-ctat genome lib [/tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.lDlSeYZwGy/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary
-sample contains 81102162 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir -J /tmp/nxf.lDlSeYZwGy/BT-20_FFPE_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction -O /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.lDlSeYZwGy/BT-20_FFPE_RNA_0001_B23LG7FLT4_3.Chimeric.out.junction
-building interval tree based on /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes
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[1760000], rate=38752.29/min -building interval tree based on /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
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[1770000], rate=36457.26/min -building interval tree based on /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
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[1750000], rate=35872.91/min
[1760000], rate=35760.24/min -building interval tree based on /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
[10000], rate=85714.29/min
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[140000], rate=71186.44/min
[150000], rate=69767.44/min
[160000], rate=70588.24/min
[170000], rate=68000.00/min
[180000], rate=67924.53/min
[190000], rate=69512.20/min
[200000], rate=71005.92/min
[210000], rate=70000.00/min
[220000], rate=72527.47/min
[230000], rate=72251.31/min
[240000], rate=70935.96/min
[250000], rate=71090.05/min
[260000], rate=71559.63/min
[270000], rate=72645.74/min
[280000], rate=72413.79/min
[290000], rate=71900.83/min
[300000], rate=70588.24/min
[310000], rate=69924.81/min
[320000], rate=70588.24/min
[330000], rate=69964.66/min
[340000], rate=69624.57/min
[350000], rate=69078.95/min
[360000], rate=68571.43/min
[370000], rate=68944.10/min
[380000], rate=69090.91/min
[390000], rate=68823.53/min
[400000], rate=68965.52/min
[410000], rate=67397.26/min
[420000], rate=67379.68/min
[430000], rate=67894.74/min
[440000], rate=66835.44/min
[450000], rate=65853.66/min
[460000], rate=58474.58/min
[470000], rate=53714.29/min
[480000], rate=49740.93/min
[490000], rate=46740.86/min
[500000], rate=44052.86/min
[510000], rate=41746.25/min
[520000], rate=39443.74/min
[530000], rate=37767.22/min
[540000], rate=36610.17/min
[550000], rate=35522.07/min
[560000], rate=34603.50/min
[570000], rate=33203.88/min
[580000], rate=32252.09/min
[590000], rate=31382.98/min
[600000], rate=30586.24/min
[610000], rate=30000.00/min
[620000], rate=29407.11/min
[630000], rate=29076.92/min
[640000], rate=28656.72/min
[650000], rate=28384.28/min
[660000], rate=28125.00/min
[670000], rate=27936.07/min
[680000], rate=27623.56/min
[690000], rate=27471.80/min
[700000], rate=27450.98/min
[710000], rate=27290.20/min
[720000], rate=27050.72/min
[730000], rate=27020.36/min
[740000], rate=26974.48/min
[750000], rate=26801.67/min
[760000], rate=26823.53/min
[770000], rate=26829.27/min
[780000], rate=26773.46/min
[790000], rate=26734.35/min
[800000], rate=26740.95/min
[810000], rate=26806.40/min
[820000], rate=26914.66/min
[830000], rate=26991.87/min
[840000], rate=27096.77/min
[850000], rate=27258.15/min
[860000], rate=27388.54/min
[870000], rate=27517.13/min
[880000], rate=27615.06/min
[890000], rate=27725.86/min
[900000], rate=27921.41/min
[910000], rate=28086.42/min
[920000], rate=28249.74/min
[930000], rate=28411.41/min
[940000], rate=28571.43/min
[950000], rate=28773.35/min
[960000], rate=28944.72/min
[970000], rate=28998.51/min
[980000], rate=29051.38/min
[990000], rate=29103.38/min
[1000000], rate=29182.88/min
[1010000], rate=29204.82/min
[1020000], rate=29212.41/min
[1030000], rate=29275.23/min
[1040000], rate=29282.03/min
[1050000], rate=29411.76/min
[1060000], rate=29499.07/min
[1070000], rate=29558.01/min
[1080000], rate=29616.09/min
[1090000], rate=29700.27/min
[1100000], rate=29796.84/min
[1110000], rate=29905.70/min
[1120000], rate=30013.40/min
