-ctat genome lib [/tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.aQkiPLPjMf/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary
-sample contains 45879746 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir  -J /tmp/nxf.aQkiPLPjMf/1173_LAF_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction  -O /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.aQkiPLPjMf/1173_LAF_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.aQkiPLPjMf/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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[3350000], rate=188732.39/min -building interval tree based on /tmp/nxf.aQkiPLPjMf/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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[2630000-building interval tree based on /tmp/nxf.aQkiPLPjMf/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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[2640000], rate=-building interval tree based on /tmp/nxf.aQkiPLPjMf/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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[3360000], rate=100850.43/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.aQkiPLPjMf/./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.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.aQkiPLPjMf/1173_LAF_T1_RNA_SLD_01_A23T55JLT4_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.aQkiPLPjMf/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -495631.400586
EM: Round [1] log likelihood: -494558.398132
EM: Round [2] log likelihood: -494207.817577
EM: Round [3] log likelihood: -494054.714427
EM: Round [4] log likelihood: -493977.010289
EM: Round [5] log likelihood: -493933.899627
EM: Round [6] log likelihood: -493908.368771
EM: Round [7] log likelihood: -493892.385490
EM: Round [8] log likelihood: -493881.872105
EM: Round [9] log likelihood: -493874.647478
EM: Round [10] log likelihood: -493869.490616
EM: Round [11] log likelihood: -493865.688173
EM: Round [12] log likelihood: -493862.806153
EM: Round [13] log likelihood: -493860.570299
EM: Round [14] log likelihood: -493858.801138
EM: Round [15] log likelihood: -493857.377450
EM: Round [16] log likelihood: -493856.215024
EM: Round [17] log likelihood: -493855.253882
EM: Round [18] log likelihood: -493854.450360
EM: Round [19] log likelihood: -493853.772050
EM: Round [20] log likelihood: -493853.194483
EM: Round [21] log likelihood: -493852.698903
EM: Round [22] log likelihood: -493852.270732
EM: Round [23] log likelihood: -493851.898499
EM: Round [24] log likelihood: -493851.573075
EM: Round [25] log likelihood: -493851.287121
EM: Round [26] log likelihood: -493851.034682
EM: Round [27] log likelihood: -493850.810879
EM: Round [28] log likelihood: -493850.611689
EM: Round [29] log likelihood: -493850.433765
EM: Round [30] log likelihood: -493850.274309
EM: Round [31] log likelihood: -493850.130961
EM: Round [32] log likelihood: -493850.001724
EM: Round [33] log likelihood: -493849.884897
EM: Round [34] log likelihood: -493849.779023
EM: Round [35] log likelihood: -493849.682849
EM: Round [36] log likelihood: -493849.595296
EM: Round [37] log likelihood: -493849.515424
EM: Round [38] log likelihood: -493849.442418
EM: Round [39] log likelihood: -493849.375564
EM: Round [40] log likelihood: -493849.314237
EM: Round [41] log likelihood: -493849.257889
EM: Round [42] log likelihood: -493849.206033
EM: Round [43] log likelihood: -493849.158242
EM: Round [44] log likelihood: -493849.114134
EM: Round [45] log likelihood: -493849.073372
EM: Round [46] log likelihood: -493849.035655
EM: Round [47] log likelihood: -493849.000712
EM: Round [48] log likelihood: -493848.968302
EM: Round [49] log likelihood: -493848.938209
EM: Round [50] log likelihood: -493848.910238
EM: Round [51] log likelihood: -493848.884213
EM: Round [52] log likelihood: -493848.859975
EM: Round [53] log likelihood: -493848.837382
