-ctat genome lib [/tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.T6UnOicKZf/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary
-sample contains 84632120 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir -J /tmp/nxf.T6UnOicKZf/tih_rna_sample_00422_23H5VFLT4_s47.Chimeric.out.junction -O /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.T6UnOicKZf/tih_rna_sample_00422_23H5VFLT4_s47.Chimeric.out.junction
-building interval tree based on /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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[1180000], rate=70168.48/min -building interval tree based on /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=66666.67/min
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[1180000], rate=65921.79/min -building interval tree based on /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=150000.00/min
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[1170000], rate=61471.10/min -building interval tree based on /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=120000.00/min
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[30000], rate=138461.54/min
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[1170000], rate=59541.98/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir --filt_file /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
6000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
5000000.00 reads per min processed...
5142857.14 reads per min processed...
4666666.67 reads per min processed...
4800000.00 reads per min processed...
4500000.00 reads per min processed...
4615384.62 reads per min processed...
4400000.00 reads per min processed...
4500000.00 reads per min processed...
4333333.33 reads per min processed...
4200000.00 reads per min processed...
4285714.29 reads per min processed...
4173913.04 reads per min processed...
4250000.00 reads per min processed...
4153846.15 reads per min processed...
4222222.22 reads per min processed...
4137931.03 reads per min processed...
4200000.00 reads per min processed...
4125000.00 reads per min processed...
4181818.18 reads per min processed...
4363636.36 reads per min processed...
4411764.71 reads per min processed...
4333333.33 reads per min processed...
4378378.38 reads per min processed...
4421052.63 reads per min processed...
4350000.00 reads per min processed...
4390243.90 reads per min processed...
4325581.40 reads per min processed...
4363636.36 reads per min processed...
4400000.00 reads per min processed...
4340425.53 reads per min processed...
4285714.29 reads per min processed...
4235294.12 reads per min processed...
4269230.77 reads per min processed...
4301886.79 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.T6UnOicKZf/tih_rna_sample_00422_23H5VFLT4_s47.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.T6UnOicKZf/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -113876.034307
EM: Round [1] log likelihood: -113780.602152
EM: Round [2] log likelihood: -113743.350704
EM: Round [3] log likelihood: -113725.174946
EM: Round [4] log likelihood: -113715.373238
EM: Round [5] log likelihood: -113709.773619
EM: Round [6] log likelihood: -113706.430757
EM: Round [7] log likelihood: -113704.350630
EM: Round [8] log likelihood: -113703.000712
EM: Round [9] log likelihood: -113702.087514
EM: Round [10] log likelihood: -113701.445116
EM: Round [11] log likelihood: -113700.976979
EM: Round [12] log likelihood: -113700.625093
EM: Round [13] log likelihood: -113700.353394
EM: Round [14] log likelihood: -113700.138704
EM: Round [15] log likelihood: -113699.965640
EM: Round [16] log likelihood: -113699.823695
EM: Round [17] log likelihood: -113699.705498
EM: Round [18] log likelihood: -113699.605754
EM: Round [19] log likelihood: -113699.520581
EM: Round [20] log likelihood: -113699.447081
EM: Round [21] log likelihood: -113699.383050
EM: Round [22] log likelihood: -113699.326794
EM: Round [23] log likelihood: -113699.276987
EM: Round [24] log likelihood: -113699.232585
EM: Round [25] log likelihood: -113699.192751
EM: Round [26] log likelihood: -113699.156812
EM: Round [27] log likelihood: -113699.124222
EM: Round [28] log likelihood: -113699.094530
EM: Round [29] log likelihood: -113699.067364
EM: Round [30] log likelihood: -113699.042415
