.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (tih_rna_sample_00164_B23WHTKLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/4e6d682297e4cc34a029876d6f3861/.command.log
Size: 85.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (tih_rna_sample_00164_B23WHTKLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/690c940fc78d72d5e9bce24b1f592e/tih_rna_sample_00164_B23WHTKLT4_1.Chimeric.out.junction
  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/11/23bd7d2e6d2c5edff04b3885be0368/tih_rna_sample_00164_B23WHTKLT4_1_2.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/4e6d682297e4cc34a029876d6f3861/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/23bd7d2e6d2c5edff04b3885be0368/tih_rna_sample_00164_B23WHTKLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/4e6d682297e4cc34a029876d6f3861/.command.run
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.6Db6Qmi4oP/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary
-sample contains 247274493 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir  -J /tmp/nxf.6Db6Qmi4oP/tih_rna_sample_00164_B23WHTKLT4_1.Chimeric.out.junction  -O /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.6Db6Qmi4oP/tih_rna_sample_00164_B23WHTKLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[2590000], rate=61277.60/min -building interval tree based on /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

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[2480000], rate=59687.12/min 
[2490000], rate=59807.85/min 
[2500000], rate=59904.15/min 
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[2560000], rate=60639.56/min 
[2570000], rate=60780.45/min 
[2580000], rate=60920.90/min 
[2590000], rate=61012.96/min -building interval tree based on /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=75000.00/min 
[20000], rate=70588.24/min 
[30000], rate=69230.77/min 
[40000], rate=68571.43/min 
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[1670000], rate=72451.19/min 
[1680000], rate=72570.19/min 
[1690000], rate=72480.34/min 
[1700000], rate=72340.43/min 
[1710000], rate=71748.25/min 
[1720000], rate=70588.24/min 
[1730000], rate=70230.04/min 
[1740000], rate=69973.19/min 
[1750000], rate=69628.65/min 
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[1770000], rate=67946.26/min 
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[1810000], rate=65619.34/min 
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[1830000], rate=64135.51/min 
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[1850000], rate=63032.37/min 
[1860000], rate=62521.01/min 
[1870000], rate=61988.95/min 
[1880000], rate=61605.68/min 
[1890000], rate=61264.18/min 
[1900000], rate=61126.01/min 
[1910000], rate=60860.33/min 
[1920000], rate=60631.58/min 
[1930000], rate=60596.55/min 
[1940000], rate=60593.44/min 
[1950000], rate=60527.68/min 
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[1970000], rate=60522.27/min 
[1980000], rate=60427.26/min 
[1990000], rate=60364.00/min 
[2000000], rate=60210.74/min 
[2010000], rate=60119.64/min 
[2020000], rate=60089.24/min 
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[2190000], rate=58556.15/min 
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[2250000], rate=57766.37/min 
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[2310000], rate=57653.91/min 
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[2450000], rate=57489.25/min 
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[2480000], rate=57853.81/min 
[2490000], rate=57974.39/min 
[2500000], rate=58094.50/min 
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[2550000], rate=58665.64/min 
[2560000], rate=58715.60/min 
[2570000], rate=58742.86/min 
[2580000], rate=58747.63/min -building interval tree based on /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=120000.00/min 
[20000], rate=150000.00/min 
[30000], rate=138461.54/min 
[40000], rate=150000.00/min 
[50000], rate=150000.00/min 
[60000], rate=156521.74/min 
[70000], rate=168000.00/min 
[80000], rate=165517.24/min 
[90000], rate=168750.00/min 
[100000], rate=181818.18/min 
[110000], rate=200000.00/min 
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[1590000], rate=51373.18/min 
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[1720000], rate=50097.09/min 
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[1740000], rate=49832.94/min 
[1750000], rate=49692.38/min 
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[2000000], rate=48038.43/min 
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[2500000], rate=47831.63/min 
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[2560000], rate=47940.07/min 
[2570000], rate=47992.53/min 
[2580000], rate=48000.00/min 
[2590000], rate=48022.25/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.6Db6Qmi4oP/./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...  
 18000000.00 reads per min processed...  
 12000000.00 reads per min processed...  
 10000000.00 reads per min processed...  
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 5333333.33 reads per min processed...  
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 3882352.94 reads per min processed...  
 3600000.00 reads per min processed...  
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 3652173.91 reads per min processed...  
 3600000.00 reads per min processed...  
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 3517241.38 reads per min processed...  
 3483870.97 reads per min processed...  
 3352941.18 reads per min processed...  
 3333333.33 reads per min processed...  
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 3272727.27 reads per min processed...  
