-ctat genome lib [/tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.NNJ2hUpcpN/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary
-sample contains 170290026 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir -J /tmp/nxf.NNJ2hUpcpN/BVT_FFPE_TRNA_liv_03_A23WKFTLT4_3.Chimeric.out.junction -O /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.NNJ2hUpcpN/BVT_FFPE_TRNA_liv_03_A23WKFTLT4_3.Chimeric.out.junction
-building interval tree based on /tmp/nxf.NNJ2hUpcpN/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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[1880000], rate=66313.93/min -building interval tree based on /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
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[1860000], rate=47009.27/min -building interval tree based on /tmp/nxf.NNJ2hUpcpN/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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[1740000], rate=41743.30/min
[1750000], rate=41816.01/min
[1760000], rate=41888.14/min
[1770000], rate=41910.02/min
[1780000], rate=41997.64/min
[1790000], rate=42101.14/min
[1800000], rate=42220.48/min
[1810000], rate=42339.18/min
[1820000], rate=42407.77/min
[1830000], rate=42508.71/min
[1840000], rate=42625.48/min
[1850000], rate=42350.25/min
[1860000], rate=42002.26/min -building interval tree based on /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=26086.96/min
[20000], rate=24000.00/min
[30000], rate=25000.00/min
[40000], rate=23762.38/min
[50000], rate=24000.00/min
[60000], rate=24000.00/min
[70000], rate=24000.00/min
[80000], rate=24120.60/min
[90000], rate=23684.21/min
[100000], rate=23529.41/min
[110000], rate=24087.59/min
[120000], rate=24573.38/min
[130000], rate=25490.20/min
[140000], rate=26168.22/min
[150000], rate=27272.73/min
[160000], rate=28152.49/min
[170000], rate=29142.86/min
[180000], rate=30252.10/min
[190000], rate=31578.95/min
[200000], rate=32697.55/min
[210000], rate=33780.16/min
[220000], rate=34554.97/min
[230000], rate=35025.38/min
[240000], rate=35910.22/min
[250000], rate=36855.04/min
[260000], rate=37590.36/min
[270000], rate=38388.63/min
[280000], rate=39069.77/min
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[300000], rate=37422.04/min
[310000], rate=36978.13/min
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[340000], rate=37158.47/min
[350000], rate=37567.08/min
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[370000], rate=38608.70/min
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[390000], rate=39795.92/min
[400000], rate=40404.04/min
[410000], rate=40931.78/min
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[440000], rate=42580.65/min
[450000], rate=42519.69/min
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[490000], rate=42363.11/min
[500000], rate=42016.81/min
[510000], rate=41689.37/min
[520000], rate=41434.26/min
[530000], rate=41352.41/min
[540000], rate=41221.37/min
[550000], rate=41147.13/min
[560000], rate=41075.79/min
[570000], rate=41204.82/min
[580000], rate=41676.65/min
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[610000], rate=42907.39/min
[620000], rate=43155.45/min
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[650000], rate=42437.43/min
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[670000], rate=40770.79/min
[680000], rate=40117.99/min
[690000], rate=40155.19/min
[700000], rate=40579.71/min
[710000], rate=40226.63/min
[720000], rate=39705.88/min
[730000], rate=39459.46/min
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[750000], rate=39198.61/min
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[770000], rate=38725.90/min
[780000], rate=38645.75/min
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[1500000], rate=42016.81/min
[1510000], rate=42178.77/min
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[1540000], rate=41528.09/min
[1550000], rate=41278.30/min
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[1570000], rate=40849.96/min
[1580000], rate=40564.83/min
[1590000], rate=40253.16/min
[1600000], rate=40066.78/min
[1610000], rate=39818.63/min
[1620000], rate=39641.11/min
[1630000], rate=39387.84/min
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[1650000], rate=38838.76/min
[1660000], rate=38515.08/min
[1670000], rate=38244.27/min
[1680000], rate=37908.99/min
[1690000], rate=37695.17/min
[1700000], rate=37555.23/min
[1710000], rate=37568.66/min
[1720000], rate=37513.63/min
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[1740000], rate=37540.45/min
[1750000], rate=37553.65/min
[1760000], rate=37566.70/min
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[1780000], rate=37618.88/min
[1790000], rate=37631.39/min
[1800000], rate=37670.04/min
[1810000], rate=37721.43/min
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[1830000], rate=37862.07/min
[1840000], rate=37951.19/min
[1850000], rate=38039.75/min
[1860000], rate=38127.78/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir --filt_file /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.NNJ2hUpcpN/./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...