EM: Round [54] log likelihood: -493848.816303
EM: Round [55] log likelihood: -493848.796619
EM: Round [56] log likelihood: -493848.778225
EM: Round [57] log likelihood: -493848.761021
EM: Round [58] log likelihood: -493848.744920
EM: Round [59] log likelihood: -493848.729838
EM: Round [60] log likelihood: -493848.715702
EM: Round [61] log likelihood: -493848.702444
EM: Round [62] log likelihood: -493848.690002
EM: Round [63] log likelihood: -493848.678316
EM: Round [64] log likelihood: -493848.667336
EM: Round [65] log likelihood: -493848.657012
EM: Round [66] log likelihood: -493848.647299
EM: Round [67] log likelihood: -493848.638156
EM: Round [68] log likelihood: -493848.629546
EM: Round [69] log likelihood: -493848.621432
EM: Round [70] log likelihood: -493848.613783
EM: Round [71] log likelihood: -493848.606568
EM: Round [72] log likelihood: -493848.599759
EM: Round [73] log likelihood: -493848.593330
EM: Round [74] log likelihood: -493848.587257
EM: Round [75] log likelihood: -493848.581518
EM: Round [76] log likelihood: -493848.576093
EM: Round [77] log likelihood: -493848.570961
EM: Round [78] log likelihood: -493848.566104
EM: Round [79] log likelihood: -493848.561507
EM: Round [80] log likelihood: -493848.557153
EM: Round [81] log likelihood: -493848.553028
EM: Round [82] log likelihood: -493848.549118
EM: Round [83] log likelihood: -493848.545411
EM: Round [84] log likelihood: -493848.541895
EM: Round [85] log likelihood: -493848.538558
EM: Round [86] log likelihood: -493848.535390
EM: Round [87] log likelihood: -493848.532382
EM: Round [88] log likelihood: -493848.529524
EM: Round [89] log likelihood: -493848.526809
EM: Round [90] log likelihood: -493848.524227
EM: Round [91] log likelihood: -493848.521772
EM: Round [92] log likelihood: -493848.519436
EM: Round [93] log likelihood: -493848.517213
EM: Round [94] log likelihood: -493848.515096
EM: Round [95] log likelihood: -493848.513081
EM: Round [96] log likelihood: -493848.511161
EM: Round [97] log likelihood: -493848.509331
EM: Round [98] log likelihood: -493848.507587
EM: Round [99] log likelihood: -493848.505923
EM: Round [100] log likelihood: -493848.504336
EM: Round [101] log likelihood: -493848.502822
EM: Round [102] log likelihood: -493848.501376
EM: Round [103] log likelihood: -493848.499996
EM: Round [104] log likelihood: -493848.498678
EM: Round [105] log likelihood: -493848.497418
EM: Round [106] log likelihood: -493848.496214
EM: Round [107] log likelihood: -493848.495062
EM: Round [108] log likelihood: -493848.493961
EM: Round [109] log likelihood: -493848.492908
EM: Round [110] log likelihood: -493848.491900
EM: Round [111] log likelihood: -493848.490935
EM: Round [112] log likelihood: -493848.490010
EM: Round [113] log likelihood: -493848.489125
EM: Round [114] log likelihood: -493848.488277
EM: Round [115] log likelihood: -493848.487463
EM: Round [116] log likelihood: -493848.486684
EM: Round [117] log likelihood: -493848.485936
EM: Round [118] log likelihood: -493848.485219
EM: Round [119] log likelihood: -493848.484530
EM: Round [120] log likelihood: -493848.483869
EM: Round [121] log likelihood: -493848.483234
EM: Round [122] log likelihood: -493848.482625
EM: Round [123] log likelihood: -493848.482039
EM: Round [124] log likelihood: -493848.481476
EM: Round [125] log likelihood: -493848.480935
EM: Round [126] log likelihood: -493848.480414
EM: Round [127] log likelihood: -493848.479913
EM: Round [128] log likelihood: -493848.479431
EM: Round [129] log likelihood: -493848.478968
EM: Round [130] log likelihood: -493848.478521
EM: Round [131] log likelihood: -493848.478091
EM: Round [132] log likelihood: -493848.477676
EM: Round [133] log likelihood: -493848.477277
EM: Round [134] log likelihood: -493848.476892
EM: Round [135] log likelihood: -493848.476521
EM: Round [136] log likelihood: -493848.476163
EM: Round [137] log likelihood: -493848.475817
