tmpdir /tmp  --min_junction_reads 0  --min_sum_frags 1  --require_LDAS 0  --max_promiscuity 10  --min_pct_dom_promiscuity 20  --min_novel_junction_support 1  --min_alt_pct_junction 10  --aggregate_novel_junction_dist 5  --min_spanning_frags_only 1  --genome_lib_dir /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -250162.845613
EM: Round [1] log likelihood: -249911.284014
EM: Round [2] log likelihood: -249810.780247
EM: Round [3] log likelihood: -249761.596966
EM: Round [4] log likelihood: -249735.193381
EM: Round [5] log likelihood: -249720.274302
EM: Round [6] log likelihood: -249711.490740
EM: Round [7] log likelihood: -249706.100187
EM: Round [8] log likelihood: -249702.648651
EM: Round [9] log likelihood: -249700.346163
EM: Round [10] log likelihood: -249698.751296
EM: Round [11] log likelihood: -249697.609201
EM: Round [12] log likelihood: -249696.767485
EM: Round [13] log likelihood: -249696.131726
EM: Round [14] log likelihood: -249695.641383
EM: Round [15] log likelihood: -249695.256374
EM: Round [16] log likelihood: -249694.949381
EM: Round [17] log likelihood: -249694.701298
EM: Round [18] log likelihood: -249694.498451
EM: Round [19] log likelihood: -249694.330858
EM: Round [20] log likelihood: -249694.191102
EM: Round [21] log likelihood: -249694.073583
EM: Round [22] log likelihood: -249693.974019
EM: Round [23] log likelihood: -249693.889089
EM: Round [24] log likelihood: -249693.816192
EM: Round [25] log likelihood: -249693.753267
EM: Round [26] log likelihood: -249693.698667
EM: Round [27] log likelihood: -249693.651064
EM: Round [28] log likelihood: -249693.609377
EM: Round [29] log likelihood: -249693.572722
EM: Round [30] log likelihood: -249693.540369
EM: Round [31] log likelihood: -249693.511712
EM: Round [32] log likelihood: -249693.486244
EM: Round [33] log likelihood: -249693.463541
EM: Round [34] log likelihood: -249693.443242
EM: Round [35] log likelihood: -249693.425044
EM: Round [36] log likelihood: -249693.408686
EM: Round [37] log likelihood: -249693.393947
EM: Round [38] log likelihood: -249693.380633
EM: Round [39] log likelihood: -249693.368581
EM: Round [40] log likelihood: -249693.357648
EM: Round [41] log likelihood: -249693.347709
EM: Round [42] log likelihood: -249693.338656
EM: Round [43] log likelihood: -249693.330395
EM: Round [44] log likelihood: -249693.322842
EM: Round [45] log likelihood: -249693.315924
EM: Round [46] log likelihood: -249693.309577
EM: Round [47] log likelihood: -249693.303745
EM: Round [48] log likelihood: -249693.298376
EM: Round [49] log likelihood: -249693.293427
EM: Round [50] log likelihood: -249693.288857
EM: Round [51] log likelihood: -249693.284630
EM: Round [52] log likelihood: -249693.280717
EM: Round [53] log likelihood: -249693.277087
EM: Round [54] log likelihood: -249693.273715
EM: Round [55] log likelihood: -249693.270580
EM: Round [56] log likelihood: -249693.267659
EM: Round [57] log likelihood: -249693.264936
EM: Round [58] log likelihood: -249693.262393
EM: Round [59] log likelihood: -249693.260015
EM: Round [60] log likelihood: -249693.257788
EM: Round [61] log likelihood: -249693.255701
EM: Round [62] log likelihood: -249693.253742
EM: Round [63] log likelihood: -249693.251901
EM: Round [64] log likelihood: -249693.250168
EM: Round [65] log likelihood: -249693.248536
EM: Round [66] log likelihood: -249693.246996
EM: Round [67] log likelihood: -249693.245543
EM: Round [68] log likelihood: -249693.244168
EM: Round [69] log likelihood: -249693.242867
EM: Round [70] log likelihood: -249693.241635