12000000.00 reads per min processed...
10000000.00 reads per min processed...
12000000.00 reads per min processed...
8400000.00 reads per min processed...
6857142.86 reads per min processed...
6000000.00 reads per min processed...
5454545.45 reads per min processed...
5500000.00 reads per min processed...
5142857.14 reads per min processed...
5200000.00 reads per min processed...
4941176.47 reads per min processed...
5000000.00 reads per min processed...
4800000.00 reads per min processed...
4857142.86 reads per min processed...
4695652.17 reads per min processed...
4750000.00 reads per min processed...
4615384.62 reads per min processed...
4666666.67 reads per min processed...
4551724.14 reads per min processed...
4451612.90 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...
4304347.83 reads per min processed...
4340425.53 reads per min processed...
4375000.00 reads per min processed...
4320000.00 reads per min processed...
4440000.00 reads per min processed...
4470588.24 reads per min processed...
4588235.29 reads per min processed...
4615384.62 reads per min processed...
4641509.43 reads per min processed...
4754716.98 reads per min processed...
4777777.78 reads per min processed...
4714285.71 reads per min processed...
4736842.11 reads per min processed...
4677966.10 reads per min processed...
4700000.00 reads per min processed...
4721311.48 reads per min processed...
4666666.67 reads per min processed...
4687500.00 reads per min processed...
4636363.64 reads per min processed...
4656716.42 reads per min processed...
4608695.65 reads per min processed...
4628571.43 reads per min processed...
4583333.33 reads per min processed...
4602739.73 reads per min processed...
4560000.00 reads per min processed...
4578947.37 reads per min processed...
4597402.60 reads per min processed...
4615384.62 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.NNJ2hUpcpN/BVT_FFPE_TRNA_liv_03_A23WKFTLT4_3.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.NNJ2hUpcpN/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -123637.642166
EM: Round [1] log likelihood: -123513.540154
EM: Round [2] log likelihood: -123466.644122
EM: Round [3] log likelihood: -123444.082462
EM: Round [4] log likelihood: -123431.895817
EM: Round [5] log likelihood: -123424.925935
EM: Round [6] log likelihood: -123420.791083
EM: Round [7] log likelihood: -123418.253896
EM: Round [8] log likelihood: -123416.639465
EM: Round [9] log likelihood: -123415.572169
EM: Round [10] log likelihood: -123414.839434
EM: Round [11] log likelihood: -123414.318305
EM: Round [12] log likelihood: -123413.935720
EM: Round [13] log likelihood: -123413.646930
EM: Round [14] log likelihood: -123413.423648
EM: Round [15] log likelihood: -123413.247432
EM: Round [16] log likelihood: -123413.105890
EM: Round [17] log likelihood: -123412.990468
EM: Round [18] log likelihood: -123412.895108
EM: Round [19] log likelihood: -123412.815423
EM: Round [20] log likelihood: -123412.748173
EM: Round [21] log likelihood: -123412.690922
EM: Round [22] log likelihood: -123412.641808
EM: Round [23] log likelihood: -123412.599388
EM: Round [24] log likelihood: -123412.562530
EM: Round [25] log likelihood: -123412.530331
EM: Round [26] log likelihood: -123412.502069
EM: Round [27] log likelihood: -123412.477156
EM: Round [28] log likelihood: -123412.455110
EM: Round [29] log likelihood: -123412.435535
EM: Round [30] log likelihood: -123412.418099
EM: Round [31] log likelihood: -123412.402523
EM: Round [32] log likelihood: -123412.388574
EM: Round [33] log likelihood: -123412.376052
EM: Round [34] log likelihood: -123412.364786
