-ctat genome lib [/tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.ZstvrXaMsb/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary
-sample contains 36146178 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir -J /tmp/nxf.ZstvrXaMsb/ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.ZstvrXaMsb/ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=100000.00/min
[20000], rate=92307.69/min
[30000], rate=105882.35/min
[40000], rate=100000.00/min
[50000], rate=103448.28/min
[60000], rate=81818.18/min
[70000], rate=71186.44/min
[80000], rate=64864.86/min
[90000], rate=61363.64/min
[100000], rate=58823.53/min
[110000], rate=57391.30/min
[120000], rate=57142.86/min
[130000], rate=57352.94/min
[140000], rate=57534.25/min
[150000], rate=58441.56/min
[160000], rate=59259.26/min
[170000], rate=59649.12/min
[180000], rate=59668.51/min
[190000], rate=60317.46/min
[200000], rate=61538.46/min
[210000], rate=63000.00/min
[220000], rate=64705.88/min
[230000], rate=66028.71/min
[240000], rate=67924.53/min
[250000], rate=68493.15/min
[260000], rate=69026.55/min
[270000], rate=69527.90/min
[280000], rate=70292.89/min
[290000], rate=70445.34/min
[300000], rate=71428.57/min
[310000], rate=72656.25/min
[320000], rate=74418.60/min
[330000], rate=75000.00/min
[340000], rate=75836.43/min
[350000], rate=77205.88/min
[360000], rate=77978.34/min
[370000], rate=78445.23/min
[380000], rate=78620.69/min
[390000], rate=78787.88/min
[400000], rate=80536.91/min
[410000], rate=81188.12/min
[420000], rate=81553.40/min
[430000], rate=82692.31/min
[440000], rate=83280.76/min
[450000], rate=84112.15/min
[460000], rate=84146.34/min
[470000], rate=83928.57/min
[480000], rate=84210.53/min
[490000], rate=84971.10/min
[500000], rate=85227.27/min
[510000], rate=85000.00/min
[520000], rate=85245.90/min
[530000], rate=85483.87/min
[540000], rate=85714.29/min
[550000], rate=85714.29/min
[560000], rate=85496.18/min
[570000], rate=85714.29/min
[580000], rate=85714.29/min
[590000], rate=85922.33/min
[600000], rate=84705.88/min
[610000], rate=83181.82/min
[620000], rate=82483.37/min
[630000], rate=81465.52/min
[640000], rate=80334.73/min
[650000], rate=79591.84/min
[660000], rate=79041.92/min
[670000], rate=78669.28/min
[680000], rate=78160.92/min
[690000], rate=77819.55/min
[700000], rate=77490.77/min
[710000], rate=77173.91/min
[720000], rate=76868.33/min
[730000], rate=76977.15/min
[740000], rate=77351.92/min
[750000], rate=76791.81/min
[760000], rate=76254.18/min
[770000], rate=75862.07/min
[780000], rate=75728.16/min -building interval tree based on /tmp/nxf.ZstvrXaMsb/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
[20000], rate=75000.00/min
[30000], rate=78260.87/min
[40000], rate=85714.29/min
[50000], rate=85714.29/min
[60000], rate=81818.18/min
[70000], rate=71186.44/min
[80000], rate=66666.67/min
[90000], rate=62790.70/min
[100000], rate=58823.53/min
[110000], rate=58407.08/min
[120000], rate=56692.91/min
[130000], rate=56521.74/min
[140000], rate=56375.84/min
[150000], rate=57324.84/min
[160000], rate=58181.82/min
[170000], rate=59302.33/min
[180000], rate=60674.16/min
[190000], rate=60962.57/min
[200000], rate=61224.49/min
[210000], rate=61165.05/min
[220000], rate=61395.35/min
[230000], rate=61607.14/min
[240000], rate=62337.66/min
[250000], rate=62500.00/min
[260000], rate=62650.60/min
[270000], rate=62790.70/min
[280000], rate=63157.89/min
[290000], rate=64684.01/min
[300000], rate=65454.55/min
[310000], rate=66192.17/min
[320000], rate=66898.95/min
[330000], rate=66666.67/min
[340000], rate=66019.42/min
[350000], rate=65625.00/min
[360000], rate=65653.50/min
[370000], rate=65680.47/min
[380000], rate=65517.24/min
[390000], rate=65181.06/min
[400000], rate=65217.39/min
[410000], rate=65425.53/min
[420000], rate=65625.00/min
[430000], rate=66153.85/min
[440000], rate=65835.41/min
[450000], rate=65853.66/min
[460000], rate=66028.71/min
[470000], rate=66352.94/min
[480000], rate=65753.42/min
[490000], rate=65333.33/min
[500000], rate=64935.06/min
[510000], rate=64693.45/min