EM: Round [71] log likelihood: -249693.240465
EM: Round [72] log likelihood: -249693.239355
EM: Round [73] log likelihood: -249693.238300
EM: Round [74] log likelihood: -249693.237295
EM: Round [75] log likelihood: -249693.236339
EM: Round [76] log likelihood: -249693.235426
EM: Round [77] log likelihood: -249693.234556
EM: Round [78] log likelihood: -249693.233724
EM: Round [79] log likelihood: -249693.232928
EM: Round [80] log likelihood: -249693.232167
EM: Round [81] log likelihood: -249693.231438
EM: Round [82] log likelihood: -249693.230739
EM: Round [83] log likelihood: -249693.230068
EM: Round [84] log likelihood: -249693.229423
EM: Round [85] log likelihood: -249693.228804
EM: Round [86] log likelihood: -249693.228208
EM: Round [87] log likelihood: -249693.227635
EM: Round [88] log likelihood: -249693.227083
EM: Round [89] log likelihood: -249693.226550
EM: Round [90] log likelihood: -249693.226037
EM: Round [91] log likelihood: -249693.225541
EM: Round [92] log likelihood: -249693.225063
EM: Round [93] log likelihood: -249693.224600
EM: Round [94] log likelihood: -249693.224153
EM: Round [95] log likelihood: -249693.223721
EM: Round [96] log likelihood: -249693.223302
EM: Round [97] log likelihood: -249693.222896
EM: Round [98] log likelihood: -249693.222503
EM: Round [99] log likelihood: -249693.222122
EM: Round [100] log likelihood: -249693.221753
EM: Round [101] log likelihood: -249693.221394
EM: Round [102] log likelihood: -249693.221046
EM: Round [103] log likelihood: -249693.220708
EM: Round [104] log likelihood: -249693.220380
EM: Round [105] log likelihood: -249693.220061
EM: Round [106] log likelihood: -249693.219750
EM: Round [107] log likelihood: -249693.219449
EM: Round [108] log likelihood: -249693.219155
EM: Round [109] log likelihood: -249693.218869
EM: Round [110] log likelihood: -249693.218591
EM: Round [111] log likelihood: -249693.218320
EM: Round [112] log likelihood: -249693.218056
EM: Round [113] log likelihood: -249693.217799
EM: Round [114] log likelihood: -249693.217549
EM: Round [115] log likelihood: -249693.217305
EM: Round [116] log likelihood: -249693.217066
EM: Round [117] log likelihood: -249693.216834
EM: Round [118] log likelihood: -249693.216607
EM: Round [119] log likelihood: -249693.216386
EM: Round [120] log likelihood: -249693.216170
EM: Round [121] log likelihood: -249693.215959
EM: Round [122] log likelihood: -249693.215753
EM: Round [123] log likelihood: -249693.215552
EM: Round [124] log likelihood: -249693.215356
EM: Round [125] log likelihood: -249693.215164
EM: Round [126] log likelihood: -249693.214977
EM: Round [127] log likelihood: -249693.214793
EM: Round [128] log likelihood: -249693.214614
EM: Round [129] log likelihood: -249693.214439
EM: Round [130] log likelihood: -249693.214267
EM: Round [131] log likelihood: -249693.214100
EM: Round [132] log likelihood: -249693.213936
EM: Round [133] log likelihood: -249693.213775
EM: Round [134] log likelihood: -249693.213618
EM: Round [135] log likelihood: -249693.213465
EM: Round [136] log likelihood: -249693.213314
EM: Round [137] log likelihood: -249693.213167
EM: Round [138] log likelihood: -249693.213023
EM: Round [139] log likelihood: -249693.212882
EM: Round [140] log likelihood: -249693.212743
EM: Round [141] log likelihood: -249693.212608
EM: Round [142] log likelihood: -249693.212475
EM: Round [143] log likelihood: -249693.212345
EM: Round [144] log likelihood: -249693.212217
EM: Round [145] log likelihood: -249693.212092
EM: Round [146] log likelihood: -249693.211970