EM: Round [31] log likelihood: -113699.019424
EM: Round [32] log likelihood: -113698.998171
EM: Round [33] log likelihood: -113698.978469
EM: Round [34] log likelihood: -113698.960160
EM: Round [35] log likelihood: -113698.943105
EM: Round [36] log likelihood: -113698.927186
EM: Round [37] log likelihood: -113698.912301
EM: Round [38] log likelihood: -113698.898358
EM: Round [39] log likelihood: -113698.885277
EM: Round [40] log likelihood: -113698.872990
EM: Round [41] log likelihood: -113698.861433
EM: Round [42] log likelihood: -113698.850551
EM: Round [43] log likelihood: -113698.840293
EM: Round [44] log likelihood: -113698.830615
EM: Round [45] log likelihood: -113698.821477
EM: Round [46] log likelihood: -113698.812841
EM: Round [47] log likelihood: -113698.804673
EM: Round [48] log likelihood: -113698.796945
EM: Round [49] log likelihood: -113698.789627
EM: Round [50] log likelihood: -113698.782693
EM: Round [51] log likelihood: -113698.776121
EM: Round [52] log likelihood: -113698.769888
EM: Round [53] log likelihood: -113698.763974
EM: Round [54] log likelihood: -113698.758361
EM: Round [55] log likelihood: -113698.753030
EM: Round [56] log likelihood: -113698.747967
EM: Round [57] log likelihood: -113698.743155
EM: Round [58] log likelihood: -113698.738581
EM: Round [59] log likelihood: -113698.734231
EM: Round [60] log likelihood: -113698.730094
EM: Round [61] log likelihood: -113698.726158
EM: Round [62] log likelihood: -113698.722411
EM: Round [63] log likelihood: -113698.718845
EM: Round [64] log likelihood: -113698.715449
EM: Round [65] log likelihood: -113698.712214
EM: Round [66] log likelihood: -113698.709133
EM: Round [67] log likelihood: -113698.706196
EM: Round [68] log likelihood: -113698.703398
EM: Round [69] log likelihood: -113698.700730
EM: Round [70] log likelihood: -113698.698186
EM: Round [71] log likelihood: -113698.695759
EM: Round [72] log likelihood: -113698.693445
EM: Round [73] log likelihood: -113698.691237
EM: Round [74] log likelihood: -113698.689130
EM: Round [75] log likelihood: -113698.687118
EM: Round [76] log likelihood: -113698.685198
EM: Round [77] log likelihood: -113698.683365
EM: Round [78] log likelihood: -113698.681615
EM: Round [79] log likelihood: -113698.679942
EM: Round [80] log likelihood: -113698.678345
EM: Round [81] log likelihood: -113698.676819
EM: Round [82] log likelihood: -113698.675360
EM: Round [83] log likelihood: -113698.673966
EM: Round [84] log likelihood: -113698.672634
EM: Round [85] log likelihood: -113698.671360
EM: Round [86] log likelihood: -113698.670141
EM: Round [87] log likelihood: -113698.668976
EM: Round [88] log likelihood: -113698.667861
EM: Round [89] log likelihood: -113698.666795
EM: Round [90] log likelihood: -113698.665775
EM: Round [91] log likelihood: -113698.664798
EM: Round [92] log likelihood: -113698.663864
EM: Round [93] log likelihood: -113698.662969
EM: Round [94] log likelihood: -113698.662113
EM: Round [95] log likelihood: -113698.661292
EM: Round [96] log likelihood: -113698.660507
EM: Round [97] log likelihood: -113698.659754
EM: Round [98] log likelihood: -113698.659034
EM: Round [99] log likelihood: -113698.658343
EM: Round [100] log likelihood: -113698.657681
EM: Round [101] log likelihood: -113698.657047
EM: Round [102] log likelihood: -113698.656439
EM: Round [103] log likelihood: -113698.655856
EM: Round [104] log likelihood: -113698.655297
EM: Round [105] log likelihood: -113698.654761
EM: Round [106] log likelihood: -113698.654247
EM: Round [107] log likelihood: -113698.653754
EM: Round [108] log likelihood: -113698.653281
EM: Round [109] log likelihood: -113698.652828
EM: Round [110] log likelihood: -113698.652392
EM: Round [111] log likelihood: -113698.651974
EM: Round [112] log likelihood: -113698.651573
EM: Round [113] log likelihood: -113698.651188
EM: Round [114] log likelihood: -113698.650818
EM: Round [115] log likelihood: -113698.650462
EM: Round [116] log likelihood: -113698.650121
EM: Round [117] log likelihood: -113698.649794
EM: Round [118] log likelihood: -113698.649479
EM: Round [119] log likelihood: -113698.649176
EM: Round [120] log likelihood: -113698.648886
EM: Round [121] log likelihood: -113698.648606
EM: Round [122] log likelihood: -113698.648337