[1130000], rate=30106.57/min
[1140000], rate=30305.72/min
[1150000], rate=30490.50/min
[1160000], rate=30647.29/min
[1170000], rate=30789.47/min
[1180000], rate=30863.12/min
[1190000], rate=31029.99/min
[1200000], rate=31182.33/min
[1210000], rate=31320.10/min
[1220000], rate=31456.81/min
[1230000], rate=31592.47/min
[1240000], rate=31619.21/min
[1250000], rate=31367.63/min
[1260000], rate=31252.58/min
[1270000], rate=31178.40/min
[1280000], rate=31017.77/min
[1290000], rate=30812.10/min
[1300000], rate=30708.66/min
[1310000], rate=30691.14/min
[1320000], rate=30685.78/min
[1330000], rate=30633.40/min
[1340000], rate=30547.11/min
[1350000], rate=30496.99/min
[1360000], rate=30527.50/min
[1370000], rate=30557.62/min
[1380000], rate=30576.07/min
[1390000], rate=30583.06/min
[1400000], rate=30623.41/min
[1410000], rate=30663.28/min
[1420000], rate=30713.77/min
[1430000], rate=30763.71/min
[1440000], rate=30824.12/min
[1450000], rate=30894.89/min
[1460000], rate=30997.88/min
[1470000], rate=31100.14/min
[1480000], rate=31223.63/min
[1490000], rate=31335.44/min
[1500000], rate=31413.61/min
[1510000], rate=31534.98/min
[1520000], rate=31633.71/min
[1530000], rate=31731.77/min
[1540000], rate=31851.09/min
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[1560000], rate=32032.85/min
[1570000], rate=31986.42/min
[1580000], rate=31940.70/min
[1590000], rate=31927.71/min
[1600000], rate=31946.76/min
[1610000], rate=31976.17/min
[1620000], rate=32005.27/min
[1630000], rate=32034.06/min
[1640000], rate=32083.47/min
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[1660000], rate=32118.67/min
[1670000], rate=32166.93/min
[1680000], rate=32225.06/min
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[1700000], rate=32339.89/min
[1710000], rate=32417.06/min
[1720000], rate=32524.42/min
[1730000], rate=32610.74/min
[1740000], rate=32696.52/min
[1750000], rate=32792.00/min
[1760000], rate=32886.95/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir --filt_file /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.lDlSeYZwGy/./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...
9000000.00 reads per min processed...
8000000.00 reads per min processed...
7500000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
5400000.00 reads per min processed...
5454545.45 reads per min processed...
5500000.00 reads per min processed...
5538461.54 reads per min processed...
5200000.00 reads per min processed...
5250000.00 reads per min processed...
5294117.65 reads per min processed...
5333333.33 reads per min processed...
5368421.05 reads per min processed...
5142857.14 reads per min processed...
5181818.18 reads per min processed...
5000000.00 reads per min processed...
4846153.85 reads per min processed...
4888888.89 reads per min processed...
4928571.43 reads per min processed...
4800000.00 reads per min processed...
4838709.68 reads per min processed...
4875000.00 reads per min processed...
4909090.91 reads per min processed...
4941176.47 reads per min processed...
4971428.57 reads per min processed...
4864864.86 reads per min processed...
4894736.84 reads per min processed...
4923076.92 reads per min processed...
5076923.08 reads per min processed...
5100000.00 reads per min processed...
5121951.22 reads per min processed...
5142857.14 reads per min processed...
5162790.70 reads per min processed...
5181818.18 reads per min processed...
5200000.00 reads per min processed...
5217391.30 reads per min processed...
5234042.55 reads per min processed...
5250000.00 reads per min processed...
5160000.00 reads per min processed...
5176470.59 reads per min processed...
5192307.69 reads per min processed...
5207547.17 reads per min processed...
5222222.22 reads per min processed...
5142857.14 reads per min processed...
5157894.74 reads per min processed...
5172413.79 reads per min processed...
5186440.68 reads per min processed...
5114754.10 reads per min processed...
