-ctat genome lib [/tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.UPRkJQ0EKL/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary
-sample contains 273616163 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir  -J /tmp/nxf.UPRkJQ0EKL/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Chimeric.out.junction  -O /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.UPRkJQ0EKL/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Chimeric.out.junction
-building interval tree based on /tmp/nxf.UPRkJQ0EKL/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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[2950000], rate=65482.80/min -building interval tree based on /tmp/nxf.UPRkJQ0EKL/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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[2560000], rate=58805.51/min 
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[2580000], rate=59038.90/min 
[2590000], rate=59132.42/min 
[2600000], rate=59248.01/min 
[2610000], rate=59363.15/min 
[2620000], rate=59477.87/min 
[2630000], rate=59592.15/min 
[2640000], rate=59616.11/min 
[2650000], rate=59639.91/min 
[2660000], rate=59663.55/min 
[2670000], rate=59664.80/min 
[2680000], rate=59688.20/min 
[2690000], rate=59755.65/min 
[2700000], rate=59822.75/min 
[2710000], rate=59845.42/min 
[2720000], rate=59867.94/min 
[2730000], rate=59912.22/min 
[2740000], rate=59956.24/min 
[2750000], rate=60021.83/min 
[2760000], rate=60087.08/min 
[2770000], rate=60173.79/min 
[2780000], rate=60238.35/min 
[2790000], rate=60280.88/min 
[2800000], rate=60388.21/min 
[2810000], rate=60473.46/min 
[2820000], rate=60558.34/min 
[2830000], rate=60642.86/min 
[2840000], rate=60748.66/min 
[2850000], rate=60832.44/min 
[2860000], rate=60937.50/min 
[2870000], rate=61042.18/min 
[2880000], rate=61146.50/min 
[2890000], rate=61272.08/min 
[2900000], rate=61418.99/min 
[2910000], rate=61522.20/min 
[2920000], rate=61646.73/min 
[2930000], rate=61749.21/min 
[2940000], rate=61873.03/min 
[2950000], rate=61974.79/min -building interval tree based on /tmp/nxf.UPRkJQ0EKL/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=85714.29/min 
[30000], rate=85714.29/min 
[40000], rate=85714.29/min 
[50000], rate=85714.29/min 
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[90000], rate=83076.92/min 
[100000], rate=83333.33/min 
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[940000], rate=51933.70/min 
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[1490000], rate=51557.09/min 
[1500000], rate=51724.14/min 
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[1570000], rate=52951.10/min 
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[1590000], rate=52941.18/min 
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[1730000], rate=50437.32/min 
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[1750000], rate=50383.88/min 
[1760000], rate=50357.65/min 
[1770000], rate=50403.42/min 
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[1980000], rate=50943.40/min 
[1990000], rate=51047.46/min 
[2000000], rate=51150.90/min 
[2010000], rate=51231.95/min 
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[2290000], rate=53359.22/min 
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[2310000], rate=53472.22/min 
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[2350000], rate=53755.24/min 
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[2380000], rate=53947.87/min 
[2390000], rate=54011.30/min 
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[2490000], rate=54287.79/min 
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[2520000], rate=54466.86/min 
[2530000], rate=54545.45/min 
[2540000], rate=54623.66/min 
[2550000], rate=54701.47/min 
[2560000], rate=54778.89/min 
[2570000], rate=54836.42/min 
[2580000], rate=54952.08/min 
