File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/efad157e853e1c2c3646f6a52a2925/.command.log
Size
70.1 KB
Attempt
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/6ff4092dd52ec3d8c9234b96f1d6b6/tih_rna_sample_00117_23H5VFLT4_s37.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/efad157e853e1c2c3646f6a52a2925/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/efad157e853e1c2c3646f6a52a2925/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/44592e76cd519b391924b7573d99bb/tih_rna_sample_00117_23H5VFLT4_s37_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/44592e76cd519b391924b7573d99bb/tih_rna_sample_00117_23H5VFLT4_s37_1.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.4W5Uf4FEVT/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary
-sample contains 207404262 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir  -J /tmp/nxf.4W5Uf4FEVT/tih_rna_sample_00117_23H5VFLT4_s37.Chimeric.out.junction  -O /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.4W5Uf4FEVT/tih_rna_sample_00117_23H5VFLT4_s37.Chimeric.out.junction
-building interval tree based on /tmp/nxf.4W5Uf4FEVT/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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[1710000], rate=84723.37/min -building interval tree based on /tmp/nxf.4W5Uf4FEVT/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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[1710000], rate=77027.03/min -building interval tree based on /tmp/nxf.4W5Uf4FEVT/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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[1670000], rate=69728.60/min 
[1680000], rate=69806.09/min 
[1690000], rate=69931.03/min 
[1700000], rate=70103.09/min -building interval tree based on /tmp/nxf.4W5Uf4FEVT/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=100000.00/min 
[30000], rate=112500.00/min 
[40000], rate=109090.91/min 
[50000], rate=107142.86/min 
[60000], rate=116129.03/min 
[70000], rate=116666.67/min 
[80000], rate=129729.73/min 
[90000], rate=142105.26/min 
[100000], rate=150000.00/min 
[110000], rate=146666.67/min 
[120000], rate=144000.00/min 
[130000], rate=144444.44/min 
[140000], rate=140000.00/min 
[150000], rate=140625.00/min 
[160000], rate=139130.43/min 
[170000], rate=141666.67/min 
[180000], rate=150000.00/min 
[190000], rate=156164.38/min 
[200000], rate=151898.73/min 
[210000], rate=148235.29/min 
[220000], rate=146666.67/min 
[230000], rate=145263.16/min 
[240000], rate=146938.78/min 
[250000], rate=145631.07/min 
[260000], rate=143119.27/min 
[270000], rate=144642.86/min 
[280000], rate=146086.96/min 
[290000], rate=148717.95/min 
[300000], rate=147540.98/min 
[310000], rate=144186.05/min 
[320000], rate=144360.90/min 
[330000], rate=145588.24/min 
[340000], rate=146762.59/min 
[350000], rate=144827.59/min 
[360000], rate=145945.95/min 
[370000], rate=147019.87/min 
[380000], rate=148051.95/min 
[390000], rate=135260.12/min 
[400000], rate=122448.98/min 
[410000], rate=113364.06/min 
[420000], rate=105882.35/min 
[430000], rate=100389.11/min 
[440000], rate=95306.86/min 
[450000], rate=91836.73/min 
[460000], rate=87898.09/min 
[470000], rate=83431.95/min 
[480000], rate=79558.01/min 
[490000], rate=77572.56/min 
[500000], rate=75949.37/min 
[510000], rate=73031.03/min 
[520000], rate=70909.09/min 
[530000], rate=69736.84/min 
[540000], rate=68936.17/min 
[550000], rate=68181.82/min 
[560000], rate=67334.67/min 
[570000], rate=66796.88/min 
[580000], rate=65909.09/min 
[590000], rate=64954.13/min 
[600000], rate=64400.72/min 
[610000], rate=64098.07/min 
[620000], rate=63807.89/min 
[630000], rate=63529.41/min 
[640000], rate=63261.94/min 
[650000], rate=63106.80/min 
[660000], rate=63157.89/min 
[670000], rate=63108.32/min 
[680000], rate=62962.96/min 
[690000], rate=62822.46/min 
[700000], rate=62686.57/min 
[710000], rate=62739.32/min 
[720000], rate=62699.56/min 
[730000], rate=62482.17/min 
[740000], rate=62535.21/min 
[750000], rate=62500.00/min 
[760000], rate=62465.75/min 
[770000], rate=62432.43/min 
[780000], rate=62483.31/min 
[790000], rate=62450.59/min 
[800000], rate=62581.49/min 
[810000], rate=62548.26/min 
[820000], rate=62515.88/min 