EM: Round [123] log likelihood: -113698.648079
EM: Round [124] log likelihood: -113698.647831
EM: Round [125] log likelihood: -113698.647592
EM: Round [126] log likelihood: -113698.647362
EM: Round [127] log likelihood: -113698.647142
EM: Round [128] log likelihood: -113698.646929
EM: Round [129] log likelihood: -113698.646724
EM: Round [130] log likelihood: -113698.646528
EM: Round [131] log likelihood: -113698.646338
EM: Round [132] log likelihood: -113698.646156
EM: Round [133] log likelihood: -113698.645980
EM: Round [134] log likelihood: -113698.645811
EM: Round [135] log likelihood: -113698.645648
EM: Round [136] log likelihood: -113698.645491
EM: Round [137] log likelihood: -113698.645340
EM: Round [138] log likelihood: -113698.645195
EM: Round [139] log likelihood: -113698.645054
EM: Round [140] log likelihood: -113698.644919
EM: Round [141] log likelihood: -113698.644789
EM: Round [142] log likelihood: -113698.644663
EM: Round [143] log likelihood: -113698.644542
EM: Round [144] log likelihood: -113698.644425
EM: Round [145] log likelihood: -113698.644313
EM: Round [146] log likelihood: -113698.644204
EM: Round [147] log likelihood: -113698.644099
EM: Round [148] log likelihood: -113698.643998
EM: Round [149] log likelihood: -113698.643900
EM: Stopping iterations at round 149 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -113772.796653
EM: Round [1] log likelihood: -113687.835527
EM: Round [2] log likelihood: -113655.566620
EM: Round [3] log likelihood: -113639.882458
EM: Round [4] log likelihood: -113631.382891
EM: Round [5] log likelihood: -113626.506057
EM: Round [6] log likelihood: -113623.589759
EM: Round [7] log likelihood: -113621.775061
EM: Round [8] log likelihood: -113620.597590
EM: Round [9] log likelihood: -113619.800390
EM: Round [10] log likelihood: -113619.238237
EM: Round [11] log likelihood: -113618.826885
EM: Round [12] log likelihood: -113618.515934
EM: Round [13] log likelihood: -113618.274205
EM: Round [14] log likelihood: -113618.081742
EM: Round [15] log likelihood: -113617.925349
EM: Round [16] log likelihood: -113617.796025
EM: Round [17] log likelihood: -113617.687465
EM: Round [18] log likelihood: -113617.595133
EM: Round [19] log likelihood: -113617.515699
EM: Round [20] log likelihood: -113617.446667
EM: Round [21] log likelihood: -113617.386134
EM: Round [22] log likelihood: -113617.332629
EM: Round [23] log likelihood: -113617.284996
EM: Round [24] log likelihood: -113617.242317
EM: Round [25] log likelihood: -113617.203855
EM: Round [26] log likelihood: -113617.169013
EM: Round [27] log likelihood: -113617.137300
EM: Round [28] log likelihood: -113617.108314
EM: Round [29] log likelihood: -113617.081717
EM: Round [30] log likelihood: -113617.057228
EM: Round [31] log likelihood: -113617.034609
EM: Round [32] log likelihood: -113617.013658
EM: Round [33] log likelihood: -113616.994203
EM: Round [34] log likelihood: -113616.976095
EM: Round [35] log likelihood: -113616.959205
EM: Round [36] log likelihood: -113616.943422
EM: Round [37] log likelihood: -113616.928648
EM: Round [38] log likelihood: -113616.914797
EM: Round [39] log likelihood: -113616.901793
EM: Round [40] log likelihood: -113616.889569
EM: Round [41] log likelihood: -113616.878064
EM: Round [42] log likelihood: -113616.867226
EM: Round [43] log likelihood: -113616.857005
EM: Round [44] log likelihood: -113616.847359
EM: Round [45] log likelihood: -113616.838246
EM: Round [46] log likelihood: -113616.829632
EM: Round [47] log likelihood: -113616.821484
EM: Round [48] log likelihood: -113616.813772
EM: Round [49] log likelihood: -113616.806468
EM: Round [50] log likelihood: -113616.799546
EM: Round [51] log likelihood: -113616.792984
EM: Round [52] log likelihood: -113616.786760
EM: Round [53] log likelihood: -113616.780854
EM: Round [54] log likelihood: -113616.775247
EM: Round [55] log likelihood: -113616.769923
EM: Round [56] log likelihood: -113616.764864
EM: Round [57] log likelihood: -113616.760057
EM: Round [58] log likelihood: -113616.755487
EM: Round [59] log likelihood: -113616.751141
EM: Round [60] log likelihood: -113616.747007
EM: Round [61] log likelihood: -113616.743074
EM: Round [62] log likelihood: -113616.739330
EM: Round [63] log likelihood: -113616.735766
EM: Round [64] log likelihood: -113616.732372