EM: Round [147] log likelihood: -249693.211850
EM: Round [148] log likelihood: -249693.211732
EM: Round [149] log likelihood: -249693.211616
EM: Round [150] log likelihood: -249693.211503
EM: Round [151] log likelihood: -249693.211392
EM: Round [152] log likelihood: -249693.211283
EM: Round [153] log likelihood: -249693.211175
EM: Round [154] log likelihood: -249693.211070
EM: Round [155] log likelihood: -249693.210967
EM: Round [156] log likelihood: -249693.210866
EM: Round [157] log likelihood: -249693.210767
EM: Stopping iterations at round 157 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -249926.885230
EM: Round [1] log likelihood: -249707.233585
EM: Round [2] log likelihood: -249621.816875
EM: Round [3] log likelihood: -249580.782773
EM: Round [4] log likelihood: -249559.117986
EM: Round [5] log likelihood: -249547.072854
EM: Round [6] log likelihood: -249540.093172
EM: Round [7] log likelihood: -249535.874321
EM: Round [8] log likelihood: -249533.210007
EM: Round [9] log likelihood: -249531.453411
EM: Round [10] log likelihood: -249530.247988
EM: Round [11] log likelihood: -249529.390705
EM: Round [12] log likelihood: -249528.761770
EM: Round [13] log likelihood: -249528.287892
EM: Round [14] log likelihood: -249527.922616
EM: Round [15] log likelihood: -249527.635507
EM: Round [16] log likelihood: -249527.406006
EM: Round [17] log likelihood: -249527.219850
EM: Round [18] log likelihood: -249527.066903
EM: Round [19] log likelihood: -249526.939807
EM: Round [20] log likelihood: -249526.833123
EM: Round [21] log likelihood: -249526.742764
EM: Round [22] log likelihood: -249526.665613
EM: Round [23] log likelihood: -249526.599260
EM: Round [24] log likelihood: -249526.541822
EM: Round [25] log likelihood: -249526.491807
EM: Round [26] log likelihood: -249526.448025
EM: Round [27] log likelihood: -249526.409512
EM: Round [28] log likelihood: -249526.375486
EM: Round [29] log likelihood: -249526.345304
EM: Round [30] log likelihood: -249526.318432
EM: Round [31] log likelihood: -249526.294429
EM: Round [32] log likelihood: -249526.272920
EM: Round [33] log likelihood: -249526.253592
EM: Round [34] log likelihood: -249526.236177
EM: Round [35] log likelihood: -249526.220447
EM: Round [36] log likelihood: -249526.206205
EM: Round [37] log likelihood: -249526.193284
EM: Round [38] log likelihood: -249526.181536
EM: Round [39] log likelihood: -249526.170834
EM: Round [40] log likelihood: -249526.161067
EM: Round [41] log likelihood: -249526.152137
EM: Round [42] log likelihood: -249526.143960
EM: Round [43] log likelihood: -249526.136459
EM: Round [44] log likelihood: -249526.129568
EM: Round [45] log likelihood: -249526.123228
EM: Round [46] log likelihood: -249526.117386
EM: Round [47] log likelihood: -249526.111995
EM: Round [48] log likelihood: -249526.107014
EM: Round [49] log likelihood: -249526.102405
EM: Round [50] log likelihood: -249526.098136
EM: Round [51] log likelihood: -249526.094175
EM: Round [52] log likelihood: -249526.090496
EM: Round [53] log likelihood: -249526.087074
EM: Round [54] log likelihood: -249526.083888
EM: Round [55] log likelihood: -249526.080918
EM: Round [56] log likelihood: -249526.078145
EM: Round [57] log likelihood: -249526.075554
EM: Round [58] log likelihood: -249526.073129
EM: Round [59] log likelihood: -249526.070858
EM: Round [60] log likelihood: -249526.068728
EM: Round [61] log likelihood: -249526.066728
EM: Round [62] log likelihood: -249526.064848
EM: Round [63] log likelihood: -249526.063079