[830000], rate=62562.81/min 
[840000], rate=62608.70/min 
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[870000], rate=62815.88/min 
[880000], rate=63007.16/min 
[890000], rate=63120.57/min 
[900000], rate=63231.85/min 
[910000], rate=63267.67/min 
[920000], rate=63521.29/min 
[930000], rate=63771.43/min 
[940000], rate=64090.91/min 
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[960000], rate=64719.10/min 
[970000], rate=65027.93/min 
[980000], rate=65333.33/min 
[990000], rate=65635.36/min 
[1000000], rate=66006.60/min 
[1010000], rate=66374.59/min 
[1020000], rate=66449.51/min 
[1030000], rate=66451.61/min 
[1040000], rate=66312.43/min 
[1050000], rate=66385.67/min 
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[1100000], rate=66599.39/min 
[1110000], rate=66666.67/min 
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[1130000], rate=66798.03/min 
[1140000], rate=66993.14/min 
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[1160000], rate=67311.41/min 
[1170000], rate=67435.16/min 
[1180000], rate=67621.78/min 
[1190000], rate=67870.72/min 
[1200000], rate=68117.31/min 
[1210000], rate=68361.58/min 
[1220000], rate=68603.56/min 
[1230000], rate=68779.12/min 
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[1250000], rate=67934.78/min 
[1260000], rate=67620.75/min 
[1270000], rate=67433.63/min 
[1280000], rate=67191.60/min 
[1290000], rate=67071.06/min 
[1300000], rate=66895.37/min 
[1310000], rate=66779.95/min 
[1320000], rate=66722.83/min 
[1330000], rate=66611.02/min 
[1340000], rate=66556.29/min 
[1350000], rate=66447.91/min 
[1360000], rate=66503.67/min 
[1370000], rate=66612.64/min 
[1380000], rate=66613.03/min 
[1390000], rate=66613.42/min 
[1400000], rate=66666.67/min 
[1410000], rate=66719.24/min 
[1420000], rate=66771.16/min 
[1430000], rate=66822.43/min 
[1440000], rate=66873.07/min 
[1450000], rate=66974.60/min 
[1460000], rate=67075.04/min 
[1470000], rate=67225.61/min 
[1480000], rate=67374.81/min 
[1490000], rate=67573.70/min 
[1500000], rate=67720.09/min 
[1510000], rate=67966.99/min 
[1520000], rate=68161.43/min 
[1530000], rate=68405.37/min 
[1540000], rate=68343.20/min 
[1550000], rate=68181.82/min 
[1560000], rate=68023.26/min 
[1570000], rate=67965.37/min 
[1580000], rate=67908.31/min 
[1590000], rate=67803.84/min 
[1600000], rate=67796.61/min 
[1610000], rate=67789.47/min 
[1620000], rate=67735.19/min 
[1630000], rate=67728.53/min 
[1640000], rate=67721.95/min 
[1650000], rate=67715.46/min 
[1660000], rate=67755.10/min 
[1670000], rate=67794.32/min 
[1680000], rate=67878.79/min 
[1690000], rate=68008.05/min 
[1700000], rate=68181.82/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 6000000.00 reads per min processed...  
 12000000.00 reads per min processed...  
 18000000.00 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...  
 5571428.57 reads per min processed...  
 5600000.00 reads per min processed...  
 5625000.00 reads per min processed...  
 5647058.82 reads per min processed...  
 5368421.05 reads per min processed...  
 5400000.00 reads per min processed...  
 5428571.43 reads per min processed...  
 5454545.45 reads per min processed...  
 5250000.00 reads per min processed...  
 5280000.00 reads per min processed...  
 5307692.31 reads per min processed...  
 5142857.14 reads per min processed...  
 5172413.79 reads per min processed...  
 5200000.00 reads per min processed...  
 5225806.45 reads per min processed...  
 5250000.00 reads per min processed...  
 5117647.06 reads per min processed...  
 5142857.14 reads per min processed...  
 5166666.67 reads per min processed...  
 5189189.19 reads per min processed...  
 5210526.32 reads per min processed...  
 5230769.23 reads per min processed...  
 5384615.38 reads per min processed...  
 5400000.00 reads per min processed...  
 5550000.00 reads per min processed...  
 5560975.61 reads per min processed...  
 5571428.57 reads per min processed...  
 5581395.35 reads per min processed...  
 5590909.09 reads per min processed...  
 5600000.00 reads per min processed...  
 5608695.65 reads per min processed...  
 5617021.28 reads per min processed...  
 5625000.00 reads per min processed...  