EM: Round [138] log likelihood: -493848.475484
EM: Round [139] log likelihood: -493848.475162
EM: Round [140] log likelihood: -493848.474852
EM: Round [141] log likelihood: -493848.474552
EM: Round [142] log likelihood: -493848.474262
EM: Round [143] log likelihood: -493848.473981
EM: Round [144] log likelihood: -493848.473711
EM: Round [145] log likelihood: -493848.473449
EM: Round [146] log likelihood: -493848.473195
EM: Round [147] log likelihood: -493848.472950
EM: Round [148] log likelihood: -493848.472713
EM: Round [149] log likelihood: -493848.472484
EM: Round [150] log likelihood: -493848.472261
EM: Round [151] log likelihood: -493848.472046
EM: Round [152] log likelihood: -493848.471838
EM: Round [153] log likelihood: -493848.471636
EM: Round [154] log likelihood: -493848.471440
EM: Round [155] log likelihood: -493848.471250
EM: Round [156] log likelihood: -493848.471066
EM: Round [157] log likelihood: -493848.470887
EM: Round [158] log likelihood: -493848.470714
EM: Round [159] log likelihood: -493848.470546
EM: Round [160] log likelihood: -493848.470383
EM: Round [161] log likelihood: -493848.470225
EM: Round [162] log likelihood: -493848.470071
EM: Round [163] log likelihood: -493848.469921
EM: Round [164] log likelihood: -493848.469776
EM: Round [165] log likelihood: -493848.469635
EM: Round [166] log likelihood: -493848.469498
EM: Round [167] log likelihood: -493848.469365
EM: Round [168] log likelihood: -493848.469235
EM: Round [169] log likelihood: -493848.469109
EM: Round [170] log likelihood: -493848.468986
EM: Round [171] log likelihood: -493848.468867
EM: Round [172] log likelihood: -493848.468751
EM: Round [173] log likelihood: -493848.468637
EM: Round [174] log likelihood: -493848.468527
EM: Round [175] log likelihood: -493848.468420
EM: Round [176] log likelihood: -493848.468315
EM: Round [177] log likelihood: -493848.468214
EM: Round [178] log likelihood: -493848.468114
EM: Stopping iterations at round 178 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -494871.560224
EM: Round [1] log likelihood: -493939.250951
EM: Round [2] log likelihood: -493642.671471
EM: Round [3] log likelihood: -493514.690709
EM: Round [4] log likelihood: -493450.242679
EM: Round [5] log likelihood: -493414.748848
EM: Round [6] log likelihood: -493393.897607
EM: Round [7] log likelihood: -493380.960619
EM: Round [8] log likelihood: -493372.533425
EM: Round [9] log likelihood: -493366.801482
EM: Round [10] log likelihood: -493362.753217
EM: Round [11] log likelihood: -493359.800355
EM: Round [12] log likelihood: -493357.586744
EM: Round [13] log likelihood: -493355.888449
EM: Round [14] log likelihood: -493354.559666
EM: Round [15] log likelihood: -493353.502408
EM: Round [16] log likelihood: -493352.648934
EM: Round [17] log likelihood: -493351.951232
EM: Round [18] log likelihood: -493351.374519
EM: Round [19] log likelihood: -493350.893105
EM: Round [20] log likelihood: -493350.487694
EM: Round [21] log likelihood: -493350.143573
EM: Round [22] log likelihood: -493349.849373
EM: Round [23] log likelihood: -493349.596200
EM: Round [24] log likelihood: -493349.377024
EM: Round [25] log likelihood: -493349.186231
EM: Round [26] log likelihood: -493349.019296
EM: Round [27] log likelihood: -493348.872543
EM: Round [28] log likelihood: -493348.742965
EM: Round [29] log likelihood: -493348.628080
EM: Round [30] log likelihood: -493348.525829
EM: Round [31] log likelihood: -493348.434493
EM: Round [32] log likelihood: -493348.352630
EM: Round [33] log likelihood: -493348.279023
EM: Round [34] log likelihood: -493348.212639
EM: Round [35] log likelihood: -493348.152597
EM: Round [36] log likelihood: -493348.098147
EM: Round [37] log likelihood: -493348.048640
EM: Round [38] log likelihood: -493348.003520
EM: Round [39] log likelihood: -493347.962304
EM: Round [40] log likelihood: -493347.924573
EM: Round [41] log likelihood: -493347.889961