[2590000], rate=55047.82/min 
[2600000], rate=55143.16/min 
[2610000], rate=55218.62/min 
[2620000], rate=55313.16/min 
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[2640000], rate=55501.05/min 
[2650000], rate=55613.85/min 
[2660000], rate=55726.26/min 
[2670000], rate=55838.27/min 
[2680000], rate=55930.43/min 
[2690000], rate=56041.67/min 
[2700000], rate=56133.06/min 
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[2720000], rate=56353.59/min 
[2730000], rate=56443.83/min 
[2740000], rate=56533.70/min 
[2750000], rate=56623.20/min 
[2760000], rate=56751.20/min 
[2770000], rate=56937.31/min 
[2780000], rate=57025.64/min 
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[2800000], rate=57201.23/min 
[2810000], rate=57288.48/min 
[2820000], rate=57394.84/min 
[2830000], rate=57500.85/min 
[2840000], rate=57606.49/min 
[2850000], rate=57731.26/min 
[2860000], rate=57719.48/min 
[2870000], rate=57649.82/min 
[2880000], rate=57580.81/min 
[2890000], rate=57531.52/min 
[2900000], rate=57463.67/min 
[2910000], rate=57434.21/min 
[2920000], rate=57386.18/min 
[2930000], rate=57338.55/min 
[2940000], rate=57291.33/min -building interval tree based on /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=120000.00/min 
[20000], rate=120000.00/min 
[30000], rate=128571.43/min 
[40000], rate=126315.79/min 
[50000], rate=157894.74/min 
[60000], rate=163636.36/min 
[70000], rate=175000.00/min 
[80000], rate=200000.00/min 
[90000], rate=186206.90/min 
[100000], rate=176470.59/min 
[110000], rate=173684.21/min 
[120000], rate=167441.86/min 
[130000], rate=181395.35/min 
[140000], rate=182608.70/min 
[150000], rate=187500.00/min 
[160000], rate=195918.37/min 
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[180000], rate=171428.57/min 
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[200000], rate=160000.00/min 
[210000], rate=151807.23/min 
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[1080000], rate=34708.09/min 
[1090000], rate=34824.28/min 
[1100000], rate=34957.63/min 
[1110000], rate=35126.58/min 
[1120000], rate=35257.08/min 
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[1180000], rate=36159.35/min 
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[1200000], rate=36474.16/min 
[1210000], rate=36648.16/min 
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[1260000], rate=37500.00/min 
[1270000], rate=37592.50/min 
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[1290000], rate=37941.18/min 
[1300000], rate=38085.94/min 
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[1330000], rate=38532.11/min 
[1340000], rate=38709.68/min 
[1350000], rate=38904.90/min 
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[1380000], rate=39447.36/min 
[1390000], rate=39638.78/min 
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[1430000], rate=40112.20/min 
[1440000], rate=40167.36/min 
[1450000], rate=40240.52/min 
[1460000], rate=40275.86/min 
[1470000], rate=40329.22/min 
[1480000], rate=40400.36/min 
[1490000], rate=40415.91/min 
[1500000], rate=40485.83/min 
[1510000], rate=40573.22/min 
[1520000], rate=40696.12/min 
[1530000], rate=40836.30/min 
[1540000], rate=40975.61/min 
[1550000], rate=41095.89/min 
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[1590000], rate=41604.88/min 
[1600000], rate=41720.99/min 
[1610000], rate=41854.42/min 
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[1630000], rate=42173.35/min 
[1640000], rate=42304.39/min 
[1650000], rate=42434.63/min 
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[1670000], rate=42729.21/min 
[1680000], rate=42857.14/min 
[1690000], rate=43020.79/min 
[1700000], rate=43165.47/min 
[1710000], rate=43309.41/min 
[1720000], rate=43489.25/min 
[1730000], rate=43631.78/min 
[1740000], rate=43791.95/min 