EM: Round [64] log likelihood: -249526.061412
EM: Round [65] log likelihood: -249526.059840
EM: Round [66] log likelihood: -249526.058356
EM: Round [67] log likelihood: -249526.056953
EM: Round [68] log likelihood: -249526.055625
EM: Round [69] log likelihood: -249526.054368
EM: Round [70] log likelihood: -249526.053175
EM: Round [71] log likelihood: -249526.052044
EM: Round [72] log likelihood: -249526.050968
EM: Round [73] log likelihood: -249526.049945
EM: Round [74] log likelihood: -249526.048971
EM: Round [75] log likelihood: -249526.048043
EM: Round [76] log likelihood: -249526.047157
EM: Round [77] log likelihood: -249526.046312
EM: Round [78] log likelihood: -249526.045504
EM: Round [79] log likelihood: -249526.044731
EM: Round [80] log likelihood: -249526.043991
EM: Round [81] log likelihood: -249526.043282
EM: Round [82] log likelihood: -249526.042602
EM: Round [83] log likelihood: -249526.041950
EM: Round [84] log likelihood: -249526.041323
EM: Round [85] log likelihood: -249526.040720
EM: Round [86] log likelihood: -249526.040141
EM: Round [87] log likelihood: -249526.039583
EM: Round [88] log likelihood: -249526.039045
EM: Round [89] log likelihood: -249526.038527
EM: Round [90] log likelihood: -249526.038027
EM: Round [91] log likelihood: -249526.037544
EM: Round [92] log likelihood: -249526.037078
EM: Round [93] log likelihood: -249526.036628
EM: Round [94] log likelihood: -249526.036192
EM: Round [95] log likelihood: -249526.035771
EM: Round [96] log likelihood: -249526.035363
EM: Round [97] log likelihood: -249526.034968
EM: Round [98] log likelihood: -249526.034585
EM: Round [99] log likelihood: -249526.034214
EM: Round [100] log likelihood: -249526.033854
EM: Round [101] log likelihood: -249526.033505
EM: Round [102] log likelihood: -249526.033166
EM: Round [103] log likelihood: -249526.032837
EM: Round [104] log likelihood: -249526.032517
EM: Round [105] log likelihood: -249526.032206
EM: Round [106] log likelihood: -249526.031904
EM: Round [107] log likelihood: -249526.031610
EM: Round [108] log likelihood: -249526.031324
EM: Round [109] log likelihood: -249526.031045
EM: Round [110] log likelihood: -249526.030775
EM: Round [111] log likelihood: -249526.030511
EM: Round [112] log likelihood: -249526.030254
EM: Round [113] log likelihood: -249526.030003
EM: Round [114] log likelihood: -249526.029759
EM: Round [115] log likelihood: -249526.029521
EM: Round [116] log likelihood: -249526.029289
EM: Round [117] log likelihood: -249526.029063
EM: Round [118] log likelihood: -249526.028842
EM: Round [119] log likelihood: -249526.028626
EM: Round [120] log likelihood: -249526.028416
EM: Round [121] log likelihood: -249526.028211
EM: Round [122] log likelihood: -249526.028010
EM: Round [123] log likelihood: -249526.027815
EM: Round [124] log likelihood: -249526.027623
EM: Round [125] log likelihood: -249526.027436
EM: Round [126] log likelihood: -249526.027254
EM: Round [127] log likelihood: -249526.027075
EM: Round [128] log likelihood: -249526.026901
EM: Round [129] log likelihood: -249526.026730
EM: Round [130] log likelihood: -249526.026563
EM: Round [131] log likelihood: -249526.026400
EM: Round [132] log likelihood: -249526.026240
EM: Round [133] log likelihood: -249526.026084
EM: Round [134] log likelihood: -249526.025931
EM: Round [135] log likelihood: -249526.025782
EM: Round [136] log likelihood: -249526.025635
EM: Round [137] log likelihood: -249526.025492
EM: Round [138] log likelihood: -249526.025351
EM: Round [139] log likelihood: -249526.025214