 5632653.06 reads per min processed...  
 5640000.00 reads per min processed...  
 5647058.82 reads per min processed...  
 5653846.15 reads per min processed...  
 5555555.56 reads per min processed...  
 5563636.36 reads per min processed...  
 5571428.57 reads per min processed...  
 5578947.37 reads per min processed...  
 5586206.90 reads per min processed...  
 5593220.34 reads per min processed...  
 5600000.00 reads per min processed...  
 5606557.38 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.4W5Uf4FEVT/tih_rna_sample_00117_23H5VFLT4_s37.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.4W5Uf4FEVT/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -202599.323527
EM: Round [1] log likelihood: -202503.195726
EM: Round [2] log likelihood: -202467.492012
EM: Round [3] log likelihood: -202450.486511
EM: Round [4] log likelihood: -202441.384669
EM: Round [5] log likelihood: -202436.188701
EM: Round [6] log likelihood: -202433.069882
EM: Round [7] log likelihood: -202431.105470
EM: Round [8] log likelihood: -202429.808509
EM: Round [9] log likelihood: -202428.913542
EM: Round [10] log likelihood: -202428.270902
EM: Round [11] log likelihood: -202427.793100
EM: Round [12] log likelihood: -202427.427083
EM: Round [13] log likelihood: -202427.139512
EM: Round [14] log likelihood: -202426.908714
EM: Round [15] log likelihood: -202426.720151
EM: Round [16] log likelihood: -202426.563779
EM: Round [17] log likelihood: -202426.432477
EM: Round [18] log likelihood: -202426.321063
EM: Round [19] log likelihood: -202426.225688
EM: Round [20] log likelihood: -202426.143429
EM: Round [21] log likelihood: -202426.072030
EM: Round [22] log likelihood: -202426.009714
EM: Round [23] log likelihood: -202425.955069
EM: Round [24] log likelihood: -202425.906949
EM: Round [25] log likelihood: -202425.864420
EM: Round [26] log likelihood: -202425.826709
EM: Round [27] log likelihood: -202425.793171
EM: Round [28] log likelihood: -202425.763265
EM: Round [29] log likelihood: -202425.736532
EM: Round [30] log likelihood: -202425.712580
EM: Round [31] log likelihood: -202425.691076
EM: Round [32] log likelihood: -202425.671730
EM: Round [33] log likelihood: -202425.654294
EM: Round [34] log likelihood: -202425.638551
EM: Round [35] log likelihood: -202425.624313
EM: Round [36] log likelihood: -202425.611415
EM: Round [37] log likelihood: -202425.599713
EM: Round [38] log likelihood: -202425.589079
EM: Round [39] log likelihood: -202425.579403
EM: Round [40] log likelihood: -202425.570586
EM: Round [41] log likelihood: -202425.562541
EM: Round [42] log likelihood: -202425.555191
EM: Round [43] log likelihood: -202425.548466
EM: Round [44] log likelihood: -202425.542306
EM: Round [45] log likelihood: -202425.536658
EM: Round [46] log likelihood: -202425.531471
EM: Round [47] log likelihood: -202425.526704
EM: Round [48] log likelihood: -202425.522317
EM: Round [49] log likelihood: -202425.518276
EM: Round [50] log likelihood: -202425.514549
EM: Round [51] log likelihood: -202425.511109
EM: Round [52] log likelihood: -202425.507931
EM: Round [53] log likelihood: -202425.504991
EM: Round [54] log likelihood: -202425.502269
EM: Round [55] log likelihood: -202425.499748
EM: Round [56] log likelihood: -202425.497409
EM: Round [57] log likelihood: -202425.495238
EM: Round [58] log likelihood: -202425.493222
EM: Round [59] log likelihood: -202425.491348
EM: Round [60] log likelihood: -202425.489604
EM: Round [61] log likelihood: -202425.487980
EM: Round [62] log likelihood: -202425.486467
EM: Round [63] log likelihood: -202425.485057
EM: Round [64] log likelihood: -202425.483741
EM: Round [65] log likelihood: -202425.482513
EM: Round [66] log likelihood: -202425.481366
EM: Round [67] log likelihood: -202425.480293
EM: Round [68] log likelihood: -202425.479290
EM: Round [69] log likelihood: -202425.478352
EM: Round [70] log likelihood: -202425.477474
EM: Round [71] log likelihood: -202425.476651
EM: Round [72] log likelihood: -202425.475880
EM: Round [73] log likelihood: -202425.475158
EM: Round [74] log likelihood: -202425.474480