[1750000], rate=43951.44/min 
[1760000], rate=43872.04/min 
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[1800000], rate=43495.77/min 
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[1850000], rate=43173.86/min 
[1860000], rate=43155.45/min 
[1870000], rate=43170.45/min 
[1880000], rate=43168.77/min 
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[1900000], rate=43165.47/min 
[1910000], rate=43180.11/min 
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[1940000], rate=43303.57/min 
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[1960000], rate=43426.88/min 
[1970000], rate=43471.86/min 
[1980000], rate=43564.36/min 
[1990000], rate=43640.35/min 
[2000000], rate=43731.78/min 
[2010000], rate=43806.76/min 
[2020000], rate=43897.14/min 
[2030000], rate=43987.00/min 
[2040000], rate=44044.62/min 
[2050000], rate=44086.02/min 
[2060000], rate=44127.10/min 
[2070000], rate=44199.29/min 
[2080000], rate=44255.32/min 
[2090000], rate=44310.95/min 
[2100000], rate=44381.82/min 
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[2120000], rate=44506.65/min 
[2130000], rate=44591.77/min 
[2140000], rate=44676.41/min 
[2150000], rate=44760.58/min 
[2160000], rate=44844.29/min 
[2170000], rate=44927.54/min 
[2180000], rate=45010.32/min 
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[2200000], rate=45205.48/min 
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[2220000], rate=45414.25/min 
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[2240000], rate=45621.18/min 
[2250000], rate=45731.71/min 
[2260000], rate=45841.78/min 
[2270000], rate=45951.42/min 
[2280000], rate=46076.12/min 
[2290000], rate=46200.40/min 
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[2310000], rate=46463.29/min 
[2320000], rate=46586.35/min 
[2330000], rate=46724.60/min 
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[2350000], rate=46750.66/min 
[2360000], rate=46748.10/min 
[2370000], rate=46730.20/min 
[2380000], rate=46712.46/min 
[2390000], rate=46679.69/min 
[2400000], rate=46692.61/min 
[2410000], rate=46735.62/min 
[2420000], rate=46763.29/min 
[2430000], rate=46790.76/min 
[2440000], rate=46818.04/min 
[2450000], rate=46860.06/min 
[2460000], rate=46886.91/min 
[2470000], rate=46913.58/min 
[2480000], rate=46969.70/min 
[2490000], rate=47010.70/min 
[2500000], rate=47066.21/min 
[2510000], rate=47136.15/min 
[2520000], rate=47191.01/min 
[2530000], rate=47216.17/min 
[2540000], rate=47211.90/min 
[2550000], rate=47251.39/min 
[2560000], rate=47305.20/min 
[2570000], rate=47373.27/min 
[2580000], rate=47441.01/min 
[2590000], rate=47522.94/min 
[2600000], rate=47575.48/min 
[2610000], rate=47627.74/min 
[2620000], rate=47708.65/min 
[2630000], rate=47774.75/min 
[2640000], rate=47840.53/min 
[2650000], rate=47906.00/min 
[2660000], rate=47956.73/min 
[2670000], rate=48021.58/min 
[2680000], rate=48071.75/min 
[2690000], rate=48136.00/min 
[2700000], rate=48214.29/min 
[2710000], rate=48277.91/min 
[2720000], rate=48341.23/min 
[2730000], rate=48418.56/min 
[2740000], rate=48495.58/min 
[2750000], rate=48586.57/min 
[2760000], rate=48662.94/min 
[2770000], rate=48753.30/min 
[2780000], rate=48843.34/min 
[2790000], rate=48947.37/min 
[2800000], rate=49036.78/min 
[2810000], rate=49140.19/min 
[2820000], rate=49243.31/min 
[2830000], rate=49346.12/min 
[2840000], rate=49448.64/min 
[2850000], rate=49565.22/min 
[2860000], rate=49667.15/min 
[2870000], rate=49783.17/min 
[2880000], rate=49884.53/min 
[2890000], rate=50000.00/min 
[2900000], rate=50100.78/min 
[2910000], rate=50215.70/min 
[2920000], rate=50344.83/min 
[2930000], rate=50473.73/min 
[2940000], rate=50587.90/min 
[2950000], rate=50716.33/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 0.00 reads per min processed...  
 0.00 reads per min processed...  