EM: Round [140] log likelihood: -249526.025079
EM: Round [141] log likelihood: -249526.024947
EM: Round [142] log likelihood: -249526.024818
EM: Round [143] log likelihood: -249526.024691
EM: Round [144] log likelihood: -249526.024567
EM: Round [145] log likelihood: -249526.024446
EM: Round [146] log likelihood: -249526.024326
EM: Round [147] log likelihood: -249526.024209
EM: Round [148] log likelihood: -249526.024095
EM: Round [149] log likelihood: -249526.023982
EM: Round [150] log likelihood: -249526.023872
EM: Round [151] log likelihood: -249526.023764
EM: Round [152] log likelihood: -249526.023658
EM: Round [153] log likelihood: -249526.023554
EM: Round [154] log likelihood: -249526.023451
EM: Round [155] log likelihood: -249526.023351
EM: Round [156] log likelihood: -249526.023253
EM: Stopping iterations at round 156 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.BEWR0nSQG6/./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.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.BEWR0nSQG6/./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.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 292294413 > /tmp/nxf.BEWR0nSQG6/./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.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir > /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir --annotate /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.BEWR0nSQG6/./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.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir
-done, see /tmp/nxf.BEWR0nSQG6/./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.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.BEWR0nSQG6/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1280, filtered: 8991)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.BEWR0nSQG6/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.BEWR0nSQG6/./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.BEWR0nSQG6/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000237296.9]
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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 [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000234152.1]
WARNING, no entry stored in dbm for [ENSG00000231929.2]
WARNING, no entry stored in dbm for [ENSG00000230239.1]
WARNING, no entry stored in dbm for [ENSG00000234667.2]
WARNING, no entry stored in dbm for [ENSG00000227110.7]
WARNING, no entry stored in dbm for [ENSG00000249395.4]
WARNING, no entry stored in dbm for [ENSG00000250421.5]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
WARNING, no entry stored in dbm for [ENSG00000249894.1]
WARNING, no entry stored in dbm for [ENSG00000287858.1]
WARNING, no entry stored in dbm for [ENSG00000253706.5]
WARNING, no entry stored in dbm for [ENSG00000234352.9]
WARNING, no entry stored in dbm for [ENSG00000267009.6]
WARNING, no entry stored in dbm for [ENSG00000186704.9]
WARNING, no entry stored in dbm for [ENSG00000230982.1]
WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [ENSG00000185904.12]
WARNING, no entry stored in dbm for [ENSG00000278733.1]
WARNING, no entry stored in dbm for [ENSG00000253557.6]
WARNING, no entry stored in dbm for [ENSG00000254275.6]
WARNING, no entry stored in dbm for [ENSG00000272870.3]
WARNING, no entry stored in dbm for [ENSG00000254363.6]
WARNING, no entry stored in dbm for [ENSG00000235903.9]
WARNING, no entry stored in dbm for [ENSG00000287578.1]
WARNING, no entry stored in dbm for [ENSG00000287923.1]
WARNING, no entry stored in dbm for [ENSG00000215908.10]