[520000], rate=64596.27/min
[530000], rate=64634.15/min
[540000], rate=64800.00/min
[550000], rate=64960.63/min
[560000], rate=65116.28/min
[570000], rate=65019.01/min
[580000], rate=64804.47/min
[590000], rate=64598.54/min
[600000], rate=64516.13/min
[610000], rate=64436.62/min
[620000], rate=64471.40/min
[630000], rate=64615.38/min
[640000], rate=65195.25/min
[650000], rate=65656.57/min
[660000], rate=66000.00/min
[670000], rate=66227.35/min
[680000], rate=66019.42/min
[690000], rate=65923.57/min
[700000], rate=65830.72/min
[710000], rate=65842.35/min
[720000], rate=65853.66/min
[730000], rate=65963.86/min
[740000], rate=66268.66/min
[750000], rate=66469.72/min
[760000], rate=66862.17/min
[770000], rate=67248.91/min
[780000], rate=67435.16/min -building interval tree based on /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=75000.00/min
[20000], rate=80000.00/min
[30000], rate=81818.18/min
[40000], rate=82758.62/min
[50000], rate=83333.33/min
[60000], rate=90000.00/min
[70000], rate=85714.29/min
[80000], rate=84210.53/min
[90000], rate=85714.29/min
[100000], rate=85714.29/min
[110000], rate=85714.29/min
[120000], rate=82758.62/min
[130000], rate=82105.26/min
[140000], rate=80769.23/min
[150000], rate=80357.14/min
[160000], rate=80000.00/min
[170000], rate=80952.38/min
[180000], rate=82442.75/min
[190000], rate=83211.68/min
[200000], rate=82191.78/min
[210000], rate=80769.23/min
[220000], rate=81481.48/min
[230000], rate=81656.80/min
[240000], rate=82285.71/min
[250000], rate=83333.33/min
[260000], rate=84324.32/min
[270000], rate=86170.21/min
[280000], rate=88421.05/min
[290000], rate=89690.72/min
[300000], rate=89108.91/min
[310000], rate=87735.85/min
[320000], rate=86877.83/min
[330000], rate=85714.29/min
[340000], rate=84647.30/min
[350000], rate=83665.34/min
[360000], rate=82758.62/min
[370000], rate=82222.22/min
[380000], rate=81138.79/min
[390000], rate=80689.66/min
[400000], rate=80267.56/min
[410000], rate=79611.65/min
[420000], rate=79245.28/min
[430000], rate=78658.54/min
[440000], rate=78106.51/min
[450000], rate=78034.68/min
[460000], rate=77966.10/min
[470000], rate=78116.34/min
[480000], rate=78474.11/min
[490000], rate=76963.35/min
[500000], rate=75566.75/min
[510000], rate=74452.55/min
[520000], rate=73411.76/min
[530000], rate=72768.88/min
[540000], rate=72000.00/min
[550000], rate=71583.51/min
[560000], rate=71186.44/min
[570000], rate=70807.45/min
[580000], rate=70445.34/min
[590000], rate=69822.49/min
[600000], rate=69767.44/min
[610000], rate=69847.33/min
[620000], rate=69793.62/min
[630000], rate=69870.61/min
[640000], rate=69818.18/min
[650000], rate=70397.11/min
[660000], rate=70337.48/min
[670000], rate=70526.32/min
[680000], rate=70466.32/min
[690000], rate=69579.83/min
[700000], rate=68852.46/min
[710000], rate=68160.00/min
[720000], rate=67817.90/min
[730000], rate=67488.44/min
[740000], rate=67069.49/min
[750000], rate=66765.58/min
[760000], rate=66375.55/min
[770000], rate=66284.07/min
[780000], rate=66195.19/min -building interval tree based on /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes
[10000], rate=100000.00/min
[20000], rate=109090.91/min
[30000], rate=105882.35/min
[40000], rate=120000.00/min
[50000], rate=120000.00/min
[60000], rate=128571.43/min
[70000], rate=120000.00/min
[80000], rate=117073.17/min
[90000], rate=114893.62/min
[100000], rate=117647.06/min
[110000], rate=122222.22/min
[120000], rate=124137.93/min
[130000], rate=121875.00/min
[140000], rate=121739.13/min
[150000], rate=120000.00/min
[160000], rate=123076.92/min
[170000], rate=122891.57/min
[180000], rate=121348.31/min
[190000], rate=120000.00/min
[200000], rate=118811.88/min
[210000], rate=121153.85/min
[220000], rate=122222.22/min
[230000], rate=112195.12/min
[240000], rate=103597.12/min
[250000], rate=96153.85/min
[260000], rate=91228.07/min
[270000], rate=88524.59/min
[280000], rate=85279.19/min
[290000], rate=82075.47/min
[300000], rate=80000.00/min
[310000], rate=78151.26/min
[320000], rate=76800.00/min
[330000], rate=76153.85/min