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 4868852.46 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.UPRkJQ0EKL/BVT_FFPE_TRNA_bst_01_01_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.UPRkJQ0EKL/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -332002.029839
EM: Round [1] log likelihood: -331875.888275
EM: Round [2] log likelihood: -331825.718197
EM: Round [3] log likelihood: -331801.175479
EM: Round [4] log likelihood: -331788.055580
EM: Round [5] log likelihood: -331780.666341
EM: Round [6] log likelihood: -331776.314862
EM: Round [7] log likelihood: -331773.636433
EM: Round [8] log likelihood: -331771.914608
EM: Round [9] log likelihood: -331770.761756
EM: Round [10] log likelihood: -331769.961225
EM: Round [11] log likelihood: -331769.387587
EM: Round [12] log likelihood: -331768.965512
EM: Round [13] log likelihood: -331768.648062
EM: Round [14] log likelihood: -331768.404925
EM: Round [15] log likelihood: -331768.215867
EM: Round [16] log likelihood: -331768.066966
EM: Round [17] log likelihood: -331767.948390
EM: Round [18] log likelihood: -331767.853036
EM: Round [19] log likelihood: -331767.775678
EM: Round [20] log likelihood: -331767.712407
EM: Round [21] log likelihood: -331767.660262
EM: Round [22] log likelihood: -331767.616975
EM: Round [23] log likelihood: -331767.580793
EM: Round [24] log likelihood: -331767.550347
EM: Round [25] log likelihood: -331767.524563
EM: Round [26] log likelihood: -331767.502591
EM: Round [27] log likelihood: -331767.483754
EM: Round [28] log likelihood: -331767.467511
EM: Round [29] log likelihood: -331767.453426
EM: Round [30] log likelihood: -331767.441145
EM: Round [31] log likelihood: -331767.430382
EM: Round [32] log likelihood: -331767.420902
EM: Round [33] log likelihood: -331767.412512
EM: Round [34] log likelihood: -331767.405053
EM: Round [35] log likelihood: -331767.398393
EM: Round [36] log likelihood: -331767.392422
EM: Round [37] log likelihood: -331767.387049
EM: Round [38] log likelihood: -331767.382194
EM: Round [39] log likelihood: -331767.377795
EM: Round [40] log likelihood: -331767.373794
EM: Round [41] log likelihood: -331767.370144
EM: Round [42] log likelihood: -331767.366806
EM: Round [43] log likelihood: -331767.363744
EM: Round [44] log likelihood: -331767.360929
EM: Round [45] log likelihood: -331767.358335
EM: Round [46] log likelihood: -331767.355938
EM: Round [47] log likelihood: -331767.353719
EM: Round [48] log likelihood: -331767.351662
EM: Round [49] log likelihood: -331767.349750
EM: Round [50] log likelihood: -331767.347970
EM: Round [51] log likelihood: -331767.346311
EM: Round [52] log likelihood: -331767.344761
EM: Round [53] log likelihood: -331767.343312
EM: Round [54] log likelihood: -331767.341955
EM: Round [55] log likelihood: -331767.340682
EM: Round [56] log likelihood: -331767.339487
EM: Round [57] log likelihood: -331767.338364
EM: Round [58] log likelihood: -331767.337306
EM: Round [59] log likelihood: -331767.336309
EM: Round [60] log likelihood: -331767.335369
EM: Round [61] log likelihood: -331767.334481
EM: Round [62] log likelihood: -331767.333641
EM: Round [63] log likelihood: -331767.332847
EM: Round [64] log likelihood: -331767.332094
EM: Round [65] log likelihood: -331767.331381
EM: Round [66] log likelihood: -331767.330704
EM: Round [67] log likelihood: -331767.330061
EM: Round [68] log likelihood: -331767.329450
EM: Round [69] log likelihood: -331767.328869
EM: Round [70] log likelihood: -331767.328315
EM: Round [71] log likelihood: -331767.327788
EM: Round [72] log likelihood: -331767.327285
EM: Round [73] log likelihood: -331767.326806
EM: Round [74] log likelihood: -331767.326348
EM: Round [75] log likelihood: -331767.325910
EM: Round [76] log likelihood: -331767.325491
EM: Round [77] log likelihood: -331767.325091
EM: Round [78] log likelihood: -331767.324708
EM: Round [79] log likelihood: -331767.324340
EM: Round [80] log likelihood: -331767.323988
EM: Round [81] log likelihood: -331767.323651
EM: Round [82] log likelihood: -331767.323326