EM: Round [65] log likelihood: -113616.729140
EM: Round [66] log likelihood: -113616.726060
EM: Round [67] log likelihood: -113616.723125
EM: Round [68] log likelihood: -113616.720328
EM: Round [69] log likelihood: -113616.717661
EM: Round [70] log likelihood: -113616.715119
EM: Round [71] log likelihood: -113616.712694
EM: Round [72] log likelihood: -113616.710380
EM: Round [73] log likelihood: -113616.708173
EM: Round [74] log likelihood: -113616.706067
EM: Round [75] log likelihood: -113616.704056
EM: Round [76] log likelihood: -113616.702137
EM: Round [77] log likelihood: -113616.700305
EM: Round [78] log likelihood: -113616.698555
EM: Round [79] log likelihood: -113616.696883
EM: Round [80] log likelihood: -113616.695287
EM: Round [81] log likelihood: -113616.693761
EM: Round [82] log likelihood: -113616.692303
EM: Round [83] log likelihood: -113616.690910
EM: Round [84] log likelihood: -113616.689577
EM: Round [85] log likelihood: -113616.688304
EM: Round [86] log likelihood: -113616.687086
EM: Round [87] log likelihood: -113616.685921
EM: Round [88] log likelihood: -113616.684807
EM: Round [89] log likelihood: -113616.683741
EM: Round [90] log likelihood: -113616.682721
EM: Round [91] log likelihood: -113616.681745
EM: Round [92] log likelihood: -113616.680810
EM: Round [93] log likelihood: -113616.679916
EM: Round [94] log likelihood: -113616.679060
EM: Round [95] log likelihood: -113616.678240
EM: Round [96] log likelihood: -113616.677454
EM: Round [97] log likelihood: -113616.676702
EM: Round [98] log likelihood: -113616.675982
EM: Round [99] log likelihood: -113616.675291
EM: Round [100] log likelihood: -113616.674630
EM: Round [101] log likelihood: -113616.673995
EM: Round [102] log likelihood: -113616.673388
EM: Round [103] log likelihood: -113616.672805
EM: Round [104] log likelihood: -113616.672246
EM: Round [105] log likelihood: -113616.671711
EM: Round [106] log likelihood: -113616.671197
EM: Round [107] log likelihood: -113616.670704
EM: Round [108] log likelihood: -113616.670231
EM: Round [109] log likelihood: -113616.669777
EM: Round [110] log likelihood: -113616.669342
EM: Round [111] log likelihood: -113616.668924
EM: Round [112] log likelihood: -113616.668523
EM: Round [113] log likelihood: -113616.668137
EM: Round [114] log likelihood: -113616.667768
EM: Round [115] log likelihood: -113616.667413
EM: Round [116] log likelihood: -113616.667071
EM: Round [117] log likelihood: -113616.666744
EM: Round [118] log likelihood: -113616.666429
EM: Round [119] log likelihood: -113616.666127
EM: Round [120] log likelihood: -113616.665836
EM: Round [121] log likelihood: -113616.665557
EM: Round [122] log likelihood: -113616.665288
EM: Round [123] log likelihood: -113616.665030
EM: Round [124] log likelihood: -113616.664782
EM: Round [125] log likelihood: -113616.664543
EM: Round [126] log likelihood: -113616.664313
EM: Round [127] log likelihood: -113616.664092
EM: Round [128] log likelihood: -113616.663880
EM: Round [129] log likelihood: -113616.663675
EM: Round [130] log likelihood: -113616.663478
EM: Round [131] log likelihood: -113616.663289
EM: Round [132] log likelihood: -113616.663107
EM: Round [133] log likelihood: -113616.662931
EM: Round [134] log likelihood: -113616.662762
EM: Round [135] log likelihood: -113616.662599
EM: Round [136] log likelihood: -113616.662442
EM: Round [137] log likelihood: -113616.662291
EM: Round [138] log likelihood: -113616.662146
EM: Round [139] log likelihood: -113616.662005
EM: Round [140] log likelihood: -113616.661870
EM: Round [141] log likelihood: -113616.661740
EM: Round [142] log likelihood: -113616.661614
EM: Round [143] log likelihood: -113616.661493
EM: Round [144] log likelihood: -113616.661376
EM: Round [145] log likelihood: -113616.661264
EM: Round [146] log likelihood: -113616.661155
EM: Round [147] log likelihood: -113616.661050
EM: Round [148] log likelihood: -113616.660949
EM: Round [149] log likelihood: -113616.660851