EM: Round [75] log likelihood: -202425.473844
EM: Round [76] log likelihood: -202425.473247
EM: Round [77] log likelihood: -202425.472686
EM: Round [78] log likelihood: -202425.472160
EM: Round [79] log likelihood: -202425.471665
EM: Round [80] log likelihood: -202425.471200
EM: Round [81] log likelihood: -202425.470762
EM: Round [82] log likelihood: -202425.470351
EM: Round [83] log likelihood: -202425.469964
EM: Round [84] log likelihood: -202425.469600
EM: Round [85] log likelihood: -202425.469257
EM: Round [86] log likelihood: -202425.468934
EM: Round [87] log likelihood: -202425.468630
EM: Round [88] log likelihood: -202425.468343
EM: Round [89] log likelihood: -202425.468073
EM: Round [90] log likelihood: -202425.467818
EM: Round [91] log likelihood: -202425.467578
EM: Round [92] log likelihood: -202425.467352
EM: Round [93] log likelihood: -202425.467138
EM: Round [94] log likelihood: -202425.466937
EM: Round [95] log likelihood: -202425.466747
EM: Round [96] log likelihood: -202425.466567
EM: Round [97] log likelihood: -202425.466398
EM: Round [98] log likelihood: -202425.466238
EM: Round [99] log likelihood: -202425.466087
EM: Round [100] log likelihood: -202425.465945
EM: Round [101] log likelihood: -202425.465810
EM: Round [102] log likelihood: -202425.465683
EM: Round [103] log likelihood: -202425.465562
EM: Round [104] log likelihood: -202425.465449
EM: Round [105] log likelihood: -202425.465341
EM: Round [106] log likelihood: -202425.465240
EM: Round [107] log likelihood: -202425.465144
EM: Stopping iterations at round 107 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -202435.944121
EM: Round [1] log likelihood: -202351.052874
EM: Round [2] log likelihood: -202320.667733
EM: Round [3] log likelihood: -202306.499782
EM: Round [4] log likelihood: -202299.010207
EM: Round [5] log likelihood: -202294.760016
EM: Round [6] log likelihood: -202292.213304
EM: Round [7] log likelihood: -202290.608870
EM: Round [8] log likelihood: -202289.548802
EM: Round [9] log likelihood: -202288.816820
EM: Round [10] log likelihood: -202288.290940
EM: Round [11] log likelihood: -202287.899764
EM: Round [12] log likelihood: -202287.599949
EM: Round [13] log likelihood: -202287.364244
EM: Round [14] log likelihood: -202287.174935
EM: Round [15] log likelihood: -202287.020139
EM: Round [16] log likelihood: -202286.891652
EM: Round [17] log likelihood: -202286.783656
EM: Round [18] log likelihood: -202286.691921
EM: Round [19] log likelihood: -202286.613302
EM: Round [20] log likelihood: -202286.545414
EM: Round [21] log likelihood: -202286.486412
EM: Round [22] log likelihood: -202286.434846
EM: Round [23] log likelihood: -202286.389560
EM: Round [24] log likelihood: -202286.349620
EM: Round [25] log likelihood: -202286.314259
EM: Round [26] log likelihood: -202286.282848
EM: Round [27] log likelihood: -202286.254859
EM: Round [28] log likelihood: -202286.229848
EM: Round [29] log likelihood: -202286.207442
EM: Round [30] log likelihood: -202286.187320
EM: Round [31] log likelihood: -202286.169210
EM: Round [32] log likelihood: -202286.152875
EM: Round [33] log likelihood: -202286.138113
EM: Round [34] log likelihood: -202286.124746
EM: Round [35] log likelihood: -202286.112621
EM: Round [36] log likelihood: -202286.101604
EM: Round [37] log likelihood: -202286.091576
EM: Round [38] log likelihood: -202286.082434
EM: Round [39] log likelihood: -202286.074088
EM: Round [40] log likelihood: -202286.066457
EM: Round [41] log likelihood: -202286.059469
EM: Round [42] log likelihood: -202286.053062
EM: Round [43] log likelihood: -202286.047180
EM: Round [44] log likelihood: -202286.041773
EM: Round [45] log likelihood: -202286.036796
EM: Round [46] log likelihood: -202286.032209
EM: Round [47] log likelihood: -202286.027978
EM: Round [48] log likelihood: -202286.024071
EM: Round [49] log likelihood: -202286.020458
EM: Round [50] log likelihood: -202286.017114
EM: Round [51] log likelihood: -202286.014016
EM: Round [52] log likelihood: -202286.011144
EM: Round [53] log likelihood: -202286.008478