5129032.26 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.lDlSeYZwGy/BT-20_FFPE_RNA_0001_B23LG7FLT4_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.lDlSeYZwGy/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -211967.263820
EM: Round [1] log likelihood: -211796.502444
EM: Round [2] log likelihood: -211724.411366
EM: Round [3] log likelihood: -211687.824397
EM: Round [4] log likelihood: -211667.703457
EM: Round [5] log likelihood: -211656.154215
EM: Round [6] log likelihood: -211649.283958
EM: Round [7] log likelihood: -211645.042427
EM: Round [8] log likelihood: -211642.322630
EM: Round [9] log likelihood: -211640.514054
EM: Round [10] log likelihood: -211639.270713
EM: Round [11] log likelihood: -211638.390190
EM: Round [12] log likelihood: -211637.750051
EM: Round [13] log likelihood: -211637.273802
EM: Round [14] log likelihood: -211636.912175
EM: Round [15] log likelihood: -211636.632556
EM: Round [16] log likelihood: -211636.412809
EM: Round [17] log likelihood: -211636.237575
EM: Round [18] log likelihood: -211636.095987
EM: Round [19] log likelihood: -211635.980217
EM: Round [20] log likelihood: -211635.884535
EM: Round [21] log likelihood: -211635.804684
EM: Round [22] log likelihood: -211635.737461
EM: Round [23] log likelihood: -211635.680420
EM: Round [24] log likelihood: -211635.631676
EM: Round [25] log likelihood: -211635.589754
EM: Round [26] log likelihood: -211635.553494
EM: Round [27] log likelihood: -211635.521967
EM: Round [28] log likelihood: -211635.494429
EM: Round [29] log likelihood: -211635.470272
EM: Round [30] log likelihood: -211635.449002
EM: Round [31] log likelihood: -211635.430207
EM: Round [32] log likelihood: -211635.413547
EM: Round [33] log likelihood: -211635.398736
EM: Round [34] log likelihood: -211635.385533
EM: Round [35] log likelihood: -211635.373736
EM: Round [36] log likelihood: -211635.363169
EM: Round [37] log likelihood: -211635.353684
EM: Round [38] log likelihood: -211635.345152
EM: Round [39] log likelihood: -211635.337464
EM: Round [40] log likelihood: -211635.330523
EM: Round [41] log likelihood: -211635.324245
EM: Round [42] log likelihood: -211635.318558
EM: Round [43] log likelihood: -211635.313398
EM: Round [44] log likelihood: -211635.308709
EM: Round [45] log likelihood: -211635.304441
EM: Round [46] log likelihood: -211635.300552
EM: Round [47] log likelihood: -211635.297002
EM: Round [48] log likelihood: -211635.293757
EM: Round [49] log likelihood: -211635.290789
EM: Round [50] log likelihood: -211635.288068
EM: Round [51] log likelihood: -211635.285572
EM: Round [52] log likelihood: -211635.283280
EM: Round [53] log likelihood: -211635.281171
EM: Round [54] log likelihood: -211635.279230
EM: Round [55] log likelihood: -211635.277440
EM: Round [56] log likelihood: -211635.275788
EM: Round [57] log likelihood: -211635.274262
EM: Round [58] log likelihood: -211635.272851
EM: Round [59] log likelihood: -211635.271544
EM: Round [60] log likelihood: -211635.270333
EM: Round [61] log likelihood: -211635.269210
EM: Round [62] log likelihood: -211635.268166
EM: Round [63] log likelihood: -211635.267196
EM: Round [64] log likelihood: -211635.266294
EM: Round [65] log likelihood: -211635.265453
EM: Round [66] log likelihood: -211635.264670
EM: Round [67] log likelihood: -211635.263939
EM: Round [68] log likelihood: -211635.263256
EM: Round [69] log likelihood: -211635.262618
EM: Round [70] log likelihood: -211635.262022
EM: Round [71] log likelihood: -211635.261463
EM: Round [72] log likelihood: -211635.260940
EM: Round [73] log likelihood: -211635.260449
EM: Round [74] log likelihood: -211635.259989
EM: Round [75] log likelihood: -211635.259556
EM: Round [76] log likelihood: -211635.259150
EM: Round [77] log likelihood: -211635.258768
EM: Round [78] log likelihood: -211635.258409
EM: Round [79] log likelihood: -211635.258070
EM: Round [80] log likelihood: -211635.257752
EM: Round [81] log likelihood: -211635.257451
EM: Round [82] log likelihood: -211635.257168
EM: Round [83] log likelihood: -211635.256900
EM: Round [84] log likelihood: -211635.256647
EM: Round [85] log likelihood: -211635.256408
EM: Round [86] log likelihood: -211635.256183