EM: Stopping iterations at round 149 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.T6UnOicKZf/./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.T6UnOicKZf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.T6UnOicKZf/./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.T6UnOicKZf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 84632120 > /tmp/nxf.T6UnOicKZf/./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.T6UnOicKZf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir > /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir --annotate /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.T6UnOicKZf/./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.T6UnOicKZf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir
-done, see /tmp/nxf.T6UnOicKZf/./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.T6UnOicKZf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.T6UnOicKZf/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 880, filtered: 7628)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.T6UnOicKZf/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.T6UnOicKZf/./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.T6UnOicKZf/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000288549.1]
WARNING, no entry stored in dbm for [ENSG00000234880.1]
WARNING, no entry stored in dbm for [ENSG00000228430.9]
WARNING, no entry stored in dbm for [ENSG00000230165.1]
WARNING, no entry stored in dbm for [ENSG00000271330.1]
WARNING, no entry stored in dbm for [ENSG00000224479.6]
WARNING, no entry stored in dbm for [ENSG00000184139.8]
WARNING, no entry stored in dbm for [ENSG00000215869.4]
WARNING, no entry stored in dbm for [ENSG00000202058.1]
WARNING, no entry stored in dbm for [ENSG00000200794.1]
WARNING, no entry stored in dbm for [ENSG00000226622.6]
WARNING, no entry stored in dbm for [ENSG00000200434.1]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000225465.10]
WARNING, no entry stored in dbm for [ENSG00000234715.2]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000272944.1]
WARNING, no entry stored in dbm for [ENSG00000213293.4]
WARNING, no entry stored in dbm for [ENSG00000214748.2]
WARNING, no entry stored in dbm for [ENSG00000267698.1]
WARNING, no entry stored in dbm for [ENSG00000223965.2]
WARNING, no entry stored in dbm for [ENSG00000234420.7]
WARNING, no entry stored in dbm for [ENSG00000213742.7]
WARNING, no entry stored in dbm for [ENSG00000225746.13]
WARNING, no entry stored in dbm for [ENSG00000229968.1]
WARNING, no entry stored in dbm for [ENSG00000222005.9]
WARNING, no entry stored in dbm for [ENSG00000279217.1]
WARNING, no entry stored in dbm for [ENSG00000201339.1]
WARNING, no entry stored in dbm for [ENSG00000260032.2]
WARNING, no entry stored in dbm for [ENSG00000229267.3]
WARNING, no entry stored in dbm for [ENSG00000234961.1]
WARNING, no entry stored in dbm for [ENSG00000282458.1]
WARNING, no entry stored in dbm for [ENSG00000234769.7]
WARNING, no entry stored in dbm for [ENSG00000234769.7]
WARNING, no entry stored in dbm for [ENSG00000213963.6]
WARNING, no entry stored in dbm for [ENSG00000194297.2]
WARNING, no entry stored in dbm for [ENSG00000267128.2]
WARNING, no entry stored in dbm for [ENSG00000267064.2]
WARNING, no entry stored in dbm for [ENSG00000275139.1]
WARNING, no entry stored in dbm for [ENSG00000233247.3]
WARNING, no entry stored in dbm for [ENSG00000237298.10]
WARNING, no entry stored in dbm for [ENSG00000255136.3]
WARNING, no entry stored in dbm for [ENSG00000186825.6]
WARNING, no entry stored in dbm for [ENSG00000262583.1]
WARNING, no entry stored in dbm for [ENSG00000274422.1]
WARNING, no entry stored in dbm for [ENSG00000204623.9]
WARNING, no entry stored in dbm for [ENSG00000235512.1]
WARNING, no entry stored in dbm for [ENSG00000080947.15]
WARNING, no entry stored in dbm for [ENSG00000286936.1]
WARNING, no entry stored in dbm for [ENSG00000205583.13]
WARNING, no entry stored in dbm for [ENSG00000245498.7]
WARNING, no entry stored in dbm for [ENSG00000248508.8]
WARNING, no entry stored in dbm for [ENSG00000227769.7]
WARNING, no entry stored in dbm for [ENSG00000236751.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000203875.13]
WARNING, no entry stored in dbm for [ENSG00000203875.13]
WARNING, no entry stored in dbm for [ENSG00000240877.3]
WARNING, no entry stored in dbm for [ENSG00000240338.6]
WARNING, no entry stored in dbm for [ENSG00000258081.4]
WARNING, no entry stored in dbm for [ENSG00000247925.2]
WARNING, no entry stored in dbm for [ENSG00000199047.3]
WARNING, no entry stored in dbm for [ENSG00000248932.6]