EM: Round [42] log likelihood: -493347.858148
EM: Round [43] log likelihood: -493347.828854
EM: Round [44] log likelihood: -493347.801834
EM: Round [45] log likelihood: -493347.776868
EM: Round [46] log likelihood: -493347.753765
EM: Round [47] log likelihood: -493347.732354
EM: Round [48] log likelihood: -493347.712482
EM: Round [49] log likelihood: -493347.694014
EM: Round [50] log likelihood: -493347.676830
EM: Round [51] log likelihood: -493347.660820
EM: Round [52] log likelihood: -493347.645887
EM: Round [53] log likelihood: -493347.631944
EM: Round [54] log likelihood: -493347.618911
EM: Round [55] log likelihood: -493347.606716
EM: Round [56] log likelihood: -493347.595295
EM: Round [57] log likelihood: -493347.584589
EM: Round [58] log likelihood: -493347.574544
EM: Round [59] log likelihood: -493347.565112
EM: Round [60] log likelihood: -493347.556249
EM: Round [61] log likelihood: -493347.547914
EM: Round [62] log likelihood: -493347.540069
EM: Round [63] log likelihood: -493347.532681
EM: Round [64] log likelihood: -493347.525718
EM: Round [65] log likelihood: -493347.519152
EM: Round [66] log likelihood: -493347.512956
EM: Round [67] log likelihood: -493347.507106
EM: Round [68] log likelihood: -493347.501579
EM: Round [69] log likelihood: -493347.496355
EM: Round [70] log likelihood: -493347.491414
EM: Round [71] log likelihood: -493347.486738
EM: Round [72] log likelihood: -493347.482311
EM: Round [73] log likelihood: -493347.478118
EM: Round [74] log likelihood: -493347.474145
EM: Round [75] log likelihood: -493347.470377
EM: Round [76] log likelihood: -493347.466804
EM: Round [77] log likelihood: -493347.463413
EM: Round [78] log likelihood: -493347.460193
EM: Round [79] log likelihood: -493347.457135
EM: Round [80] log likelihood: -493347.454230
EM: Round [81] log likelihood: -493347.451468
EM: Round [82] log likelihood: -493347.448842
EM: Round [83] log likelihood: -493347.446344
EM: Round [84] log likelihood: -493347.443966
EM: Round [85] log likelihood: -493347.441703
EM: Round [86] log likelihood: -493347.439548
EM: Round [87] log likelihood: -493347.437494
EM: Round [88] log likelihood: -493347.435537
EM: Round [89] log likelihood: -493347.433671
EM: Round [90] log likelihood: -493347.431892
EM: Round [91] log likelihood: -493347.430194
EM: Round [92] log likelihood: -493347.428574
EM: Round [93] log likelihood: -493347.427028
EM: Round [94] log likelihood: -493347.425551
EM: Round [95] log likelihood: -493347.424140
EM: Round [96] log likelihood: -493347.422792
EM: Round [97] log likelihood: -493347.421504
EM: Round [98] log likelihood: -493347.420272
EM: Round [99] log likelihood: -493347.419093
EM: Round [100] log likelihood: -493347.417966
EM: Round [101] log likelihood: -493347.416887
EM: Round [102] log likelihood: -493347.415854
EM: Round [103] log likelihood: -493347.414865
EM: Round [104] log likelihood: -493347.413917
EM: Round [105] log likelihood: -493347.413009
EM: Round [106] log likelihood: -493347.412139
EM: Round [107] log likelihood: -493347.411305
EM: Round [108] log likelihood: -493347.410505
EM: Round [109] log likelihood: -493347.409737
EM: Round [110] log likelihood: -493347.409001
EM: Round [111] log likelihood: -493347.408294
EM: Round [112] log likelihood: -493347.407615
EM: Round [113] log likelihood: -493347.406964
EM: Round [114] log likelihood: -493347.406338
EM: Round [115] log likelihood: -493347.405736
EM: Round [116] log likelihood: -493347.405158
EM: Round [117] log likelihood: -493347.404602
EM: Round [118] log likelihood: -493347.404067
EM: Round [119] log likelihood: -493347.403553
EM: Round [120] log likelihood: -493347.403058
EM: Round [121] log likelihood: -493347.402582
EM: Round [122] log likelihood: -493347.402123
EM: Round [123] log likelihood: -493347.401682
EM: Round [124] log likelihood: -493347.401256
EM: Round [125] log likelihood: -493347.400847