[340000], rate=75836.43/min
[350000], rate=75000.00/min
[360000], rate=74482.76/min
[370000], rate=73754.15/min
[380000], rate=73311.90/min
[390000], rate=73125.00/min
[400000], rate=72948.33/min
[410000], rate=72781.07/min
[420000], rate=73043.48/min
[430000], rate=73087.82/min
[440000], rate=73743.02/min
[450000], rate=72972.97/min
[460000], rate=72440.94/min
[470000], rate=71938.78/min
[480000], rate=71820.45/min
[490000], rate=71359.22/min
[500000], rate=71258.91/min
[510000], rate=71328.67/min
[520000], rate=71395.88/min
[530000], rate=71621.62/min
[540000], rate=71840.35/min
[550000], rate=72052.40/min
[560000], rate=70886.08/min
[570000], rate=70370.37/min
[580000], rate=69461.08/min
[590000], rate=68604.65/min
[600000], rate=68311.20/min
[610000], rate=67903.53/min
[620000], rate=67513.61/min
[630000], rate=67140.32/min
[640000], rate=66782.61/min
[650000], rate=66666.67/min
[660000], rate=66554.62/min
[670000], rate=66446.28/min
[680000], rate=66449.51/min
[690000], rate=66666.67/min
[700000], rate=66666.67/min
[710000], rate=66046.51/min
[720000], rate=65454.55/min
[730000], rate=64985.16/min
[740000], rate=64817.52/min
[750000], rate=64562.41/min
[760000], rate=64225.35/min
[770000], rate=63988.92/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir --filt_file /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
0.00 reads per min processed...
12000000.00 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...
4285714.29 reads per min processed...
4400000.00 reads per min processed...
4235294.12 reads per min processed...
4333333.33 reads per min processed...
4200000.00 reads per min processed...
4285714.29 reads per min processed...
4363636.36 reads per min processed...
4434782.61 reads per min processed...
4500000.00 reads per min processed...
4560000.00 reads per min processed...
4444444.44 reads per min processed...
4500000.00 reads per min processed...
4551724.14 reads per min processed...
4451612.90 reads per min processed...
4500000.00 reads per min processed...
4411764.71 reads per min processed...
4457142.86 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.ZstvrXaMsb/ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.Chimeric.out.junction --tmpdir /tmp --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --max_promiscuity 10 --min_pct_dom_promiscuity 20 --min_novel_junction_support 1 --min_alt_pct_junction 10 --aggregate_novel_junction_dist 5 --min_spanning_frags_only 1 --genome_lib_dir /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -39353.731836
EM: Round [1] log likelihood: -39292.386365
EM: Round [2] log likelihood: -39266.850467
EM: Round [3] log likelihood: -39254.071362
EM: Round [4] log likelihood: -39247.091559
EM: Round [5] log likelihood: -39243.059322
EM: Round [6] log likelihood: -39240.612009
EM: Round [7] log likelihood: -39239.055325
EM: Round [8] log likelihood: -39238.021286
EM: Round [9] log likelihood: -39237.307504
EM: Round [10] log likelihood: -39236.798248
EM: Round [11] log likelihood: -39236.424654
EM: Round [12] log likelihood: -39236.144129
EM: Round [13] log likelihood: -39235.929348
EM: Round [14] log likelihood: -39235.762191
EM: Round [15] log likelihood: -39235.630278
EM: Round [16] log likelihood: -39235.524926
EM: Round [17] log likelihood: -39235.439908
EM: Round [18] log likelihood: -39235.370668
EM: Round [19] log likelihood: -39235.313815
EM: Round [20] log likelihood: -39235.266791
EM: Round [21] log likelihood: -39235.227637
EM: Round [22] log likelihood: -39235.194839
EM: Round [23] log likelihood: -39235.167214
EM: Round [24] log likelihood: -39235.143827
EM: Round [25] log likelihood: -39235.123934
EM: Round [26] log likelihood: -39235.106941
EM: Round [27] log likelihood: -39235.092366
EM: Round [28] log likelihood: -39235.079818
EM: Round [29] log likelihood: -39235.068977
EM: Round [30] log likelihood: -39235.059581
EM: Round [31] log likelihood: -39235.051412
EM: Round [32] log likelihood: -39235.044289
EM: Round [33] log likelihood: -39235.038062
EM: Round [34] log likelihood: -39235.032604