WARNING, no entry stored in dbm for [ENSG00000260083.2]
WARNING, no entry stored in dbm for [ENSG00000226419.8]
WARNING, no entry stored in dbm for [ENSG00000266053.2]
WARNING, no entry stored in dbm for [ENSG00000228463.10]
WARNING, no entry stored in dbm for [ENSG00000228463.10]
WARNING, no entry stored in dbm for [ENSG00000287411.1]
WARNING, no entry stored in dbm for [ENSG00000267342.1]
WARNING, no entry stored in dbm for [ENSG00000224413.1]
WARNING, no entry stored in dbm for [ENSG00000176700.20]
WARNING, no entry stored in dbm for [ENSG00000224897.8]
WARNING, no entry stored in dbm for [ENSG00000227681.5]
WARNING, no entry stored in dbm for [ENSG00000228697.4]
WARNING, no entry stored in dbm for [ENSG00000226356.2]
WARNING, no entry stored in dbm for [ENSG00000244217.1]
WARNING, no entry stored in dbm for [ENSG00000241318.3]
WARNING, no entry stored in dbm for [ENSG00000242071.3]
WARNING, no entry stored in dbm for [ENSG00000220370.1]
WARNING, no entry stored in dbm for [ENSG00000241582.1]
WARNING, no entry stored in dbm for [ENSG00000243964.1]
WARNING, no entry stored in dbm for [ENSG00000213122.4]
WARNING, no entry stored in dbm for [ENSG00000213935.3]
WARNING, no entry stored in dbm for [ENSG00000241129.3]
WARNING, no entry stored in dbm for [ENSG00000226217.1]
WARNING, no entry stored in dbm for [ENSG00000230559.1]
WARNING, no entry stored in dbm for [ENSG00000139239.7]
WARNING, no entry stored in dbm for [ENSG00000206899.1]
WARNING, no entry stored in dbm for [ENSG00000275834.1]
WARNING, no entry stored in dbm for [ENSG00000222969.1]
WARNING, no entry stored in dbm for [ENSG00000201901.1]
WARNING, no entry stored in dbm for [ENSG00000222969.1]
WARNING, no entry stored in dbm for [ENSG00000200673.1]
WARNING, no entry stored in dbm for [ENSG00000222969.1]
WARNING, no entry stored in dbm for [ENSG00000200674.1]
WARNING, no entry stored in dbm for [ENSG00000180525.13]
WARNING, no entry stored in dbm for [ENSG00000224100.1]
WARNING, no entry stored in dbm for [ENSG00000235777.1]
WARNING, no entry stored in dbm for [ENSG00000231404.2]
WARNING, no entry stored in dbm for [ENSG00000283103.3]
WARNING, no entry stored in dbm for [ENSG00000248927.1]
WARNING, no entry stored in dbm for [ENSG00000230510.7]
WARNING, no entry stored in dbm for [ENSG00000232220.2]
WARNING, no entry stored in dbm for [ENSG00000284740.1]
WARNING, no entry stored in dbm for [ENSG00000244257.5]
WARNING, no entry stored in dbm for [ENSG00000227617.9]
WARNING, no entry stored in dbm for [ENSG00000214106.9]
WARNING, no entry stored in dbm for [ENSG00000235605.1]
WARNING, no entry stored in dbm for [ENSG00000253619.1]
WARNING, no entry stored in dbm for [ENSG00000231690.3]
WARNING, no entry stored in dbm for [ENSG00000235823.3]
WARNING, no entry stored in dbm for [ENSG00000236552.2]
WARNING, no entry stored in dbm for [ENSG00000260088.1]
WARNING, no entry stored in dbm for [ENSG00000286907.1]
WARNING, no entry stored in dbm for [ENSG00000229511.1]
WARNING, no entry stored in dbm for [ENSG00000181577.16]
WARNING, no entry stored in dbm for [ENSG00000236596.1]
WARNING, no entry stored in dbm for [ENSG00000279701.1]
WARNING, no entry stored in dbm for [ENSG00000271918.1]
WARNING, no entry stored in dbm for [ENSG00000203825.4]
WARNING, no entry stored in dbm for [ENSG00000203825.4]
WARNING, no entry stored in dbm for [ENSG00000203825.4]
WARNING, no entry stored in dbm for [ENSG00000203825.4]
WARNING, no entry stored in dbm for [ENSG00000224071.1]
WARNING, no entry stored in dbm for [ENSG00000288577.1]
WARNING, no entry stored in dbm for [ENSG00000205360.6]
WARNING, no entry stored in dbm for [ENSG00000234587.1]
WARNING, no entry stored in dbm for [ENSG00000276027.1]
WARNING, no entry stored in dbm for [ENSG00000269929.3]
WARNING, no entry stored in dbm for [ENSG00000172965.17]
WARNING, no entry stored in dbm for [ENSG00000234231.4]
WARNING, no entry stored in dbm for [ENSG00000215417.13]
WARNING, no entry stored in dbm for [ENSG00000285894.2]
WARNING, no entry stored in dbm for [ENSG00000225783.8]
WARNING, no entry stored in dbm for [ENSG00000275708.1]
WARNING, no entry stored in dbm for [ENSG00000234931.1]
WARNING, no entry stored in dbm for [ENSG00000232709.1]
WARNING, no entry stored in dbm for [ENSG00000267433.1]