EM: Round [35] log likelihood: -123412.354630
EM: Round [36] log likelihood: -123412.345458
EM: Round [37] log likelihood: -123412.337160
EM: Round [38] log likelihood: -123412.329641
EM: Round [39] log likelihood: -123412.322817
EM: Round [40] log likelihood: -123412.316616
EM: Round [41] log likelihood: -123412.310972
EM: Round [42] log likelihood: -123412.305830
EM: Round [43] log likelihood: -123412.301138
EM: Round [44] log likelihood: -123412.296854
EM: Round [45] log likelihood: -123412.292936
EM: Round [46] log likelihood: -123412.289350
EM: Round [47] log likelihood: -123412.286065
EM: Round [48] log likelihood: -123412.283051
EM: Round [49] log likelihood: -123412.280285
EM: Round [50] log likelihood: -123412.277743
EM: Round [51] log likelihood: -123412.275405
EM: Round [52] log likelihood: -123412.273253
EM: Round [53] log likelihood: -123412.271270
EM: Round [54] log likelihood: -123412.269442
EM: Round [55] log likelihood: -123412.267755
EM: Round [56] log likelihood: -123412.266196
EM: Round [57] log likelihood: -123412.264756
EM: Round [58] log likelihood: -123412.263423
EM: Round [59] log likelihood: -123412.262189
EM: Round [60] log likelihood: -123412.261046
EM: Round [61] log likelihood: -123412.259986
EM: Round [62] log likelihood: -123412.259002
EM: Round [63] log likelihood: -123412.258088
EM: Round [64] log likelihood: -123412.257239
EM: Round [65] log likelihood: -123412.256449
EM: Round [66] log likelihood: -123412.255714
EM: Round [67] log likelihood: -123412.255030
EM: Round [68] log likelihood: -123412.254392
EM: Round [69] log likelihood: -123412.253797
EM: Round [70] log likelihood: -123412.253241
EM: Round [71] log likelihood: -123412.252722
EM: Round [72] log likelihood: -123412.252237
EM: Round [73] log likelihood: -123412.251784
EM: Round [74] log likelihood: -123412.251359
EM: Round [75] log likelihood: -123412.250962
EM: Round [76] log likelihood: -123412.250589
EM: Round [77] log likelihood: -123412.250240
EM: Round [78] log likelihood: -123412.249912
EM: Round [79] log likelihood: -123412.249604
EM: Round [80] log likelihood: -123412.249315
EM: Round [81] log likelihood: -123412.249043
EM: Round [82] log likelihood: -123412.248787
EM: Round [83] log likelihood: -123412.248547
EM: Round [84] log likelihood: -123412.248320
EM: Round [85] log likelihood: -123412.248106
EM: Round [86] log likelihood: -123412.247905
EM: Round [87] log likelihood: -123412.247715
EM: Round [88] log likelihood: -123412.247535
EM: Round [89] log likelihood: -123412.247366
EM: Round [90] log likelihood: -123412.247205
EM: Round [91] log likelihood: -123412.247054
EM: Round [92] log likelihood: -123412.246911
EM: Round [93] log likelihood: -123412.246775
EM: Round [94] log likelihood: -123412.246647
EM: Round [95] log likelihood: -123412.246525
EM: Round [96] log likelihood: -123412.246410
EM: Round [97] log likelihood: -123412.246300
EM: Round [98] log likelihood: -123412.246196
EM: Round [99] log likelihood: -123412.246098
EM: Stopping iterations at round 99 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -123605.097191
EM: Round [1] log likelihood: -123490.827864
EM: Round [2] log likelihood: -123448.946648
EM: Round [3] log likelihood: -123429.160542
EM: Round [4] log likelihood: -123418.602350
EM: Round [5] log likelihood: -123412.608103
EM: Round [6] log likelihood: -123409.063955
EM: Round [7] log likelihood: -123406.890159
EM: Round [8] log likelihood: -123405.504977
EM: Round [9] log likelihood: -123404.587119
EM: Round [10] log likelihood: -123403.955463
EM: Round [11] log likelihood: -123403.505336
EM: Round [12] log likelihood: -123403.174445