EM: Round [126] log likelihood: -493347.400452
EM: Round [127] log likelihood: -493347.400071
EM: Round [128] log likelihood: -493347.399704
EM: Round [129] log likelihood: -493347.399350
EM: Round [130] log likelihood: -493347.399008
EM: Round [131] log likelihood: -493347.398679
EM: Round [132] log likelihood: -493347.398360
EM: Round [133] log likelihood: -493347.398053
EM: Round [134] log likelihood: -493347.397757
EM: Round [135] log likelihood: -493347.397470
EM: Round [136] log likelihood: -493347.397193
EM: Round [137] log likelihood: -493347.396926
EM: Round [138] log likelihood: -493347.396667
EM: Round [139] log likelihood: -493347.396417
EM: Round [140] log likelihood: -493347.396175
EM: Round [141] log likelihood: -493347.395941
EM: Round [142] log likelihood: -493347.395714
EM: Round [143] log likelihood: -493347.395495
EM: Round [144] log likelihood: -493347.395283
EM: Round [145] log likelihood: -493347.395077
EM: Round [146] log likelihood: -493347.394878
EM: Round [147] log likelihood: -493347.394685
EM: Round [148] log likelihood: -493347.394499
EM: Round [149] log likelihood: -493347.394318
EM: Round [150] log likelihood: -493347.394142
EM: Round [151] log likelihood: -493347.393972
EM: Round [152] log likelihood: -493347.393806
EM: Round [153] log likelihood: -493347.393646
EM: Round [154] log likelihood: -493347.393491
EM: Round [155] log likelihood: -493347.393340
EM: Round [156] log likelihood: -493347.393193
EM: Round [157] log likelihood: -493347.393051
EM: Round [158] log likelihood: -493347.392913
EM: Round [159] log likelihood: -493347.392779
EM: Round [160] log likelihood: -493347.392648
EM: Round [161] log likelihood: -493347.392522
EM: Round [162] log likelihood: -493347.392398
EM: Round [163] log likelihood: -493347.392279
EM: Round [164] log likelihood: -493347.392162
EM: Round [165] log likelihood: -493347.392049
EM: Round [166] log likelihood: -493347.391939
EM: Round [167] log likelihood: -493347.391831
EM: Round [168] log likelihood: -493347.391727
EM: Round [169] log likelihood: -493347.391625
EM: Round [170] log likelihood: -493347.391526
EM: Stopping iterations at round 170 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.aQkiPLPjMf/./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.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.aQkiPLPjMf/./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.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 45879746 > /tmp/nxf.aQkiPLPjMf/./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.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir > /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir --annotate /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.aQkiPLPjMf/./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.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir
-done, see /tmp/nxf.aQkiPLPjMf/./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.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.aQkiPLPjMf/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 619, filtered: 6777)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.aQkiPLPjMf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.aQkiPLPjMf/./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.aQkiPLPjMf/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
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WARNING, no entry stored in dbm for [ENSG00000253187.2]
WARNING, no entry stored in dbm for [ENSG00000272677.1]
WARNING, no entry stored in dbm for [ENSG00000229367.1]
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 [ENSG00000285806.1]
WARNING, no entry stored in dbm for [ENSG00000181126.13]
WARNING, no entry stored in dbm for [ENSG00000275834.1]
WARNING, no entry stored in dbm for [ENSG00000276550.4]
WARNING, no entry stored in dbm for [ENSG00000203875.13]
WARNING, no entry stored in dbm for [ENSG00000226877.9]
