-ctat genome lib [/tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.nhLzySAF68/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.nhLzySAF68/./star-fusion.preliminary
-sample contains 106860155 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir -J /tmp/nxf.nhLzySAF68/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -O /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.nhLzySAF68/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Chimeric.out.junction
-building interval tree based on /tmp/nxf.nhLzySAF68/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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[2130000], rate=68746.64/min -building interval tree based on /tmp/nxf.nhLzySAF68/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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[2110000], rate=59886.47/min -building interval tree based on /tmp/nxf.nhLzySAF68/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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[2100000], rate=54973.82/min
[2110000], rate=55067.42/min -building interval tree based on /tmp/nxf.nhLzySAF68/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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[2110000], rate=46906.26/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir --filt_file /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
6000000.00 reads per min processed...
12000000.00 reads per min processed...
9000000.00 reads per min processed...
8000000.00 reads per min processed...
10000000.00 reads per min processed...
9000000.00 reads per min processed...
10500000.00 reads per min processed...
9600000.00 reads per min processed...
10800000.00 reads per min processed...
10000000.00 reads per min processed...
9428571.43 reads per min processed...
9000000.00 reads per min processed...
7800000.00 reads per min processed...
7636363.64 reads per min processed...
7500000.00 reads per min processed...
7384615.38 reads per min processed...
6800000.00 reads per min processed...
6750000.00 reads per min processed...
6705882.35 reads per min processed...
6315789.47 reads per min processed...
6300000.00 reads per min processed...
6285714.29 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
5769230.77 reads per min processed...
5777777.78 reads per min processed...
5586206.90 reads per min processed...
5419354.84 reads per min processed...
5437500.00 reads per min processed...
5454545.45 reads per min processed...
5314285.71 reads per min processed...
5333333.33 reads per min processed...
5351351.35 reads per min processed...
5368421.05 reads per min processed...
5384615.38 reads per min processed...
5268292.68 reads per min processed...
5285714.29 reads per min processed...
5302325.58 reads per min processed...
5318181.82 reads per min processed...
5333333.33 reads per min processed...
5347826.09 reads per min processed...
5361702.13 reads per min processed...
5489361.70 reads per min processed...
5500000.00 reads per min processed...
5625000.00 reads per min processed...
5632653.06 reads per min processed...
5640000.00 reads per min processed...
5760000.00 reads per min processed...
5764705.88 reads per min processed...
5882352.94 reads per min processed...
5773584.91 reads per min processed...
5777777.78 reads per min processed...
5781818.18 reads per min processed...
5785714.29 reads per min processed...
5689655.17 reads per min processed...
5694915.25 reads per min processed...
5700000.00 reads per min processed...
5704918.03 reads per min processed...
5709677.42 reads per min processed...
5714285.71 reads per min processed...
5630769.23 reads per min processed...
5636363.64 reads per min processed...
5558823.53 reads per min processed...
5485714.29 reads per min processed...
5492957.75 reads per min processed...
5424657.53 reads per min processed...
5360000.00 reads per min processed...
5368421.05 reads per min processed...
5376623.38 reads per min processed...
5316455.70 reads per min processed...
5325000.00 reads per min processed...
5333333.33 reads per min processed...
5341463.41 reads per min processed...