EM: Round [54] log likelihood: -202286.006001
EM: Round [55] log likelihood: -202286.003698
EM: Round [56] log likelihood: -202286.001556
EM: Round [57] log likelihood: -202285.999561
EM: Round [58] log likelihood: -202285.997701
EM: Round [59] log likelihood: -202285.995967
EM: Round [60] log likelihood: -202285.994349
EM: Round [61] log likelihood: -202285.992838
EM: Round [62] log likelihood: -202285.991426
EM: Round [63] log likelihood: -202285.990106
EM: Round [64] log likelihood: -202285.988871
EM: Round [65] log likelihood: -202285.987715
EM: Round [66] log likelihood: -202285.986632
EM: Round [67] log likelihood: -202285.985618
EM: Round [68] log likelihood: -202285.984667
EM: Round [69] log likelihood: -202285.983775
EM: Round [70] log likelihood: -202285.982938
EM: Round [71] log likelihood: -202285.982153
EM: Round [72] log likelihood: -202285.981416
EM: Round [73] log likelihood: -202285.980723
EM: Round [74] log likelihood: -202285.980072
EM: Round [75] log likelihood: -202285.979460
EM: Round [76] log likelihood: -202285.978885
EM: Round [77] log likelihood: -202285.978343
EM: Round [78] log likelihood: -202285.977834
EM: Round [79] log likelihood: -202285.977355
EM: Round [80] log likelihood: -202285.976904
EM: Round [81] log likelihood: -202285.976479
EM: Round [82] log likelihood: -202285.976078
EM: Round [83] log likelihood: -202285.975701
EM: Round [84] log likelihood: -202285.975346
EM: Round [85] log likelihood: -202285.975011
EM: Round [86] log likelihood: -202285.974695
EM: Round [87] log likelihood: -202285.974398
EM: Round [88] log likelihood: -202285.974117
EM: Round [89] log likelihood: -202285.973852
EM: Round [90] log likelihood: -202285.973602
EM: Round [91] log likelihood: -202285.973366
EM: Round [92] log likelihood: -202285.973143
EM: Round [93] log likelihood: -202285.972933
EM: Round [94] log likelihood: -202285.972735
EM: Round [95] log likelihood: -202285.972547
EM: Round [96] log likelihood: -202285.972370
EM: Round [97] log likelihood: -202285.972203
EM: Round [98] log likelihood: -202285.972045
EM: Round [99] log likelihood: -202285.971896
EM: Round [100] log likelihood: -202285.971755
EM: Round [101] log likelihood: -202285.971622
EM: Round [102] log likelihood: -202285.971496
EM: Round [103] log likelihood: -202285.971377
EM: Round [104] log likelihood: -202285.971264
EM: Round [105] log likelihood: -202285.971158
EM: Round [106] log likelihood: -202285.971057
EM: Round [107] log likelihood: -202285.970961
EM: Stopping iterations at round 107 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.4W5Uf4FEVT/./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.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.4W5Uf4FEVT/./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.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 207404262 > /tmp/nxf.4W5Uf4FEVT/./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.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir > /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir --annotate /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.4W5Uf4FEVT/./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.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir
-done, see /tmp/nxf.4W5Uf4FEVT/./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.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.4W5Uf4FEVT/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1637, filtered: 10792)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.4W5Uf4FEVT/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.4W5Uf4FEVT/./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.4W5Uf4FEVT/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000245958.6]
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WARNING, no entry stored in dbm for [ENSG00000271933.1]
WARNING, no entry stored in dbm for [ENSG00000254418.1]
WARNING, no entry stored in dbm for [ENSG00000270583.1]
WARNING, no entry stored in dbm for [ENSG00000258454.1]
WARNING, no entry stored in dbm for [ENSG00000202538.1]