WARNING, no entry stored in dbm for [ENSG00000228225.1]
WARNING, no entry stored in dbm for [ENSG00000259663.2]
WARNING, no entry stored in dbm for [ENSG00000266729.5]
WARNING, no entry stored in dbm for [ENSG00000270429.1]
WARNING, no entry stored in dbm for [ENSG00000273509.1]
WARNING, no entry stored in dbm for [ENSG00000283541.1]
WARNING, no entry stored in dbm for [ENSG00000283541.1]
WARNING, no entry stored in dbm for [ENSG00000230219.3]
WARNING, no entry stored in dbm for [ENSG00000259755.1]
WARNING, no entry stored in dbm for [ENSG00000197182.14]
WARNING, no entry stored in dbm for [ENSG00000223960.7]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000239224.3]
WARNING, no entry stored in dbm for [ENSG00000226312.7]
WARNING, no entry stored in dbm for [ENSG00000234425.1]
WARNING, no entry stored in dbm for [ENSG00000213071.11]
WARNING, no entry stored in dbm for [ENSG00000177946.7]
WARNING, no entry stored in dbm for [ENSG00000234825.3]
WARNING, no entry stored in dbm for [ENSG00000238045.9]
WARNING, no entry stored in dbm for [ENSG00000273693.1]
WARNING, no entry stored in dbm for [ENSG00000260071.2]
WARNING, no entry stored in dbm for [ENSG00000287601.1]
WARNING, no entry stored in dbm for [ENSG00000236813.1]
WARNING, no entry stored in dbm for [ENSG00000222019.7]
WARNING, no entry stored in dbm for [ENSG00000254605.1]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000258794.3]
WARNING, no entry stored in dbm for [ENSG00000255216.2]
WARNING, no entry stored in dbm for [ENSG00000244198.7]
WARNING, no entry stored in dbm for [ENSG00000204959.4]
WARNING, no entry stored in dbm for [ENSG00000219807.2]
WARNING, no entry stored in dbm for [ENSG00000253282.1]
WARNING, no entry stored in dbm for [ENSG00000247137.9]
WARNING, no entry stored in dbm for [ENSG00000285545.1]
WARNING, no entry stored in dbm for [ENSG00000241170.3]
WARNING, no entry stored in dbm for [ENSG00000231259.5]
WARNING, no entry stored in dbm for [ENSG00000237666.2]
WARNING, no entry stored in dbm for [ENSG00000248671.8]
WARNING, no entry stored in dbm for [ENSG00000248671.8]
WARNING, no entry stored in dbm for [ENSG00000287823.1]
WARNING, no entry stored in dbm for [ENSG00000284640.1]
WARNING, no entry stored in dbm for [ENSG00000287220.1]
WARNING, no entry stored in dbm for [ENSG00000287530.1]
WARNING, no entry stored in dbm for [ENSG00000254602.2]
WARNING, no entry stored in dbm for [ENSG00000225096.3]
WARNING, no entry stored in dbm for [ENSG00000276248.1]
WARNING, no entry stored in dbm for [ENSG00000275285.1]
WARNING, no entry stored in dbm for [ENSG00000285280.2]
WARNING, no entry stored in dbm for [ENSG00000232347.1]
WARNING, no entry stored in dbm for [ENSG00000217801.10]
WARNING, no entry stored in dbm for [ENSG00000259008.1]
WARNING, no entry stored in dbm for [ENSG00000278291.1]
WARNING, no entry stored in dbm for [ENSG00000228830.1]
WARNING, no entry stored in dbm for [ENSG00000286171.1]
WARNING, no entry stored in dbm for [ENSG00000233379.2]
WARNING, no entry stored in dbm for [ENSG00000287156.1]
WARNING, no entry stored in dbm for [ENSG00000244757.1]
WARNING, no entry stored in dbm for [ENSG00000258875.6]
WARNING, no entry stored in dbm for [ENSG00000288044.1]
WARNING, no entry stored in dbm for [ENSG00000279175.1]
WARNING, no entry stored in dbm for [ENSG00000236740.6]
WARNING, no entry stored in dbm for [ENSG00000225311.1]
WARNING, no entry stored in dbm for [ENSG00000233508.3]
WARNING, no entry stored in dbm for [ENSG00000188002.10]
WARNING, no entry stored in dbm for [ENSG00000276850.5]