EM: Round [35] log likelihood: -39235.027809
EM: Round [36] log likelihood: -39235.023587
EM: Round [37] log likelihood: -39235.019862
EM: Round [38] log likelihood: -39235.016568
EM: Round [39] log likelihood: -39235.013651
EM: Round [40] log likelihood: -39235.011062
EM: Round [41] log likelihood: -39235.008760
EM: Round [42] log likelihood: -39235.006712
EM: Round [43] log likelihood: -39235.004885
EM: Round [44] log likelihood: -39235.003253
EM: Round [45] log likelihood: -39235.001795
EM: Round [46] log likelihood: -39235.000489
EM: Round [47] log likelihood: -39234.999319
EM: Round [48] log likelihood: -39234.998268
EM: Round [49] log likelihood: -39234.997324
EM: Round [50] log likelihood: -39234.996475
EM: Round [51] log likelihood: -39234.995711
EM: Round [52] log likelihood: -39234.995022
EM: Round [53] log likelihood: -39234.994401
EM: Round [54] log likelihood: -39234.993840
EM: Round [55] log likelihood: -39234.993333
EM: Round [56] log likelihood: -39234.992874
EM: Round [57] log likelihood: -39234.992459
EM: Round [58] log likelihood: -39234.992083
EM: Round [59] log likelihood: -39234.991742
EM: Round [60] log likelihood: -39234.991433
EM: Round [61] log likelihood: -39234.991152
EM: Round [62] log likelihood: -39234.990897
EM: Round [63] log likelihood: -39234.990665
EM: Round [64] log likelihood: -39234.990454
EM: Round [65] log likelihood: -39234.990262
EM: Round [66] log likelihood: -39234.990087
EM: Round [67] log likelihood: -39234.989927
EM: Round [68] log likelihood: -39234.989782
EM: Round [69] log likelihood: -39234.989649
EM: Round [70] log likelihood: -39234.989527
EM: Round [71] log likelihood: -39234.989416
EM: Round [72] log likelihood: -39234.989315
EM: Round [73] log likelihood: -39234.989222
EM: Stopping iterations at round 73 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -39343.133834
EM: Round [1] log likelihood: -39285.451452
EM: Round [2] log likelihood: -39262.185038
EM: Round [3] log likelihood: -39250.887531
EM: Round [4] log likelihood: -39244.872207
EM: Round [5] log likelihood: -39241.479201
EM: Round [6] log likelihood: -39239.467413
EM: Round [7] log likelihood: -39238.215012
EM: Round [8] log likelihood: -39237.397700
EM: Round [9] log likelihood: -39236.840505
EM: Round [10] log likelihood: -39236.445642
EM: Round [11] log likelihood: -39236.156388
EM: Round [12] log likelihood: -39235.938553
EM: Round [13] log likelihood: -39235.770723
EM: Round [14] log likelihood: -39235.638982
EM: Round [15] log likelihood: -39235.533967
EM: Round [16] log likelihood: -39235.449184
EM: Round [17] log likelihood: -39235.379995
EM: Round [18] log likelihood: -39235.323014
EM: Round [19] log likelihood: -39235.275715
EM: Round [20] log likelihood: -39235.236180
EM: Round [21] log likelihood: -39235.202931
EM: Round [22] log likelihood: -39235.174813
EM: Round [23] log likelihood: -39235.150917
EM: Round [24] log likelihood: -39235.130517
EM: Round [25] log likelihood: -39235.113027
EM: Round [26] log likelihood: -39235.097976
EM: Round [27] log likelihood: -39235.084977
EM: Round [28] log likelihood: -39235.073713
EM: Round [29] log likelihood: -39235.063922
EM: Round [30] log likelihood: -39235.055386
EM: Round [31] log likelihood: -39235.047926
EM: Round [32] log likelihood: -39235.041387
EM: Round [33] log likelihood: -39235.035644
EM: Round [34] log likelihood: -39235.030586
EM: Round [35] log likelihood: -39235.026124
EM: Round [36] log likelihood: -39235.022179
EM: Round [37] log likelihood: -39235.018685
EM: Round [38] log likelihood: -39235.015583
EM: Round [39] log likelihood: -39235.012826
EM: Round [40] log likelihood: -39235.010372
EM: Round [41] log likelihood: -39235.008183
EM: Round [42] log likelihood: -39235.006228
EM: Round [43] log likelihood: -39235.004480
EM: Round [44] log likelihood: -39235.002915
EM: Round [45] log likelihood: -39235.001511
EM: Round [46] log likelihood: -39235.000252
EM: Round [47] log likelihood: -39234.999120
EM: Round [48] log likelihood: -39234.998102