WARNING, no entry stored in dbm for [ENSG00000200795.1]
WARNING, no entry stored in dbm for [ENSG00000286232.1]
WARNING, no entry stored in dbm for [ENSG00000223508.5]
WARNING, no entry stored in dbm for [ENSG00000280414.1]
WARNING, no entry stored in dbm for [ENSG00000220505.2]
WARNING, no entry stored in dbm for [ENSG00000250320.6]
WARNING, no entry stored in dbm for [ENSG00000231793.5]
WARNING, no entry stored in dbm for [ENSG00000280038.1]
WARNING, no entry stored in dbm for [ENSG00000260897.1]
WARNING, no entry stored in dbm for [ENSG00000258598.1]
WARNING, no entry stored in dbm for [ENSG00000269900.3]
WARNING, no entry stored in dbm for [ENSG00000286694.1]
WARNING, no entry stored in dbm for [ENSG00000232624.8]
WARNING, no entry stored in dbm for [ENSG00000249072.1]
WARNING, no entry stored in dbm for [ENSG00000245025.3]
WARNING, no entry stored in dbm for [ENSG00000231871.5]
WARNING, no entry stored in dbm for [ENSG00000232811.1]
WARNING, no entry stored in dbm for [ENSG00000269516.6]
WARNING, no entry stored in dbm for [ENSG00000231437.3]
WARNING, no entry stored in dbm for [ENSG00000259605.3]
WARNING, no entry stored in dbm for [ENSG00000196810.5]
WARNING, no entry stored in dbm for [ENSG00000233111.1]
WARNING, no entry stored in dbm for [ENSG00000269001.2]
WARNING, no entry stored in dbm for [ENSG00000283443.1]
WARNING, no entry stored in dbm for [ENSG00000233025.1]
WARNING, no entry stored in dbm for [ENSG00000237363.1]
WARNING, no entry stored in dbm for [ENSG00000215908.10]
WARNING, no entry stored in dbm for [ENSG00000229585.4]
WARNING, no entry stored in dbm for [ENSG00000274265.5]
WARNING, no entry stored in dbm for [ENSG00000257998.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000259469.1]
WARNING, no entry stored in dbm for [ENSG00000285051.2]
WARNING, no entry stored in dbm for [ENSG00000262413.1]
WARNING, no entry stored in dbm for [ENSG00000223960.7]
WARNING, no entry stored in dbm for [ENSG00000200463.1]
WARNING, no entry stored in dbm for [ENSG00000272888.7]
WARNING, no entry stored in dbm for [ENSG00000243389.1]
WARNING, no entry stored in dbm for [ENSG00000234715.2]
WARNING, no entry stored in dbm for [ENSG00000227617.9]
WARNING, no entry stored in dbm for [ENSG00000261795.1]
WARNING, no entry stored in dbm for [ENSG00000176124.15]
WARNING, no entry stored in dbm for [ENSG00000247828.8]
WARNING, no entry stored in dbm for [ENSG00000227252.2]
WARNING, no entry stored in dbm for [ENSG00000223773.7]
WARNING, no entry stored in dbm for [ENSG00000250406.2]
WARNING, no entry stored in dbm for [ENSG00000249072.1]
WARNING, no entry stored in dbm for [ENSG00000215039.7]
WARNING, no entry stored in dbm for [ENSG00000249392.1]
WARNING, no entry stored in dbm for [ENSG00000247381.3]
WARNING, no entry stored in dbm for [ENSG00000231163.6]
WARNING, no entry stored in dbm for [ENSG00000279968.3]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000230773.9]
WARNING, no entry stored in dbm for [ENSG00000228205.1]
WARNING, no entry stored in dbm for [ENSG00000253773.3]
WARNING, no entry stored in dbm for [ENSG00000272994.1]
WARNING, no entry stored in dbm for [ENSG00000225783.8]
WARNING, no entry stored in dbm for [ENSG00000197734.10]
WARNING, no entry stored in dbm for [ENSG00000222047.9]
WARNING, no entry stored in dbm for [ENSG00000234996.4]
WARNING, no entry stored in dbm for [ENSG00000263647.1]
WARNING, no entry stored in dbm for [ENSG00000214035.3]
WARNING, no entry stored in dbm for [ENSG00000231329.8]
WARNING, no entry stored in dbm for [ENSG00000244137.1]
WARNING, no entry stored in dbm for [ENSG00000233967.7]
WARNING, no entry stored in dbm for [ENSG00000254560.6]
WARNING, no entry stored in dbm for [ENSG00000247081.8]
WARNING, no entry stored in dbm for [ENSG00000214176.9]
WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [ENSG00000237222.4]
WARNING, no entry stored in dbm for [ENSG00000207089.1]
WARNING, no entry stored in dbm for [ENSG00000212215.1]
WARNING, no entry stored in dbm for [ENSG00000202229.1]
WARNING, no entry stored in dbm for [ENSG00000238021.6]