EM: Round [83] log likelihood: -331767.323015
EM: Round [84] log likelihood: -331767.322716
EM: Round [85] log likelihood: -331767.322429
EM: Round [86] log likelihood: -331767.322153
EM: Round [87] log likelihood: -331767.321887
EM: Round [88] log likelihood: -331767.321631
EM: Round [89] log likelihood: -331767.321384
EM: Round [90] log likelihood: -331767.321147
EM: Round [91] log likelihood: -331767.320918
EM: Round [92] log likelihood: -331767.320697
EM: Round [93] log likelihood: -331767.320484
EM: Round [94] log likelihood: -331767.320279
EM: Round [95] log likelihood: -331767.320080
EM: Round [96] log likelihood: -331767.319889
EM: Round [97] log likelihood: -331767.319703
EM: Round [98] log likelihood: -331767.319524
EM: Round [99] log likelihood: -331767.319351
EM: Round [100] log likelihood: -331767.319184
EM: Round [101] log likelihood: -331767.319022
EM: Round [102] log likelihood: -331767.318865
EM: Round [103] log likelihood: -331767.318714
EM: Round [104] log likelihood: -331767.318567
EM: Round [105] log likelihood: -331767.318425
EM: Round [106] log likelihood: -331767.318287
EM: Round [107] log likelihood: -331767.318153
EM: Round [108] log likelihood: -331767.318024
EM: Round [109] log likelihood: -331767.317898
EM: Round [110] log likelihood: -331767.317777
EM: Round [111] log likelihood: -331767.317658
EM: Round [112] log likelihood: -331767.317544
EM: Round [113] log likelihood: -331767.317433
EM: Round [114] log likelihood: -331767.317325
EM: Round [115] log likelihood: -331767.317220
EM: Round [116] log likelihood: -331767.317119
EM: Round [117] log likelihood: -331767.317020
EM: Stopping iterations at round 117 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -331821.614951
EM: Round [1] log likelihood: -331712.991576
EM: Round [2] log likelihood: -331671.702479
EM: Round [3] log likelihood: -331652.011524
EM: Round [4] log likelihood: -331641.654425
EM: Round [5] log likelihood: -331635.898066
EM: Round [6] log likelihood: -331632.554925
EM: Round [7] log likelihood: -331630.529282
EM: Round [8] log likelihood: -331629.249557
EM: Round [9] log likelihood: -331628.408207
EM: Round [10] log likelihood: -331627.834548
EM: Round [11] log likelihood: -331627.430681
EM: Round [12] log likelihood: -331627.138491
EM: Round [13] log likelihood: -331626.922241
EM: Round [14] log likelihood: -331626.759179
EM: Round [15] log likelihood: -331626.634328
EM: Round [16] log likelihood: -331626.537518
EM: Round [17] log likelihood: -331626.461655
EM: Round [18] log likelihood: -331626.401668
EM: Round [19] log likelihood: -331626.353859
EM: Round [20] log likelihood: -331626.315488
EM: Round [21] log likelihood: -331626.284493
EM: Round [22] log likelihood: -331626.259308
EM: Round [23] log likelihood: -331626.238727
EM: Round [24] log likelihood: -331626.221818
EM: Round [25] log likelihood: -331626.207853
EM: Round [26] log likelihood: -331626.196260
EM: Round [27] log likelihood: -331626.186587
EM: Round [28] log likelihood: -331626.178476
EM: Round [29] log likelihood: -331626.171640
EM: Round [30] log likelihood: -331626.165849
EM: Round [31] log likelihood: -331626.160919
EM: Round [32] log likelihood: -331626.156701
EM: Round [33] log likelihood: -331626.153073
EM: Round [34] log likelihood: -331626.149936
EM: Round [35] log likelihood: -331626.147210
EM: Round [36] log likelihood: -331626.144828
EM: Round [37] log likelihood: -331626.142737
EM: Round [38] log likelihood: -331626.140891
EM: Round [39] log likelihood: -331626.139253
EM: Round [40] log likelihood: -331626.137792
EM: Round [41] log likelihood: -331626.136483
EM: Round [42] log likelihood: -331626.135303
EM: Round [43] log likelihood: -331626.134236
EM: Round [44] log likelihood: -331626.133266
EM: Round [45] log likelihood: -331626.132380
EM: Round [46] log likelihood: -331626.131567
EM: Round [47] log likelihood: -331626.130818
EM: Round [48] log likelihood: -331626.130126
EM: Round [49] log likelihood: -331626.129484
EM: Round [50] log likelihood: -331626.128886