EM: Round [49] log likelihood: -39234.997185
EM: Round [50] log likelihood: -39234.996358
EM: Round [51] log likelihood: -39234.995613
EM: Round [52] log likelihood: -39234.994940
EM: Round [53] log likelihood: -39234.994331
EM: Round [54] log likelihood: -39234.993781
EM: Round [55] log likelihood: -39234.993283
EM: Round [56] log likelihood: -39234.992832
EM: Round [57] log likelihood: -39234.992423
EM: Round [58] log likelihood: -39234.992052
EM: Round [59] log likelihood: -39234.991715
EM: Round [60] log likelihood: -39234.991409
EM: Round [61] log likelihood: -39234.991131
EM: Round [62] log likelihood: -39234.990879
EM: Round [63] log likelihood: -39234.990648
EM: Round [64] log likelihood: -39234.990439
EM: Round [65] log likelihood: -39234.990248
EM: Round [66] log likelihood: -39234.990074
EM: Round [67] log likelihood: -39234.989915
EM: Round [68] log likelihood: -39234.989770
EM: Round [69] log likelihood: -39234.989637
EM: Round [70] log likelihood: -39234.989516
EM: Round [71] log likelihood: -39234.989406
EM: Round [72] log likelihood: -39234.989304
EM: Round [73] log likelihood: -39234.989212
EM: Stopping iterations at round 73 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.ZstvrXaMsb/./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.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.ZstvrXaMsb/./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.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 36146178 > /tmp/nxf.ZstvrXaMsb/./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.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir > /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir --annotate /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.ZstvrXaMsb/./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.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir
-done, see /tmp/nxf.ZstvrXaMsb/./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.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.ZstvrXaMsb/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 277, filtered: 3454)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.ZstvrXaMsb/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.ZstvrXaMsb/./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.ZstvrXaMsb/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000229739.4]
WARNING, no entry stored in dbm for [ENSG00000264538.6]
WARNING, no entry stored in dbm for [ENSG00000232732.11]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000283696.1]
WARNING, no entry stored in dbm for [ENSG00000180747.15]
WARNING, no entry stored in dbm for [ENSG00000261702.2]
WARNING, no entry stored in dbm for [ENSG00000214535.3]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000279217.1]
WARNING, no entry stored in dbm for [ENSG00000230666.5]
WARNING, no entry stored in dbm for [ENSG00000212694.8]
WARNING, no entry stored in dbm for [ENSG00000240549.2]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000158482.10]
WARNING, no entry stored in dbm for [ENSG00000277458.1]
WARNING, no entry stored in dbm for [ENSG00000277142.1]
WARNING, no entry stored in dbm for [ENSG00000224209.8]
WARNING, no entry stored in dbm for [ENSG00000223508.5]
WARNING, no entry stored in dbm for [ENSG00000254762.1]
WARNING, no entry stored in dbm for [ENSG00000265735.2]
WARNING, no entry stored in dbm for [ENSG00000240116.3]
WARNING, no entry stored in dbm for [ENSG00000276168.1]
WARNING, no entry stored in dbm for [ENSG00000240116.3]
WARNING, no entry stored in dbm for [ENSG00000202058.1]
WARNING, no entry stored in dbm for [ENSG00000200708.1]
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 [ENSG00000202058.1]
WARNING, no entry stored in dbm for [ENSG00000202406.1]
WARNING, no entry stored in dbm for [ENSG00000202058.1]
WARNING, no entry stored in dbm for [ENSG00000201287.1]
WARNING, no entry stored in dbm for [ENSG00000202415.1]
WARNING, no entry stored in dbm for [ENSG00000200488.1]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000248764.1]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000273129.2]