5349397.59 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.nhLzySAF68/SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Chimeric.out.junction --tmpdir /tmp --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --max_promiscuity 10 --min_pct_dom_promiscuity 20 --min_novel_junction_support 1 --min_alt_pct_junction 10 --aggregate_novel_junction_dist 5 --min_spanning_frags_only 1 --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -112494.361475
EM: Round [1] log likelihood: -112175.484426
EM: Round [2] log likelihood: -112048.788578
EM: Round [3] log likelihood: -111986.608629
EM: Round [4] log likelihood: -111952.783192
EM: Round [5] log likelihood: -111933.322613
EM: Round [6] log likelihood: -111921.648124
EM: Round [7] log likelihood: -111914.353125
EM: Round [8] log likelihood: -111909.603440
EM: Round [9] log likelihood: -111906.387806
EM: Round [10] log likelihood: -111904.133204
EM: Round [11] log likelihood: -111902.503905
EM: Round [12] log likelihood: -111901.295896
EM: Round [13] log likelihood: -111900.380619
EM: Round [14] log likelihood: -111899.674254
EM: Round [15] log likelihood: -111899.120440
EM: Round [16] log likelihood: -111898.680238
EM: Round [17] log likelihood: -111898.326100
EM: Round [18] log likelihood: -111898.038132
EM: Round [19] log likelihood: -111897.801711
EM: Round [20] log likelihood: -111897.605917
EM: Round [21] log likelihood: -111897.442481
EM: Round [22] log likelihood: -111897.305065
EM: Round [23] log likelihood: -111897.188755
EM: Round [24] log likelihood: -111897.089704
EM: Round [25] log likelihood: -111897.004870
EM: Round [26] log likelihood: -111896.931828
EM: Round [27] log likelihood: -111896.868628
EM: Round [28] log likelihood: -111896.813691
EM: Round [29] log likelihood: -111896.765731
EM: Round [30] log likelihood: -111896.723690
EM: Round [31] log likelihood: -111896.686697
EM: Round [32] log likelihood: -111896.654028
EM: Round [33] log likelihood: -111896.625078
EM: Round [34] log likelihood: -111896.599339
EM: Round [35] log likelihood: -111896.576385
EM: Round [36] log likelihood: -111896.555853
EM: Round [37] log likelihood: -111896.537435
EM: Round [38] log likelihood: -111896.520869
EM: Round [39] log likelihood: -111896.505929
EM: Round [40] log likelihood: -111896.492423
EM: Round [41] log likelihood: -111896.480182
EM: Round [42] log likelihood: -111896.469062
EM: Round [43] log likelihood: -111896.458939
EM: Round [44] log likelihood: -111896.449702
EM: Round [45] log likelihood: -111896.441256
EM: Round [46] log likelihood: -111896.433518
EM: Round [47] log likelihood: -111896.426413
EM: Round [48] log likelihood: -111896.419879
EM: Round [49] log likelihood: -111896.413858
EM: Round [50] log likelihood: -111896.408299
EM: Round [51] log likelihood: -111896.403158
EM: Round [52] log likelihood: -111896.398396
EM: Round [53] log likelihood: -111896.393977
EM: Round [54] log likelihood: -111896.389871
EM: Round [55] log likelihood: -111896.386048
EM: Round [56] log likelihood: -111896.382485
EM: Round [57] log likelihood: -111896.379159
EM: Round [58] log likelihood: -111896.376049
EM: Round [59] log likelihood: -111896.373138
EM: Round [60] log likelihood: -111896.370409
EM: Round [61] log likelihood: -111896.367847
EM: Round [62] log likelihood: -111896.365440
EM: Round [63] log likelihood: -111896.363176
EM: Round [64] log likelihood: -111896.361043
EM: Round [65] log likelihood: -111896.359031
EM: Round [66] log likelihood: -111896.357132
EM: Round [67] log likelihood: -111896.355338
EM: Round [68] log likelihood: -111896.353640
EM: Round [69] log likelihood: -111896.352033
EM: Round [70] log likelihood: -111896.350510
EM: Round [71] log likelihood: -111896.349065
EM: Round [72] log likelihood: -111896.347693
EM: Round [73] log likelihood: -111896.346390
EM: Round [74] log likelihood: -111896.345151
EM: Round [75] log likelihood: -111896.343971
EM: Round [76] log likelihood: -111896.342847
EM: Round [77] log likelihood: -111896.341777
EM: Round [78] log likelihood: -111896.340755
EM: Round [79] log likelihood: -111896.339781
EM: Round [80] log likelihood: -111896.338850
EM: Round [81] log likelihood: -111896.337961
EM: Round [82] log likelihood: -111896.337110
EM: Round [83] log likelihood: -111896.336297
EM: Round [84] log likelihood: -111896.335518
EM: Round [85] log likelihood: -111896.334772