EM: Round [13] log likelihood: -123402.924527
EM: Round [14] log likelihood: -123402.731310
EM: Round [15] log likelihood: -123402.578909
EM: Round [16] log likelihood: -123402.456623
EM: Round [17] log likelihood: -123402.357042
EM: Round [18] log likelihood: -123402.274910
EM: Round [19] log likelihood: -123402.206418
EM: Round [20] log likelihood: -123402.148750
EM: Round [21] log likelihood: -123402.099786
EM: Round [22] log likelihood: -123402.057906
EM: Round [23] log likelihood: -123402.021854
EM: Round [24] log likelihood: -123401.990644
EM: Round [25] log likelihood: -123401.963489
EM: Round [26] log likelihood: -123401.939759
EM: Round [27] log likelihood: -123401.918942
EM: Round [28] log likelihood: -123401.900615
EM: Round [29] log likelihood: -123401.884433
EM: Round [30] log likelihood: -123401.870104
EM: Round [31] log likelihood: -123401.857385
EM: Round [32] log likelihood: -123401.846070
EM: Round [33] log likelihood: -123401.835984
EM: Round [34] log likelihood: -123401.826978
EM: Round [35] log likelihood: -123401.818921
EM: Round [36] log likelihood: -123401.811705
EM: Round [37] log likelihood: -123401.805231
EM: Round [38] log likelihood: -123401.799417
EM: Round [39] log likelihood: -123401.794189
EM: Round [40] log likelihood: -123401.789483
EM: Round [41] log likelihood: -123401.785242
EM: Round [42] log likelihood: -123401.781417
EM: Round [43] log likelihood: -123401.777964
EM: Round [44] log likelihood: -123401.774845
EM: Round [45] log likelihood: -123401.772025
EM: Round [46] log likelihood: -123401.769473
EM: Round [47] log likelihood: -123401.767162
EM: Round [48] log likelihood: -123401.765068
EM: Round [49] log likelihood: -123401.763170
EM: Round [50] log likelihood: -123401.761448
EM: Round [51] log likelihood: -123401.759884
EM: Round [52] log likelihood: -123401.758464
EM: Round [53] log likelihood: -123401.757174
EM: Round [54] log likelihood: -123401.756000
EM: Round [55] log likelihood: -123401.754933
EM: Round [56] log likelihood: -123401.753961
EM: Round [57] log likelihood: -123401.753076
EM: Round [58] log likelihood: -123401.752269
EM: Round [59] log likelihood: -123401.751534
EM: Round [60] log likelihood: -123401.750863
EM: Round [61] log likelihood: -123401.750251
EM: Round [62] log likelihood: -123401.749692
EM: Round [63] log likelihood: -123401.749181
EM: Round [64] log likelihood: -123401.748714
EM: Round [65] log likelihood: -123401.748287
EM: Round [66] log likelihood: -123401.747897
EM: Round [67] log likelihood: -123401.747539
EM: Round [68] log likelihood: -123401.747212
EM: Round [69] log likelihood: -123401.746912
EM: Round [70] log likelihood: -123401.746637
EM: Round [71] log likelihood: -123401.746385
EM: Round [72] log likelihood: -123401.746153
EM: Round [73] log likelihood: -123401.745941
EM: Round [74] log likelihood: -123401.745745
EM: Round [75] log likelihood: -123401.745566
EM: Round [76] log likelihood: -123401.745401
EM: Round [77] log likelihood: -123401.745249
EM: Round [78] log likelihood: -123401.745109
EM: Round [79] log likelihood: -123401.744980
EM: Round [80] log likelihood: -123401.744861
EM: Round [81] log likelihood: -123401.744752
EM: Round [82] log likelihood: -123401.744651
EM: Round [83] log likelihood: -123401.744558
EM: Stopping iterations at round 83 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.NNJ2hUpcpN/./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.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.NNJ2hUpcpN/./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.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 170290026 > /tmp/nxf.NNJ2hUpcpN/./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.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir > /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir --annotate /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.NNJ2hUpcpN/./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.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir
-done, see /tmp/nxf.NNJ2hUpcpN/./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.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.NNJ2hUpcpN/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1131, filtered: 6925)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.NNJ2hUpcpN/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.NNJ2hUpcpN/./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.NNJ2hUpcpN/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000229739.4]
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WARNING, no entry stored in dbm for [ENSG00000253882.6]
WARNING, no entry stored in dbm for [ENSG00000255910.2]
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 [ENSG00000285062.1]
WARNING, no entry stored in dbm for [ENSG00000275140.1]
WARNING, no entry stored in dbm for [ENSG00000237017.1]
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000265041.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000201758.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000201901.1]
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 [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 [ENSG00000274670.1]
WARNING, no entry stored in dbm for [ENSG00000283345.1]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000279658.1]
WARNING, no entry stored in dbm for [ENSG00000273724.1]
WARNING, no entry stored in dbm for [ENSG00000272505.1]
WARNING, no entry stored in dbm for [ENSG00000264647.1]
WARNING, no entry stored in dbm for [ENSG00000277096.1]
WARNING, no entry stored in dbm for [ENSG00000254350.1]
WARNING, no entry stored in dbm for [ENSG00000253784.1]
WARNING, no entry stored in dbm for [ENSG00000259375.1]
WARNING, no entry stored in dbm for [ENSG00000246339.6]
WARNING, no entry stored in dbm for [ENSG00000286171.1]
WARNING, no entry stored in dbm for [ENSG00000283674.3]
WARNING, no entry stored in dbm for [ENSG00000241570.8]
WARNING, no entry stored in dbm for [ENSG00000227157.2]
WARNING, no entry stored in dbm for [ENSG00000257817.2]
WARNING, no entry stored in dbm for [ENSG00000260413.1]
WARNING, no entry stored in dbm for [ENSG00000286093.1]
WARNING, no entry stored in dbm for [ENSG00000287060.1]
WARNING, no entry stored in dbm for [ENSG00000249863.2]
WARNING, no entry stored in dbm for [ENSG00000240418.1]
WARNING, no entry stored in dbm for [ENSG00000232767.2]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000269473.1]
WARNING, no entry stored in dbm for [ENSG00000254363.6]
WARNING, no entry stored in dbm for [ENSG00000226266.6]
WARNING, no entry stored in dbm for [ENSG00000229195.1]
WARNING, no entry stored in dbm for [ENSG00000259331.1]
WARNING, no entry stored in dbm for [ENSG00000255458.7]
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 [ENSG00000226472.8]
WARNING, no entry stored in dbm for [ENSG00000270571.2]
WARNING, no entry stored in dbm for [ENSG00000277458.1]
WARNING, no entry stored in dbm for [ENSG00000214331.8]
WARNING, no entry stored in dbm for [ENSG00000227719.1]
WARNING, no entry stored in dbm for [ENSG00000241057.2]
WARNING, no entry stored in dbm for [ENSG00000241057.2]
WARNING, no entry stored in dbm for [ENSG00000277283.1]
* STAR-Fusion complete. See output: /tmp/nxf.NNJ2hUpcpN/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)