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 [ENSG00000233836.7]
WARNING, no entry stored in dbm for [ENSG00000261569.5]
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 [ENSG00000287737.1]
WARNING, no entry stored in dbm for [ENSG00000260563.3]
WARNING, no entry stored in dbm for [ENSG00000243655.2]
WARNING, no entry stored in dbm for [ENSG00000250777.2]
WARNING, no entry stored in dbm for [ENSG00000214999.3]
WARNING, no entry stored in dbm for [ENSG00000214999.3]
WARNING, no entry stored in dbm for [ENSG00000283345.1]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000277511.1]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000278408.1]
WARNING, no entry stored in dbm for [ENSG00000277332.1]
WARNING, no entry stored in dbm for [ENSG00000243415.2]
WARNING, no entry stored in dbm for [ENSG00000253176.3]
WARNING, no entry stored in dbm for [ENSG00000251314.2]
WARNING, no entry stored in dbm for [ENSG00000255491.3]
WARNING, no entry stored in dbm for [ENSG00000242396.1]
WARNING, no entry stored in dbm for [ENSG00000220256.4]
WARNING, no entry stored in dbm for [ENSG00000244021.4]
WARNING, no entry stored in dbm for [ENSG00000241251.2]
WARNING, no entry stored in dbm for [ENSG00000265401.1]
WARNING, no entry stored in dbm for [ENSG00000173209.23]
WARNING, no entry stored in dbm for [ENSG00000243176.6]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000278577.1]
WARNING, no entry stored in dbm for [ENSG00000268362.6]
WARNING, no entry stored in dbm for [ENSG00000259363.6]
WARNING, no entry stored in dbm for [ENSG00000286402.1]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000250007.7]
WARNING, no entry stored in dbm for [ENSG00000250869.2]
WARNING, no entry stored in dbm for [ENSG00000204745.4]
WARNING, no entry stored in dbm for [ENSG00000233673.7]
WARNING, no entry stored in dbm for [ENSG00000249609.1]
WARNING, no entry stored in dbm for [ENSG00000284627.1]
WARNING, no entry stored in dbm for [ENSG00000266718.2]
WARNING, no entry stored in dbm for [ENSG00000286957.1]
WARNING, no entry stored in dbm for [ENSG00000223703.1]
WARNING, no entry stored in dbm for [ENSG00000257817.2]
WARNING, no entry stored in dbm for [ENSG00000257817.2]
WARNING, no entry stored in dbm for [ENSG00000268093.1]
WARNING, no entry stored in dbm for [ENSG00000267169.2]
WARNING, no entry stored in dbm for [ENSG00000279569.1]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000226994.9]
WARNING, no entry stored in dbm for [ENSG00000267934.1]
WARNING, no entry stored in dbm for [ENSG00000225963.8]
WARNING, no entry stored in dbm for [ENSG00000216895.9]
WARNING, no entry stored in dbm for [ENSG00000279198.1]
WARNING, no entry stored in dbm for [ENSG00000281026.1]
WARNING, no entry stored in dbm for [ENSG00000269371.1]
WARNING, no entry stored in dbm for [ENSG00000261804.2]
WARNING, no entry stored in dbm for [ENSG00000236540.7]
WARNING, no entry stored in dbm for [ENSG00000243696.5]
WARNING, no entry stored in dbm for [ENSG00000243696.5]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000243554.1]
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 [ENSG00000243797.6]
WARNING, no entry stored in dbm for [ENSG00000181123.8]
WARNING, no entry stored in dbm for [ENSG00000215908.10]
WARNING, no entry stored in dbm for [ENSG00000277283.1]
WARNING, no entry stored in dbm for [ENSG00000248290.1]
WARNING, no entry stored in dbm for [ENSG00000229913.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.BEWR0nSQG6/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)