WARNING, no entry stored in dbm for [ENSG00000228393.4]
WARNING, no entry stored in dbm for [ENSG00000214433.4]
WARNING, no entry stored in dbm for [ENSG00000237187.9]
WARNING, no entry stored in dbm for [ENSG00000251504.1]
WARNING, no entry stored in dbm for [ENSG00000283103.3]
WARNING, no entry stored in dbm for [ENSG00000287032.1]
WARNING, no entry stored in dbm for [ENSG00000219201.4]
WARNING, no entry stored in dbm for [ENSG00000228021.7]
WARNING, no entry stored in dbm for [ENSG00000231971.6]
WARNING, no entry stored in dbm for [ENSG00000080947.15]
WARNING, no entry stored in dbm for [ENSG00000266962.2]
WARNING, no entry stored in dbm for [ENSG00000288093.1]
WARNING, no entry stored in dbm for [ENSG00000204177.10]
WARNING, no entry stored in dbm for [ENSG00000222094.1]
WARNING, no entry stored in dbm for [ENSG00000287063.1]
WARNING, no entry stored in dbm for [ENSG00000260879.1]
WARNING, no entry stored in dbm for [ENSG00000271459.1]
WARNING, no entry stored in dbm for [ENSG00000234318.1]
WARNING, no entry stored in dbm for [ENSG00000240751.1]
WARNING, no entry stored in dbm for [ENSG00000225872.4]
WARNING, no entry stored in dbm for [ENSG00000241155.1]
WARNING, no entry stored in dbm for [ENSG00000241155.1]
WARNING, no entry stored in dbm for [ENSG00000248837.7]
WARNING, no entry stored in dbm for [ENSG00000251567.5]
WARNING, no entry stored in dbm for [ENSG00000261028.1]
WARNING, no entry stored in dbm for [ENSG00000261028.1]
WARNING, no entry stored in dbm for [ENSG00000227741.1]
WARNING, no entry stored in dbm for [ENSG00000271860.7]
WARNING, no entry stored in dbm for [ENSG00000285802.1]
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 [ENSG00000271551.2]
WARNING, no entry stored in dbm for [ENSG00000167046.4]
WARNING, no entry stored in dbm for [ENSG00000243289.1]
WARNING, no entry stored in dbm for [ENSG00000261011.1]
WARNING, no entry stored in dbm for [ENSG00000176318.8]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000286830.1]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000224888.4]
WARNING, no entry stored in dbm for [ENSG00000213587.3]
WARNING, no entry stored in dbm for [ENSG00000199395.1]
WARNING, no entry stored in dbm for [ENSG00000213587.3]
WARNING, no entry stored in dbm for [ENSG00000274408.1]
WARNING, no entry stored in dbm for [ENSG00000213587.3]
WARNING, no entry stored in dbm for [ENSG00000223019.1]
WARNING, no entry stored in dbm for [ENSG00000213587.3]
WARNING, no entry stored in dbm for [ENSG00000200275.1]
WARNING, no entry stored in dbm for [ENSG00000286692.1]
WARNING, no entry stored in dbm for [ENSG00000265218.1]
WARNING, no entry stored in dbm for [ENSG00000131484.4]
WARNING, no entry stored in dbm for [ENSG00000232760.1]
WARNING, no entry stored in dbm for [ENSG00000232626.3]
WARNING, no entry stored in dbm for [ENSG00000286152.1]
WARNING, no entry stored in dbm for [ENSG00000213250.5]
WARNING, no entry stored in dbm for [ENSG00000248126.1]
WARNING, no entry stored in dbm for [ENSG00000273391.1]
WARNING, no entry stored in dbm for [ENSG00000263823.1]
WARNING, no entry stored in dbm for [ENSG00000279861.1]
WARNING, no entry stored in dbm for [ENSG00000254951.7]
WARNING, no entry stored in dbm for [ENSG00000249722.1]
WARNING, no entry stored in dbm for [ENSG00000250764.1]
WARNING, no entry stored in dbm for [ENSG00000236283.5]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000274499.1]
WARNING, no entry stored in dbm for [ENSG00000238045.9]
WARNING, no entry stored in dbm for [ENSG00000233175.2]
WARNING, no entry stored in dbm for [ENSG00000233175.2]
WARNING, no entry stored in dbm for [ENSG00000280007.1]
WARNING, no entry stored in dbm for [ENSG00000239467.6]
WARNING, no entry stored in dbm for [ENSG00000259577.2]
WARNING, no entry stored in dbm for [ENSG00000233891.8]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000267207.1]


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