EM: Round [86] log likelihood: -111896.334057
EM: Round [87] log likelihood: -111896.333372
EM: Round [88] log likelihood: -111896.332715
EM: Round [89] log likelihood: -111896.332084
EM: Round [90] log likelihood: -111896.331479
EM: Round [91] log likelihood: -111896.330897
EM: Round [92] log likelihood: -111896.330338
EM: Round [93] log likelihood: -111896.329801
EM: Round [94] log likelihood: -111896.329285
EM: Round [95] log likelihood: -111896.328788
EM: Round [96] log likelihood: -111896.328310
EM: Round [97] log likelihood: -111896.327849
EM: Round [98] log likelihood: -111896.327406
EM: Round [99] log likelihood: -111896.326979
EM: Round [100] log likelihood: -111896.326568
EM: Round [101] log likelihood: -111896.326171
EM: Round [102] log likelihood: -111896.325788
EM: Round [103] log likelihood: -111896.325420
EM: Round [104] log likelihood: -111896.325064
EM: Round [105] log likelihood: -111896.324720
EM: Round [106] log likelihood: -111896.324389
EM: Round [107] log likelihood: -111896.324068
EM: Round [108] log likelihood: -111896.323759
EM: Round [109] log likelihood: -111896.323460
EM: Round [110] log likelihood: -111896.323172
EM: Round [111] log likelihood: -111896.322892
EM: Round [112] log likelihood: -111896.322623
EM: Round [113] log likelihood: -111896.322362
EM: Round [114] log likelihood: -111896.322109
EM: Round [115] log likelihood: -111896.321865
EM: Round [116] log likelihood: -111896.321629
EM: Round [117] log likelihood: -111896.321400
EM: Round [118] log likelihood: -111896.321179
EM: Round [119] log likelihood: -111896.320965
EM: Round [120] log likelihood: -111896.320757
EM: Round [121] log likelihood: -111896.320556
EM: Round [122] log likelihood: -111896.320361
EM: Round [123] log likelihood: -111896.320172
EM: Round [124] log likelihood: -111896.319989
EM: Round [125] log likelihood: -111896.319812
EM: Round [126] log likelihood: -111896.319640
EM: Round [127] log likelihood: -111896.319473
EM: Round [128] log likelihood: -111896.319311
EM: Round [129] log likelihood: -111896.319154
EM: Round [130] log likelihood: -111896.319002
EM: Round [131] log likelihood: -111896.318854
EM: Round [132] log likelihood: -111896.318711
EM: Round [133] log likelihood: -111896.318571
EM: Round [134] log likelihood: -111896.318436
EM: Round [135] log likelihood: -111896.318305
EM: Round [136] log likelihood: -111896.318177
EM: Round [137] log likelihood: -111896.318054
EM: Round [138] log likelihood: -111896.317933
EM: Round [139] log likelihood: -111896.317816
EM: Round [140] log likelihood: -111896.317703
EM: Round [141] log likelihood: -111896.317592
EM: Round [142] log likelihood: -111896.317485
EM: Round [143] log likelihood: -111896.317380
EM: Round [144] log likelihood: -111896.317279
EM: Round [145] log likelihood: -111896.317180
EM: Stopping iterations at round 145 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -112365.910957
EM: Round [1] log likelihood: -112092.139743
EM: Round [2] log likelihood: -111990.174493
EM: Round [3] log likelihood: -111942.121346
EM: Round [4] log likelihood: -111916.625851
EM: Round [5] log likelihood: -111902.200300
EM: Round [6] log likelihood: -111893.651299
EM: Round [7] log likelihood: -111888.359932
EM: Round [8] log likelihood: -111884.940377
EM: Round [9] log likelihood: -111882.638071
EM: Round [10] log likelihood: -111881.029924
EM: Round [11] log likelihood: -111879.870415
EM: Round [12] log likelihood: -111879.011648
EM: Round [13] log likelihood: -111878.361127
EM: Round [14] log likelihood: -111877.858917
EM: Round [15] log likelihood: -111877.464902
EM: Round [16] log likelihood: -111877.151453
EM: Round [17] log likelihood: -111876.899064
EM: Round [18] log likelihood: -111876.693657
EM: Round [19] log likelihood: -111876.524887
EM: Round [20] log likelihood: -111876.385022
EM: Round [21] log likelihood: -111876.268205
EM: Round [22] log likelihood: -111876.169938
EM: Round [23] log likelihood: -111876.086732
EM: Round [24] log likelihood: -111876.015850
EM: Round [25] log likelihood: -111875.955126
EM: Round [26] log likelihood: -111875.902830
EM: Round [27] log likelihood: -111875.857570
EM: Round [28] log likelihood: -111875.818218
EM: Round [29] log likelihood: -111875.783855
EM: Round [30] log likelihood: -111875.753724
EM: Round [31] log likelihood: -111875.727201
EM: Round [32] log likelihood: -111875.703767