WARNING, no entry stored in dbm for [ENSG00000207291.1]
WARNING, no entry stored in dbm for [ENSG00000250033.5]
WARNING, no entry stored in dbm for [ENSG00000286147.1]
WARNING, no entry stored in dbm for [ENSG00000243766.8]
WARNING, no entry stored in dbm for [ENSG00000286293.1]
WARNING, no entry stored in dbm for [ENSG00000287426.1]
WARNING, no entry stored in dbm for [ENSG00000281097.1]
WARNING, no entry stored in dbm for [ENSG00000254460.1]
WARNING, no entry stored in dbm for [ENSG00000250390.2]
WARNING, no entry stored in dbm for [ENSG00000286731.1]
WARNING, no entry stored in dbm for [ENSG00000266456.1]
WARNING, no entry stored in dbm for [ENSG00000247363.2]
WARNING, no entry stored in dbm for [ENSG00000225756.1]
WARNING, no entry stored in dbm for [ENSG00000205716.4]
WARNING, no entry stored in dbm for [ENSG00000235550.1]
WARNING, no entry stored in dbm for [ENSG00000196593.9]
WARNING, no entry stored in dbm for [ENSG00000215386.13]
WARNING, no entry stored in dbm for [ENSG00000238764.1]
WARNING, no entry stored in dbm for [ENSG00000286378.1]
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 [ENSG00000232576.2]
WARNING, no entry stored in dbm for [ENSG00000235749.3]
WARNING, no entry stored in dbm for [ENSG00000217801.10]
WARNING, no entry stored in dbm for [ENSG00000228818.1]
WARNING, no entry stored in dbm for [ENSG00000286215.1]
WARNING, no entry stored in dbm for [ENSG00000225339.4]
WARNING, no entry stored in dbm for [ENSG00000230303.6]
WARNING, no entry stored in dbm for [ENSG00000233817.1]
WARNING, no entry stored in dbm for [ENSG00000272030.1]
WARNING, no entry stored in dbm for [ENSG00000286162.2]
WARNING, no entry stored in dbm for [ENSG00000286162.2]
WARNING, no entry stored in dbm for [ENSG00000228830.1]
WARNING, no entry stored in dbm for [ENSG00000284977.2]
WARNING, no entry stored in dbm for [ENSG00000258666.1]
WARNING, no entry stored in dbm for [ENSG00000272078.1]
WARNING, no entry stored in dbm for [ENSG00000223745.8]
WARNING, no entry stored in dbm for [ENSG00000230490.3]
WARNING, no entry stored in dbm for [ENSG00000230490.3]
WARNING, no entry stored in dbm for [ENSG00000233183.3]
WARNING, no entry stored in dbm for [ENSG00000217648.1]
WARNING, no entry stored in dbm for [ENSG00000279593.1]
WARNING, no entry stored in dbm for [ENSG00000227486.2]
WARNING, no entry stored in dbm for [ENSG00000261116.1]
WARNING, no entry stored in dbm for [ENSG00000277301.1]
WARNING, no entry stored in dbm for [ENSG00000272097.2]
WARNING, no entry stored in dbm for [ENSG00000233508.3]
WARNING, no entry stored in dbm for [ENSG00000285646.2]
WARNING, no entry stored in dbm for [ENSG00000285646.2]
WARNING, no entry stored in dbm for [ENSG00000269155.2]
WARNING, no entry stored in dbm for [ENSG00000215022.7]
WARNING, no entry stored in dbm for [ENSG00000215022.7]
WARNING, no entry stored in dbm for [ENSG00000225705.2]
WARNING, no entry stored in dbm for [ENSG00000264057.1]
WARNING, no entry stored in dbm for [ENSG00000207291.1]
WARNING, no entry stored in dbm for [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000286437.1]
WARNING, no entry stored in dbm for [ENSG00000248692.5]
WARNING, no entry stored in dbm for [ENSG00000249669.10]
WARNING, no entry stored in dbm for [ENSG00000259868.3]
WARNING, no entry stored in dbm for [ENSG00000249189.1]
WARNING, no entry stored in dbm for [ENSG00000276216.1]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000275557.1]
WARNING, no entry stored in dbm for [ENSG00000274423.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000287411.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000254468.2]
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000282572.2]
WARNING, no entry stored in dbm for [ENSG00000241860.7]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000215158.9]
WARNING, no entry stored in dbm for [ENSG00000229930.1]
WARNING, no entry stored in dbm for [ENSG00000238035.8]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
WARNING, no entry stored in dbm for [ENSG00000257883.1]
WARNING, no entry stored in dbm for [ENSG00000257654.1]