WARNING, no entry stored in dbm for [ENSG00000143429.10]
WARNING, no entry stored in dbm for [ENSG00000224893.7]
WARNING, no entry stored in dbm for [ENSG00000234476.3]
WARNING, no entry stored in dbm for [ENSG00000256582.1]
WARNING, no entry stored in dbm for [ENSG00000235160.2]
WARNING, no entry stored in dbm for [ENSG00000232190.3]
WARNING, no entry stored in dbm for [ENSG00000226125.2]
WARNING, no entry stored in dbm for [ENSG00000234948.2]
WARNING, no entry stored in dbm for [ENSG00000237751.2]
WARNING, no entry stored in dbm for [ENSG00000260807.7]
WARNING, no entry stored in dbm for [ENSG00000228794.10]
WARNING, no entry stored in dbm for [ENSG00000175772.11]
WARNING, no entry stored in dbm for [ENSG00000249346.7]
WARNING, no entry stored in dbm for [ENSG00000182648.13]
WARNING, no entry stored in dbm for [ENSG00000225269.3]
WARNING, no entry stored in dbm for [ENSG00000269220.1]
WARNING, no entry stored in dbm for [ENSG00000188185.13]
WARNING, no entry stored in dbm for [ENSG00000283945.1]
WARNING, no entry stored in dbm for [ENSG00000276758.1]
WARNING, no entry stored in dbm for [ENSG00000261303.6]
WARNING, no entry stored in dbm for [ENSG00000229957.1]
WARNING, no entry stored in dbm for [ENSG00000260776.6]
WARNING, no entry stored in dbm for [ENSG00000232000.3]
WARNING, no entry stored in dbm for [ENSG00000258847.1]
WARNING, no entry stored in dbm for [ENSG00000187847.4]
WARNING, no entry stored in dbm for [ENSG00000189223.15]
WARNING, no entry stored in dbm for [ENSG00000267007.1]
WARNING, no entry stored in dbm for [ENSG00000243945.1]
WARNING, no entry stored in dbm for [ENSG00000235864.1]
WARNING, no entry stored in dbm for [ENSG00000235217.6]
WARNING, no entry stored in dbm for [ENSG00000251557.2]
WARNING, no entry stored in dbm for [ENSG00000233680.4]
WARNING, no entry stored in dbm for [ENSG00000243188.1]
WARNING, no entry stored in dbm for [ENSG00000267801.1]
WARNING, no entry stored in dbm for [ENSG00000250980.1]
WARNING, no entry stored in dbm for [ENSG00000247498.10]
WARNING, no entry stored in dbm for [ENSG00000255621.1]
WARNING, no entry stored in dbm for [ENSG00000234420.7]
WARNING, no entry stored in dbm for [ENSG00000204091.8]
WARNING, no entry stored in dbm for [ENSG00000235590.7]
WARNING, no entry stored in dbm for [ENSG00000224692.1]
WARNING, no entry stored in dbm for [ENSG00000200434.1]
WARNING, no entry stored in dbm for [ENSG00000234285.1]
WARNING, no entry stored in dbm for [ENSG00000254349.6]
WARNING, no entry stored in dbm for [ENSG00000265374.1]
WARNING, no entry stored in dbm for [ENSG00000228264.1]
WARNING, no entry stored in dbm for [ENSG00000180769.10]
WARNING, no entry stored in dbm for [ENSG00000212855.5]
WARNING, no entry stored in dbm for [ENSG00000286217.2]
WARNING, no entry stored in dbm for [ENSG00000108958.4]
WARNING, no entry stored in dbm for [ENSG00000224032.7]
WARNING, no entry stored in dbm for [ENSG00000184991.3]
WARNING, no entry stored in dbm for [ENSG00000232015.2]
WARNING, no entry stored in dbm for [ENSG00000236493.2]
WARNING, no entry stored in dbm for [ENSG00000263883.1]
WARNING, no entry stored in dbm for [ENSG00000285825.2]
WARNING, no entry stored in dbm for [ENSG00000216906.2]
WARNING, no entry stored in dbm for [ENSG00000287376.1]
WARNING, no entry stored in dbm for [ENSG00000226954.1]
WARNING, no entry stored in dbm for [ENSG00000237125.11]
WARNING, no entry stored in dbm for [ENSG00000236493.2]
WARNING, no entry stored in dbm for [ENSG00000279066.1]
WARNING, no entry stored in dbm for [ENSG00000226625.1]
WARNING, no entry stored in dbm for [ENSG00000239828.7]
WARNING, no entry stored in dbm for [ENSG00000225889.9]
WARNING, no entry stored in dbm for [ENSG00000249691.1]
WARNING, no entry stored in dbm for [ENSG00000088340.17]
WARNING, no entry stored in dbm for [ENSG00000212664.5]
WARNING, no entry stored in dbm for [ENSG00000231412.2]
WARNING, no entry stored in dbm for [ENSG00000240498.9]
WARNING, no entry stored in dbm for [ENSG00000239622.1]
WARNING, no entry stored in dbm for [ENSG00000287390.1]
WARNING, no entry stored in dbm for [ENSG00000285551.2]
WARNING, no entry stored in dbm for [ENSG00000261670.1]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000182586.9]
WARNING, no entry stored in dbm for [ENSG00000256422.6]