EM: Round [51] log likelihood: -331626.128328
EM: Round [52] log likelihood: -331626.127804
EM: Round [53] log likelihood: -331626.127312
EM: Round [54] log likelihood: -331626.126849
EM: Round [55] log likelihood: -331626.126411
EM: Round [56] log likelihood: -331626.125996
EM: Round [57] log likelihood: -331626.125603
EM: Round [58] log likelihood: -331626.125228
EM: Round [59] log likelihood: -331626.124872
EM: Round [60] log likelihood: -331626.124532
EM: Round [61] log likelihood: -331626.124207
EM: Round [62] log likelihood: -331626.123895
EM: Round [63] log likelihood: -331626.123597
EM: Round [64] log likelihood: -331626.123311
EM: Round [65] log likelihood: -331626.123036
EM: Round [66] log likelihood: -331626.122771
EM: Round [67] log likelihood: -331626.122516
EM: Round [68] log likelihood: -331626.122271
EM: Round [69] log likelihood: -331626.122034
EM: Round [70] log likelihood: -331626.121806
EM: Round [71] log likelihood: -331626.121585
EM: Round [72] log likelihood: -331626.121371
EM: Round [73] log likelihood: -331626.121165
EM: Round [74] log likelihood: -331626.120965
EM: Round [75] log likelihood: -331626.120772
EM: Round [76] log likelihood: -331626.120584
EM: Round [77] log likelihood: -331626.120402
EM: Round [78] log likelihood: -331626.120226
EM: Round [79] log likelihood: -331626.120055
EM: Round [80] log likelihood: -331626.119889
EM: Round [81] log likelihood: -331626.119728
EM: Round [82] log likelihood: -331626.119571
EM: Round [83] log likelihood: -331626.119419
EM: Round [84] log likelihood: -331626.119272
EM: Round [85] log likelihood: -331626.119128
EM: Round [86] log likelihood: -331626.118988
EM: Round [87] log likelihood: -331626.118853
EM: Round [88] log likelihood: -331626.118720
EM: Round [89] log likelihood: -331626.118592
EM: Round [90] log likelihood: -331626.118467
EM: Round [91] log likelihood: -331626.118345
EM: Round [92] log likelihood: -331626.118226
EM: Round [93] log likelihood: -331626.118111
EM: Round [94] log likelihood: -331626.117999
EM: Round [95] log likelihood: -331626.117889
EM: Round [96] log likelihood: -331626.117782
EM: Round [97] log likelihood: -331626.117678
EM: Round [98] log likelihood: -331626.117577
EM: Round [99] log likelihood: -331626.117479
EM: Stopping iterations at round 99 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.UPRkJQ0EKL/./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.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.UPRkJQ0EKL/./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.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 273616163 > /tmp/nxf.UPRkJQ0EKL/./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.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir > /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir --annotate /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.UPRkJQ0EKL/./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.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir
-done, see /tmp/nxf.UPRkJQ0EKL/./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.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.UPRkJQ0EKL/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1582, filtered: 14210)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.UPRkJQ0EKL/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.UPRkJQ0EKL/./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.UPRkJQ0EKL/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000237296.9]
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WARNING, no entry stored in dbm for [ENSG00000246203.2]
WARNING, no entry stored in dbm for [ENSG00000278932.4]
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WARNING, no entry stored in dbm for [ENSG00000224540.1]
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WARNING, no entry stored in dbm for [ENSG00000279021.1]
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WARNING, no entry stored in dbm for [ENSG00000275613.2]
WARNING, no entry stored in dbm for [ENSG00000272195.1]