EM: Round [33] log likelihood: -111875.682989
EM: Round [34] log likelihood: -111875.664504
EM: Round [35] log likelihood: -111875.648006
EM: Round [36] log likelihood: -111875.633235
EM: Round [37] log likelihood: -111875.619972
EM: Round [38] log likelihood: -111875.608028
EM: Round [39] log likelihood: -111875.597243
EM: Round [40] log likelihood: -111875.587478
EM: Round [41] log likelihood: -111875.578613
EM: Round [42] log likelihood: -111875.570547
EM: Round [43] log likelihood: -111875.563188
EM: Round [44] log likelihood: -111875.556460
EM: Round [45] log likelihood: -111875.550295
EM: Round [46] log likelihood: -111875.544632
EM: Round [47] log likelihood: -111875.539420
EM: Round [48] log likelihood: -111875.534613
EM: Round [49] log likelihood: -111875.530171
EM: Round [50] log likelihood: -111875.526058
EM: Round [51] log likelihood: -111875.522243
EM: Round [52] log likelihood: -111875.518697
EM: Round [53] log likelihood: -111875.515395
EM: Round [54] log likelihood: -111875.512317
EM: Round [55] log likelihood: -111875.509441
EM: Round [56] log likelihood: -111875.506750
EM: Round [57] log likelihood: -111875.504229
EM: Round [58] log likelihood: -111875.501862
EM: Round [59] log likelihood: -111875.499639
EM: Round [60] log likelihood: -111875.497546
EM: Round [61] log likelihood: -111875.495574
EM: Round [62] log likelihood: -111875.493713
EM: Round [63] log likelihood: -111875.491956
EM: Round [64] log likelihood: -111875.490293
EM: Round [65] log likelihood: -111875.488719
EM: Round [66] log likelihood: -111875.487227
EM: Round [67] log likelihood: -111875.485811
EM: Round [68] log likelihood: -111875.484466
EM: Round [69] log likelihood: -111875.483188
EM: Round [70] log likelihood: -111875.481971
EM: Round [71] log likelihood: -111875.480812
EM: Round [72] log likelihood: -111875.479707
EM: Round [73] log likelihood: -111875.478653
EM: Round [74] log likelihood: -111875.477647
EM: Round [75] log likelihood: -111875.476686
EM: Round [76] log likelihood: -111875.475767
EM: Round [77] log likelihood: -111875.474888
EM: Round [78] log likelihood: -111875.474046
EM: Round [79] log likelihood: -111875.473240
EM: Round [80] log likelihood: -111875.472467
EM: Round [81] log likelihood: -111875.471726
EM: Round [82] log likelihood: -111875.471014
EM: Round [83] log likelihood: -111875.470332
EM: Round [84] log likelihood: -111875.469676
EM: Round [85] log likelihood: -111875.469046
EM: Round [86] log likelihood: -111875.468440
EM: Round [87] log likelihood: -111875.467857
EM: Round [88] log likelihood: -111875.467297
EM: Round [89] log likelihood: -111875.466757
EM: Round [90] log likelihood: -111875.466238
EM: Round [91] log likelihood: -111875.465737
EM: Round [92] log likelihood: -111875.465255
EM: Round [93] log likelihood: -111875.464790
EM: Round [94] log likelihood: -111875.464342
EM: Round [95] log likelihood: -111875.463910
EM: Round [96] log likelihood: -111875.463493
EM: Round [97] log likelihood: -111875.463090
EM: Round [98] log likelihood: -111875.462702
EM: Round [99] log likelihood: -111875.462327
EM: Round [100] log likelihood: -111875.461964
EM: Round [101] log likelihood: -111875.461614
EM: Round [102] log likelihood: -111875.461276
EM: Round [103] log likelihood: -111875.460949
EM: Round [104] log likelihood: -111875.460633
EM: Round [105] log likelihood: -111875.460328
EM: Round [106] log likelihood: -111875.460032
EM: Round [107] log likelihood: -111875.459746
EM: Round [108] log likelihood: -111875.459469
EM: Round [109] log likelihood: -111875.459202
EM: Round [110] log likelihood: -111875.458943
EM: Round [111] log likelihood: -111875.458692
EM: Round [112] log likelihood: -111875.458449
EM: Round [113] log likelihood: -111875.458214
EM: Round [114] log likelihood: -111875.457986
EM: Round [115] log likelihood: -111875.457765
EM: Round [116] log likelihood: -111875.457551
EM: Round [117] log likelihood: -111875.457344
EM: Round [118] log likelihood: -111875.457143
EM: Round [119] log likelihood: -111875.456948
EM: Round [120] log likelihood: -111875.456759
EM: Round [121] log likelihood: -111875.456576
EM: Round [122] log likelihood: -111875.456398
EM: Round [123] log likelihood: -111875.456226
EM: Round [124] log likelihood: -111875.456059
EM: Round [125] log likelihood: -111875.455896
EM: Round [126] log likelihood: -111875.455739
EM: Round [127] log likelihood: -111875.455586