EM: Round [87] log likelihood: -211635.255969
EM: Round [88] log likelihood: -211635.255767
EM: Round [89] log likelihood: -211635.255575
EM: Round [90] log likelihood: -211635.255394
EM: Round [91] log likelihood: -211635.255221
EM: Round [92] log likelihood: -211635.255058
EM: Round [93] log likelihood: -211635.254903
EM: Round [94] log likelihood: -211635.254756
EM: Round [95] log likelihood: -211635.254617
EM: Round [96] log likelihood: -211635.254484
EM: Round [97] log likelihood: -211635.254358
EM: Round [98] log likelihood: -211635.254238
EM: Round [99] log likelihood: -211635.254123
EM: Round [100] log likelihood: -211635.254015
EM: Round [101] log likelihood: -211635.253911
EM: Round [102] log likelihood: -211635.253812
EM: Stopping iterations at round 102 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -211708.826664
EM: Round [1] log likelihood: -211563.796094
EM: Round [2] log likelihood: -211505.924964
EM: Round [3] log likelihood: -211477.364650
EM: Round [4] log likelihood: -211461.863126
EM: Round [5] log likelihood: -211453.030183
EM: Round [6] log likelihood: -211447.808087
EM: Round [7] log likelihood: -211444.606972
EM: Round [8] log likelihood: -211442.572025
EM: Round [9] log likelihood: -211441.232315
EM: Round [10] log likelihood: -211440.321220
EM: Round [11] log likelihood: -211439.683121
EM: Round [12] log likelihood: -211439.224289
EM: Round [13] log likelihood: -211438.886510
EM: Round [14] log likelihood: -211438.632570
EM: Round [15] log likelihood: -211438.438034
EM: Round [16] log likelihood: -211438.286465
EM: Round [17] log likelihood: -211438.166561
EM: Round [18] log likelihood: -211438.070395
EM: Round [19] log likelihood: -211437.992304
EM: Round [20] log likelihood: -211437.928178
EM: Round [21] log likelihood: -211437.874988
EM: Round [22] log likelihood: -211437.830468
EM: Round [23] log likelihood: -211437.792901
EM: Round [24] log likelihood: -211437.760973
EM: Round [25] log likelihood: -211437.733659
EM: Round [26] log likelihood: -211437.710158
EM: Round [27] log likelihood: -211437.689832
EM: Round [28] log likelihood: -211437.672171
EM: Round [29] log likelihood: -211437.656763
EM: Round [30] log likelihood: -211437.643269
EM: Round [31] log likelihood: -211437.631412
EM: Round [32] log likelihood: -211437.620963
EM: Round [33] log likelihood: -211437.611728
EM: Round [34] log likelihood: -211437.603547
EM: Round [35] log likelihood: -211437.596282
EM: Round [36] log likelihood: -211437.589817
EM: Round [37] log likelihood: -211437.584053
EM: Round [38] log likelihood: -211437.578905
EM: Round [39] log likelihood: -211437.574299
EM: Round [40] log likelihood: -211437.570171
EM: Round [41] log likelihood: -211437.566466
EM: Round [42] log likelihood: -211437.563137
EM: Round [43] log likelihood: -211437.560140
EM: Round [44] log likelihood: -211437.557439
EM: Round [45] log likelihood: -211437.555002
EM: Round [46] log likelihood: -211437.552801
EM: Round [47] log likelihood: -211437.550809
EM: Round [48] log likelihood: -211437.549006
EM: Round [49] log likelihood: -211437.547371
EM: Round [50] log likelihood: -211437.545887
EM: Round [51] log likelihood: -211437.544539
EM: Round [52] log likelihood: -211437.543312
EM: Round [53] log likelihood: -211437.542195
EM: Round [54] log likelihood: -211437.541177
EM: Round [55] log likelihood: -211437.540248
EM: Round [56] log likelihood: -211437.539399
EM: Round [57] log likelihood: -211437.538622
EM: Round [58] log likelihood: -211437.537912
EM: Round [59] log likelihood: -211437.537261
EM: Round [60] log likelihood: -211437.536663
EM: Round [61] log likelihood: -211437.536115
EM: Round [62] log likelihood: -211437.535610
EM: Round [63] log likelihood: -211437.535146
EM: Round [64] log likelihood: -211437.534719
EM: Round [65] log likelihood: -211437.534325
EM: Round [66] log likelihood: -211437.533961
EM: Round [67] log likelihood: -211437.533625
EM: Round [68] log likelihood: -211437.533314
EM: Round [69] log likelihood: -211437.533026
EM: Round [70] log likelihood: -211437.532760
EM: Round [71] log likelihood: -211437.532513
EM: Round [72] log likelihood: -211437.532283
EM: Round [73] log likelihood: -211437.532069