WARNING, no entry stored in dbm for [ENSG00000244198.7]
WARNING, no entry stored in dbm for [ENSG00000215158.9]
WARNING, no entry stored in dbm for [ENSG00000255503.1]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000256035.1]
WARNING, no entry stored in dbm for [ENSG00000230551.4]
WARNING, no entry stored in dbm for [ENSG00000219529.2]
WARNING, no entry stored in dbm for [ENSG00000239393.1]
WARNING, no entry stored in dbm for [ENSG00000266931.2]
WARNING, no entry stored in dbm for [ENSG00000240237.1]
WARNING, no entry stored in dbm for [ENSG00000288531.1]
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 [ENSG00000288088.1]
WARNING, no entry stored in dbm for [ENSG00000283696.1]
WARNING, no entry stored in dbm for [ENSG00000287356.1]
WARNING, no entry stored in dbm for [ENSG00000231073.1]
WARNING, no entry stored in dbm for [ENSG00000170161.7]
WARNING, no entry stored in dbm for [ENSG00000231212.1]
WARNING, no entry stored in dbm for [ENSG00000237208.1]
WARNING, no entry stored in dbm for [ENSG00000227619.3]
WARNING, no entry stored in dbm for [ENSG00000234640.1]
WARNING, no entry stored in dbm for [ENSG00000272405.1]
WARNING, no entry stored in dbm for [ENSG00000229953.1]
WARNING, no entry stored in dbm for [ENSG00000286215.1]
WARNING, no entry stored in dbm for [ENSG00000285637.2]
WARNING, no entry stored in dbm for [ENSG00000239665.8]
WARNING, no entry stored in dbm for [ENSG00000258377.1]
WARNING, no entry stored in dbm for [ENSG00000258377.1]
WARNING, no entry stored in dbm for [ENSG00000274261.2]
WARNING, no entry stored in dbm for [ENSG00000258875.6]
WARNING, no entry stored in dbm for [ENSG00000286587.1]
WARNING, no entry stored in dbm for [ENSG00000231881.2]
WARNING, no entry stored in dbm for [ENSG00000183239.5]
WARNING, no entry stored in dbm for [ENSG00000243730.2]
WARNING, no entry stored in dbm for [ENSG00000279930.1]
WARNING, no entry stored in dbm for [ENSG00000280011.1]
WARNING, no entry stored in dbm for [ENSG00000284633.1]
WARNING, no entry stored in dbm for [ENSG00000279136.1]
WARNING, no entry stored in dbm for [ENSG00000207579.1]
WARNING, no entry stored in dbm for [ENSG00000226310.1]
WARNING, no entry stored in dbm for [ENSG00000223756.7]
WARNING, no entry stored in dbm for [ENSG00000248692.5]
WARNING, no entry stored in dbm for [ENSG00000161912.18]
WARNING, no entry stored in dbm for [ENSG00000286912.1]
WARNING, no entry stored in dbm for [ENSG00000180139.11]
WARNING, no entry stored in dbm for [ENSG00000229800.1]
WARNING, no entry stored in dbm for [ENSG00000279278.1]
WARNING, no entry stored in dbm for [ENSG00000237017.1]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000281741.2]
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 [ENSG00000249574.1]
WARNING, no entry stored in dbm for [ENSG00000229797.2]
WARNING, no entry stored in dbm for [ENSG00000261404.7]
WARNING, no entry stored in dbm for [ENSG00000236792.1]
WARNING, no entry stored in dbm for [ENSG00000229930.1]
WARNING, no entry stored in dbm for [ENSG00000264107.1]
WARNING, no entry stored in dbm for [ENSG00000250999.2]
WARNING, no entry stored in dbm for [ENSG00000280064.1]
WARNING, no entry stored in dbm for [ENSG00000276484.1]
WARNING, no entry stored in dbm for [ENSG00000276484.1]
WARNING, no entry stored in dbm for [ENSG00000276484.1]
WARNING, no entry stored in dbm for [ENSG00000276484.1]
WARNING, no entry stored in dbm for [ENSG00000257398.8]
WARNING, no entry stored in dbm for [ENSG00000233031.1]
WARNING, no entry stored in dbm for [ENSG00000260196.1]
WARNING, no entry stored in dbm for [ENSG00000280248.1]
WARNING, no entry stored in dbm for [ENSG00000286619.1]
WARNING, no entry stored in dbm for [ENSG00000284675.1]
WARNING, no entry stored in dbm for [ENSG00000215692.2]
WARNING, no entry stored in dbm for [ENSG00000250159.7]
WARNING, no entry stored in dbm for [ENSG00000260522.1]
WARNING, no entry stored in dbm for [ENSG00000258130.8]
WARNING, no entry stored in dbm for [ENSG00000225108.1]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