WARNING, no entry stored in dbm for [ENSG00000260261.2]
WARNING, no entry stored in dbm for [ENSG00000214135.8]
WARNING, no entry stored in dbm for [ENSG00000238387.1]
WARNING, no entry stored in dbm for [ENSG00000253535.5]
WARNING, no entry stored in dbm for [ENSG00000284675.1]
WARNING, no entry stored in dbm for [ENSG00000228043.5]
WARNING, no entry stored in dbm for [ENSG00000287030.1]
WARNING, no entry stored in dbm for [ENSG00000250159.7]
WARNING, no entry stored in dbm for [ENSG00000261714.2]
WARNING, no entry stored in dbm for [ENSG00000232963.1]
WARNING, no entry stored in dbm for [ENSG00000253843.1]
WARNING, no entry stored in dbm for [ENSG00000287780.1]
WARNING, no entry stored in dbm for [ENSG00000205794.4]
WARNING, no entry stored in dbm for [ENSG00000277096.1]
WARNING, no entry stored in dbm for [ENSG00000286720.1]
WARNING, no entry stored in dbm for [ENSG00000287676.1]
WARNING, no entry stored in dbm for [ENSG00000228303.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000260417.1]
WARNING, no entry stored in dbm for [ENSG00000249782.2]
WARNING, no entry stored in dbm for [ENSG00000228998.4]
WARNING, no entry stored in dbm for [ENSG00000257239.1]
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 [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000266208.1]
WARNING, no entry stored in dbm for [ENSG00000250546.6]
WARNING, no entry stored in dbm for [ENSG00000234129.8]
WARNING, no entry stored in dbm for [ENSG00000287529.1]
WARNING, no entry stored in dbm for [ENSG00000284663.1]
WARNING, no entry stored in dbm for [ENSG00000254527.1]
WARNING, no entry stored in dbm for [ENSG00000267409.1]
WARNING, no entry stored in dbm for [ENSG00000287710.1]
WARNING, no entry stored in dbm for [ENSG00000240535.8]
WARNING, no entry stored in dbm for [ENSG00000267040.6]
WARNING, no entry stored in dbm for [ENSG00000262262.1]
WARNING, no entry stored in dbm for [ENSG00000257663.1]
WARNING, no entry stored in dbm for [ENSG00000177738.4]
WARNING, no entry stored in dbm for [ENSG00000280238.1]
WARNING, no entry stored in dbm for [ENSG00000255401.1]
WARNING, no entry stored in dbm for [ENSG00000259397.3]
WARNING, no entry stored in dbm for [ENSG00000213963.6]
WARNING, no entry stored in dbm for [ENSG00000221849.2]
WARNING, no entry stored in dbm for [ENSG00000267640.6]
WARNING, no entry stored in dbm for [ENSG00000232386.9]
WARNING, no entry stored in dbm for [ENSG00000261526.2]
WARNING, no entry stored in dbm for [ENSG00000280048.1]
WARNING, no entry stored in dbm for [ENSG00000261670.1]
WARNING, no entry stored in dbm for [ENSG00000277369.1]
WARNING, no entry stored in dbm for [ENSG00000239137.1]
WARNING, no entry stored in dbm for [ENSG00000260865.1]
WARNING, no entry stored in dbm for [ENSG00000111788.10]
WARNING, no entry stored in dbm for [ENSG00000257612.2]
WARNING, no entry stored in dbm for [ENSG00000286797.1]
WARNING, no entry stored in dbm for [ENSG00000234352.9]
WARNING, no entry stored in dbm for [ENSG00000214331.8]
WARNING, no entry stored in dbm for [ENSG00000214331.8]
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 [ENSG00000287202.1]
WARNING, no entry stored in dbm for [ENSG00000262202.4]
WARNING, no entry stored in dbm for [ENSG00000245750.10]
WARNING, no entry stored in dbm for [ENSG00000281195.1]
WARNING, no entry stored in dbm for [ENSG00000279865.1]
WARNING, no entry stored in dbm for [ENSG00000196205.8]
WARNING, no entry stored in dbm for [ENSG00000268650.3]
WARNING, no entry stored in dbm for [ENSG00000277200.1]
WARNING, no entry stored in dbm for [ENSG00000266368.1]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000214243.3]
WARNING, no entry stored in dbm for [ENSG00000214243.3]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000258376.2]
WARNING, no entry stored in dbm for [ENSG00000268163.1]
WARNING, no entry stored in dbm for [ENSG00000267698.1]
WARNING, no entry stored in dbm for [ENSG00000232310.8]
WARNING, no entry stored in dbm for [ENSG00000237036.5]


	* STAR-Fusion complete.  See output: /tmp/nxf.4W5Uf4FEVT/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)