WARNING, no entry stored in dbm for [ENSG00000261046.1]
WARNING, no entry stored in dbm for [ENSG00000267107.8]
WARNING, no entry stored in dbm for [ENSG00000225072.1]
WARNING, no entry stored in dbm for [ENSG00000224367.6]
WARNING, no entry stored in dbm for [ENSG00000266916.7]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000198496.12]
WARNING, no entry stored in dbm for [ENSG00000262879.6]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000215386.13]
WARNING, no entry stored in dbm for [ENSG00000283774.1]
WARNING, no entry stored in dbm for [ENSG00000221063.3]
WARNING, no entry stored in dbm for [ENSG00000244171.4]
WARNING, no entry stored in dbm for [ENSG00000229382.1]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000213247.3]
WARNING, no entry stored in dbm for [ENSG00000237929.1]
WARNING, no entry stored in dbm for [ENSG00000254401.2]
WARNING, no entry stored in dbm for [ENSG00000231566.2]
WARNING, no entry stored in dbm for [ENSG00000281721.1]
WARNING, no entry stored in dbm for [ENSG00000229433.2]
WARNING, no entry stored in dbm for [ENSG00000261008.7]
WARNING, no entry stored in dbm for [ENSG00000281912.1]
WARNING, no entry stored in dbm for [ENSG00000249069.8]
WARNING, no entry stored in dbm for [ENSG00000235703.6]
WARNING, no entry stored in dbm for [ENSG00000241769.7]
WARNING, no entry stored in dbm for [ENSG00000259905.7]
WARNING, no entry stored in dbm for [ENSG00000225718.2]
WARNING, no entry stored in dbm for [ENSG00000230202.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000279128.1]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000231074.9]
WARNING, no entry stored in dbm for [ENSG00000166104.15]
WARNING, no entry stored in dbm for [ENSG00000166104.15]
WARNING, no entry stored in dbm for [ENSG00000124835.2]
WARNING, no entry stored in dbm for [ENSG00000124835.2]
WARNING, no entry stored in dbm for [ENSG00000124835.2]
WARNING, no entry stored in dbm for [ENSG00000255410.2]
WARNING, no entry stored in dbm for [ENSG00000283103.3]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000262870.1]
WARNING, no entry stored in dbm for [ENSG00000229212.8]
WARNING, no entry stored in dbm for [ENSG00000236204.6]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000272578.5]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000279484.2]
WARNING, no entry stored in dbm for [ENSG00000285799.1]
WARNING, no entry stored in dbm for [ENSG00000254741.1]
WARNING, no entry stored in dbm for [ENSG00000282885.2]
WARNING, no entry stored in dbm for [ENSG00000244236.3]
WARNING, no entry stored in dbm for [ENSG00000287356.1]
WARNING, no entry stored in dbm for [ENSG00000225032.5]
WARNING, no entry stored in dbm for [ENSG00000236740.6]
WARNING, no entry stored in dbm for [ENSG00000286073.1]
WARNING, no entry stored in dbm for [ENSG00000226499.1]
WARNING, no entry stored in dbm for [ENSG00000239670.1]
WARNING, no entry stored in dbm for [ENSG00000258875.6]
WARNING, no entry stored in dbm for [ENSG00000244237.1]
WARNING, no entry stored in dbm for [ENSG00000181524.6]
WARNING, no entry stored in dbm for [ENSG00000259121.2]
WARNING, no entry stored in dbm for [ENSG00000274717.1]
WARNING, no entry stored in dbm for [ENSG00000279738.1]
WARNING, no entry stored in dbm for [ENSG00000259456.4]
WARNING, no entry stored in dbm for [ENSG00000285492.1]
WARNING, no entry stored in dbm for [ENSG00000227242.4]
WARNING, no entry stored in dbm for [ENSG00000282375.1]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000269001.2]
WARNING, no entry stored in dbm for [ENSG00000258320.1]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000222043.2]
WARNING, no entry stored in dbm for [ENSG00000273765.1]
WARNING, no entry stored in dbm for [ENSG00000205682.2]
WARNING, no entry stored in dbm for [ENSG00000213963.6]
WARNING, no entry stored in dbm for [ENSG00000230073.1]
WARNING, no entry stored in dbm for [ENSG00000249631.6]
* STAR-Fusion complete. See output: /tmp/nxf.ZstvrXaMsb/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)