WARNING, no entry stored in dbm for [ENSG00000251574.8]
WARNING, no entry stored in dbm for [ENSG00000285042.1]
WARNING, no entry stored in dbm for [ENSG00000244538.1]
WARNING, no entry stored in dbm for [ENSG00000251378.1]
WARNING, no entry stored in dbm for [ENSG00000249275.1]
WARNING, no entry stored in dbm for [ENSG00000279811.1]
WARNING, no entry stored in dbm for [ENSG00000228852.6]
WARNING, no entry stored in dbm for [ENSG00000228830.1]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000287588.1]
WARNING, no entry stored in dbm for [ENSG00000272953.1]
WARNING, no entry stored in dbm for [ENSG00000279901.1]
WARNING, no entry stored in dbm for [ENSG00000287826.1]
WARNING, no entry stored in dbm for [ENSG00000264164.1]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000277229.1]
WARNING, no entry stored in dbm for [ENSG00000184616.9]
WARNING, no entry stored in dbm for [ENSG00000286935.1]
WARNING, no entry stored in dbm for [ENSG00000216285.5]
WARNING, no entry stored in dbm for [ENSG00000286069.2]
WARNING, no entry stored in dbm for [ENSG00000234072.1]
WARNING, no entry stored in dbm for [ENSG00000239985.2]
WARNING, no entry stored in dbm for [ENSG00000224365.1]
WARNING, no entry stored in dbm for [ENSG00000287250.1]
WARNING, no entry stored in dbm for [ENSG00000287188.1]
WARNING, no entry stored in dbm for [ENSG00000257337.7]
WARNING, no entry stored in dbm for [ENSG00000236172.7]
WARNING, no entry stored in dbm for [ENSG00000197099.8]
WARNING, no entry stored in dbm for [ENSG00000228801.6]
WARNING, no entry stored in dbm for [ENSG00000212664.5]
WARNING, no entry stored in dbm for [ENSG00000263887.7]
WARNING, no entry stored in dbm for [ENSG00000259433.2]
WARNING, no entry stored in dbm for [ENSG00000253919.1]
WARNING, no entry stored in dbm for [ENSG00000279523.1]
WARNING, no entry stored in dbm for [ENSG00000267040.6]
WARNING, no entry stored in dbm for [ENSG00000260963.2]
WARNING, no entry stored in dbm for [ENSG00000260693.1]
WARNING, no entry stored in dbm for [ENSG00000245904.4]
WARNING, no entry stored in dbm for [ENSG00000236833.1]
WARNING, no entry stored in dbm for [ENSG00000242327.1]
WARNING, no entry stored in dbm for [ENSG00000240669.1]
WARNING, no entry stored in dbm for [ENSG00000244436.2]
WARNING, no entry stored in dbm for [ENSG00000174171.6]
WARNING, no entry stored in dbm for [ENSG00000285106.2]
WARNING, no entry stored in dbm for [ENSG00000218175.2]
WARNING, no entry stored in dbm for [ENSG00000269032.1]
WARNING, no entry stored in dbm for [ENSG00000253166.2]
WARNING, no entry stored in dbm for [ENSG00000272384.1]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000267784.1]
WARNING, no entry stored in dbm for [ENSG00000268884.1]
WARNING, no entry stored in dbm for [ENSG00000230721.1]
WARNING, no entry stored in dbm for [ENSG00000283459.1]
WARNING, no entry stored in dbm for [ENSG00000238045.9]
WARNING, no entry stored in dbm for [ENSG00000259780.3]
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 [ENSG00000230189.7]
WARNING, no entry stored in dbm for [ENSG00000244657.1]
WARNING, no entry stored in dbm for [ENSG00000276651.1]
WARNING, no entry stored in dbm for [ENSG00000267009.6]
WARNING, no entry stored in dbm for [ENSG00000233565.1]
WARNING, no entry stored in dbm for [ENSG00000257074.3]
WARNING, no entry stored in dbm for [ENSG00000244055.2]
WARNING, no entry stored in dbm for [ENSG00000218586.3]
WARNING, no entry stored in dbm for [ENSG00000268460.2]
WARNING, no entry stored in dbm for [ENSG00000226040.3]
WARNING, no entry stored in dbm for [ENSG00000264044.1]
WARNING, no entry stored in dbm for [ENSG00000262879.6]
WARNING, no entry stored in dbm for [ENSG00000274712.2]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000267698.1]
WARNING, no entry stored in dbm for [ENSG00000214330.4]
WARNING, no entry stored in dbm for [ENSG00000251595.7]
WARNING, no entry stored in dbm for [ENSG00000285756.2]


	* STAR-Fusion complete.  See output: /tmp/nxf.UPRkJQ0EKL/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)