WARNING, no entry stored in dbm for [ENSG00000188511.12]
WARNING, no entry stored in dbm for [ENSG00000225746.13]
WARNING, no entry stored in dbm for [ENSG00000251079.6]
WARNING, no entry stored in dbm for [ENSG00000279022.1]
WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [ENSG00000232489.1]
WARNING, no entry stored in dbm for [ENSG00000254837.2]
WARNING, no entry stored in dbm for [ENSG00000242125.3]
WARNING, no entry stored in dbm for [ENSG00000213371.4]
WARNING, no entry stored in dbm for [ENSG00000237636.3]
WARNING, no entry stored in dbm for [ENSG00000218476.2]
WARNING, no entry stored in dbm for [ENSG00000187472.4]
WARNING, no entry stored in dbm for [ENSG00000236779.1]
WARNING, no entry stored in dbm for [ENSG00000283907.1]
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 [ENSG00000271277.1]
WARNING, no entry stored in dbm for [ENSG00000234648.1]
WARNING, no entry stored in dbm for [ENSG00000244313.3]
WARNING, no entry stored in dbm for [ENSG00000260000.2]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000288543.1]
WARNING, no entry stored in dbm for [ENSG00000261003.1]
WARNING, no entry stored in dbm for [ENSG00000173209.23]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000242338.6]
WARNING, no entry stored in dbm for [ENSG00000249306.6]
WARNING, no entry stored in dbm for [ENSG00000286912.1]
WARNING, no entry stored in dbm for [ENSG00000240197.1]
WARNING, no entry stored in dbm for [ENSG00000273598.1]
WARNING, no entry stored in dbm for [ENSG00000286830.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000249072.1]
WARNING, no entry stored in dbm for [ENSG00000260261.2]
WARNING, no entry stored in dbm for [ENSG00000253392.3]
WARNING, no entry stored in dbm for [ENSG00000251314.2]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
WARNING, no entry stored in dbm for [ENSG00000271680.1]
WARNING, no entry stored in dbm for [ENSG00000267053.8]
WARNING, no entry stored in dbm for [ENSG00000288633.1]
WARNING, no entry stored in dbm for [ENSG00000264497.1]
WARNING, no entry stored in dbm for [ENSG00000262879.6]
WARNING, no entry stored in dbm for [ENSG00000264164.1]
WARNING, no entry stored in dbm for [ENSG00000225205.5]
WARNING, no entry stored in dbm for [ENSG00000213468.7]
WARNING, no entry stored in dbm for [ENSG00000249228.1]
WARNING, no entry stored in dbm for [ENSG00000237161.4]
WARNING, no entry stored in dbm for [ENSG00000288077.1]
WARNING, no entry stored in dbm for [ENSG00000257817.2]
WARNING, no entry stored in dbm for [ENSG00000273771.1]
WARNING, no entry stored in dbm for [ENSG00000272800.3]
WARNING, no entry stored in dbm for [ENSG00000279649.1]
WARNING, no entry stored in dbm for [ENSG00000287858.1]
WARNING, no entry stored in dbm for [ENSG00000234584.1]
WARNING, no entry stored in dbm for [ENSG00000287306.1]
WARNING, no entry stored in dbm for [ENSG00000234997.2]
WARNING, no entry stored in dbm for [ENSG00000249406.3]
WARNING, no entry stored in dbm for [ENSG00000269473.1]
WARNING, no entry stored in dbm for [ENSG00000225840.2]
WARNING, no entry stored in dbm for [ENSG00000214331.8]
WARNING, no entry stored in dbm for [ENSG00000249637.2]
WARNING, no entry stored in dbm for [ENSG00000267058.1]
WARNING, no entry stored in dbm for [ENSG00000275850.1]
WARNING, no entry stored in dbm for [ENSG00000268205.1]
WARNING, no entry stored in dbm for [ENSG00000239224.3]
WARNING, no entry stored in dbm for [ENSG00000268205.1]
WARNING, no entry stored in dbm for [ENSG00000275878.1]
WARNING, no entry stored in dbm for [ENSG00000268205.1]
WARNING, no entry stored in dbm for [ENSG00000265813.2]
WARNING, no entry stored in dbm for [ENSG00000268205.1]
WARNING, no entry stored in dbm for [ENSG00000275090.1]
WARNING, no entry stored in dbm for [ENSG00000239556.4]
WARNING, no entry stored in dbm for [ENSG00000267328.1]
WARNING, no entry stored in dbm for [ENSG00000230613.1]
WARNING, no entry stored in dbm for [ENSG00000283366.2]
WARNING, no entry stored in dbm for [ENSG00000220804.8]
WARNING, no entry stored in dbm for [ENSG00000228506.2]
WARNING, no entry stored in dbm for [ENSG00000231749.3]
WARNING, no entry stored in dbm for [ENSG00000251595.7]
* STAR-Fusion complete. See output: /tmp/nxf.T6UnOicKZf/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)