EM: Round [128] log likelihood: -111875.455438
EM: Round [129] log likelihood: -111875.455294
EM: Round [130] log likelihood: -111875.455154
EM: Round [131] log likelihood: -111875.455018
EM: Round [132] log likelihood: -111875.454886
EM: Round [133] log likelihood: -111875.454758
EM: Round [134] log likelihood: -111875.454633
EM: Round [135] log likelihood: -111875.454513
EM: Round [136] log likelihood: -111875.454395
EM: Round [137] log likelihood: -111875.454281
EM: Round [138] log likelihood: -111875.454170
EM: Round [139] log likelihood: -111875.454062
EM: Round [140] log likelihood: -111875.453957
EM: Round [141] log likelihood: -111875.453855
EM: Round [142] log likelihood: -111875.453756
EM: Stopping iterations at round 142 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 106860155 > /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir > /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir --annotate /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir
-done, see /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.nhLzySAF68/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 467, filtered: 5219)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.nhLzySAF68/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.nhLzySAF68/./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.nhLzySAF68/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000234715.2]
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WARNING, no entry stored in dbm for [ENSG00000201428.1]
WARNING, no entry stored in dbm for [ENSG00000200047.1]
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WARNING, no entry stored in dbm for [ENSG00000250198.3]
WARNING, no entry stored in dbm for [ENSG00000277654.6]
WARNING, no entry stored in dbm for [ENSG00000286558.1]
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WARNING, no entry stored in dbm for [ENSG00000215448.3]
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WARNING, no entry stored in dbm for [ENSG00000255875.2]
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WARNING, no entry stored in dbm for [ENSG00000254453.1]
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WARNING, no entry stored in dbm for [ENSG00000253230.9]
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WARNING, no entry stored in dbm for [ENSG00000235605.1]
WARNING, no entry stored in dbm for [ENSG00000266680.1]
WARNING, no entry stored in dbm for [ENSG00000197558.13]
WARNING, no entry stored in dbm for [ENSG00000216519.2]
WARNING, no entry stored in dbm for [ENSG00000279738.1]
WARNING, no entry stored in dbm for [ENSG00000215353.2]
WARNING, no entry stored in dbm for [ENSG00000278983.1]
WARNING, no entry stored in dbm for [ENSG00000236263.1]
WARNING, no entry stored in dbm for [ENSG00000283662.1]
WARNING, no entry stored in dbm for [ENSG00000285668.1]
WARNING, no entry stored in dbm for [ENSG00000235421.1]
WARNING, no entry stored in dbm for [ENSG00000227113.2]
WARNING, no entry stored in dbm for [ENSG00000271943.2]
WARNING, no entry stored in dbm for [ENSG00000237666.2]
WARNING, no entry stored in dbm for [ENSG00000243503.2]
WARNING, no entry stored in dbm for [ENSG00000280362.1]
WARNING, no entry stored in dbm for [ENSG00000261586.2]
WARNING, no entry stored in dbm for [ENSG00000254581.1]
WARNING, no entry stored in dbm for [ENSG00000235027.1]
WARNING, no entry stored in dbm for [ENSG00000234017.1]
WARNING, no entry stored in dbm for [ENSG00000272267.2]
WARNING, no entry stored in dbm for [ENSG00000205682.2]
WARNING, no entry stored in dbm for [ENSG00000205682.2]
WARNING, no entry stored in dbm for [ENSG00000205682.2]
WARNING, no entry stored in dbm for [ENSG00000286970.1]
WARNING, no entry stored in dbm for [ENSG00000218175.2]
WARNING, no entry stored in dbm for [ENSG00000188850.9]
WARNING, no entry stored in dbm for [ENSG00000093100.13]
WARNING, no entry stored in dbm for [ENSG00000257403.2]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000268460.2]
WARNING, no entry stored in dbm for [ENSG00000278920.1]
WARNING, no entry stored in dbm for [ENSG00000239224.3]
WARNING, no entry stored in dbm for [ENSG00000241057.2]
WARNING, no entry stored in dbm for [ENSG00000228204.2]
WARNING, no entry stored in dbm for [ENSG00000228113.7]
* STAR-Fusion complete. See output: /tmp/nxf.nhLzySAF68/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)