EM: Round [74] log likelihood: -211437.531871
EM: Round [75] log likelihood: -211437.531686
EM: Round [76] log likelihood: -211437.531514
EM: Round [77] log likelihood: -211437.531353
EM: Round [78] log likelihood: -211437.531203
EM: Round [79] log likelihood: -211437.531063
EM: Round [80] log likelihood: -211437.530931
EM: Round [81] log likelihood: -211437.530808
EM: Round [82] log likelihood: -211437.530693
EM: Round [83] log likelihood: -211437.530585
EM: Round [84] log likelihood: -211437.530484
EM: Round [85] log likelihood: -211437.530388
EM: Stopping iterations at round 85 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.lDlSeYZwGy/./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.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.lDlSeYZwGy/./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.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 81102162 > /tmp/nxf.lDlSeYZwGy/./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.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir > /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir --annotate /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.lDlSeYZwGy/./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.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir
-done, see /tmp/nxf.lDlSeYZwGy/./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.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.lDlSeYZwGy/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1042, filtered: 9219)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.lDlSeYZwGy/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.lDlSeYZwGy/./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.lDlSeYZwGy/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000279273.1]
WARNING, no entry stored in dbm for [ENSG00000237135.1]
WARNING, no entry stored in dbm for [ENSG00000287952.1]
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WARNING, no entry stored in dbm for [ENSG00000242477.1]
WARNING, no entry stored in dbm for [ENSG00000242407.1]
WARNING, no entry stored in dbm for [ENSG00000267198.1]
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WARNING, no entry stored in dbm for [ENSG00000284783.1]
WARNING, no entry stored in dbm for [ENSG00000285035.1]
WARNING, no entry stored in dbm for [ENSG00000253107.1]
WARNING, no entry stored in dbm for [ENSG00000268895.6]
WARNING, no entry stored in dbm for [ENSG00000264164.1]
WARNING, no entry stored in dbm for [ENSG00000131484.4]
WARNING, no entry stored in dbm for [ENSG00000266356.1]
WARNING, no entry stored in dbm for [ENSG00000213650.3]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000276805.2]
WARNING, no entry stored in dbm for [ENSG00000258119.1]
WARNING, no entry stored in dbm for [ENSG00000255487.1]
WARNING, no entry stored in dbm for [ENSG00000257337.7]
WARNING, no entry stored in dbm for [ENSG00000237087.1]
WARNING, no entry stored in dbm for [ENSG00000287721.1]
WARNING, no entry stored in dbm for [ENSG00000287431.1]
WARNING, no entry stored in dbm for [ENSG00000287431.1]
WARNING, no entry stored in dbm for [ENSG00000287431.1]
WARNING, no entry stored in dbm for [ENSG00000286934.1]
WARNING, no entry stored in dbm for [ENSG00000286646.1]
WARNING, no entry stored in dbm for [ENSG00000267070.1]
WARNING, no entry stored in dbm for [ENSG00000272800.3]
WARNING, no entry stored in dbm for [ENSG00000268516.2]
WARNING, no entry stored in dbm for [ENSG00000267078.1]
WARNING, no entry stored in dbm for [ENSG00000262202.4]
WARNING, no entry stored in dbm for [ENSG00000204929.13]
WARNING, no entry stored in dbm for [ENSG00000267469.1]
WARNING, no entry stored in dbm for [ENSG00000287374.1]
WARNING, no entry stored in dbm for [ENSG00000274712.2]
WARNING, no entry stored in dbm for [ENSG00000266378.1]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000255306.1]
WARNING, no entry stored in dbm for [ENSG00000232759.1]
WARNING, no entry stored in dbm for [ENSG00000225722.1]
WARNING, no entry stored in dbm for [ENSG00000267083.1]
WARNING, no entry stored in dbm for [ENSG00000279569.1]
* STAR-Fusion complete. See output: /tmp/nxf.lDlSeYZwGy/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)