 3260869.57 reads per min processed...  
 3250000.00 reads per min processed...  
 3240000.00 reads per min processed...  
 3230769.23 reads per min processed...  
 3222222.22 reads per min processed...  
 3214285.71 reads per min processed...  
 3206896.55 reads per min processed...  
 3200000.00 reads per min processed...  
 3142857.14 reads per min processed...  
 3138461.54 reads per min processed...  
 3088235.29 reads per min processed...  
 3042253.52 reads per min processed...  
 3041095.89 reads per min processed...  
 3040000.00 reads per min processed...  
 3038961.04 reads per min processed...  
 3037974.68 reads per min processed...  
 3037037.04 reads per min processed...  
 3000000.00 reads per min processed...  
 3000000.00 reads per min processed...  
 3000000.00 reads per min processed...  
 3033707.87 reads per min processed...  
 3032967.03 reads per min processed...  
 3065217.39 reads per min processed...  
 3063829.79 reads per min processed...  
 3062500.00 reads per min processed...  
 3092783.51 reads per min processed...  
 3090909.09 reads per min processed...  
 3089108.91 reads per min processed...  
 3087378.64 reads per min processed...  
 3085714.29 reads per min processed...  
 3084112.15 reads per min processed...  
 3082568.81 reads per min processed...  
 3109090.91 reads per min processed...  
 3107142.86 reads per min processed...  
 3132743.36 reads per min processed...  
 3157894.74 reads per min processed...  
 3182608.70 reads per min processed...  
 3179487.18 reads per min processed...  
 3176470.59 reads per min processed...  
 3173553.72 reads per min processed...  
 3196721.31 reads per min processed...  
 3193548.39 reads per min processed...  
 3190476.19 reads per min processed...  
 3187500.00 reads per min processed...  
 3184615.38 reads per min processed...  
 3181818.18 reads per min processed...  
 3179104.48 reads per min processed...  
 3176470.59 reads per min processed...  
 3173913.04 reads per min processed...  
 3171428.57 reads per min processed...  
 3146853.15 reads per min processed...  
 3144827.59 reads per min processed...  
 3142857.14 reads per min processed...  
 3140939.60 reads per min processed...  
 3139072.85 reads per min processed...  
 3137254.90 reads per min processed...  
 3135483.87 reads per min processed...  
 3153846.15 reads per min processed...  
 3151898.73 reads per min processed...  
 3150000.00 reads per min processed...  
 3128834.36 reads per min processed...  
 3127272.73 reads per min processed...  
 3125748.50 reads per min processed...  
 3124260.36 reads per min processed...  
 3122807.02 reads per min processed...  
 3121387.28 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.6Db6Qmi4oP/tih_rna_sample_00164_B23WHTKLT4_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.6Db6Qmi4oP/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -227701.550825
EM: Round [1] log likelihood: -227553.380593
EM: Round [2] log likelihood: -227500.946580
EM: Round [3] log likelihood: -227476.778452
EM: Round [4] log likelihood: -227464.230950
EM: Round [5] log likelihood: -227457.302772
EM: Round [6] log likelihood: -227453.300514
EM: Round [7] log likelihood: -227450.886336
EM: Round [8] log likelihood: -227449.364653
EM: Round [9] log likelihood: -227448.362919
EM: Round [10] log likelihood: -227447.675847
EM: Round [11] log likelihood: -227447.186748
EM: Round [12] log likelihood: -227446.827035
EM: Round [13] log likelihood: -227446.554951
EM: Round [14] log likelihood: -227446.344158
EM: Round [15] log likelihood: -227446.177468
EM: Round [16] log likelihood: -227446.043302
EM: Round [17] log likelihood: -227445.933630
EM: Round [18] log likelihood: -227445.842745
EM: Round [19] log likelihood: -227445.766500
EM: Round [20] log likelihood: -227445.701821
EM: Round [21] log likelihood: -227445.646395
EM: Round [22] log likelihood: -227445.598456
EM: Round [23] log likelihood: -227445.556638
EM: Round [24] log likelihood: -227445.519870
EM: Round [25] log likelihood: -227445.487308
EM: Round [26] log likelihood: -227445.458277
EM: Round [27] log likelihood: -227445.432234
EM: Round [28] log likelihood: -227445.408738
EM: Round [29] log likelihood: -227445.387427
EM: Round [30] log likelihood: -227445.368006
EM: Round [31] log likelihood: -227445.350227
EM: Round [32] log likelihood: -227445.333883
EM: Round [33] log likelihood: -227445.318803
EM: Round [34] log likelihood: -227445.304839
EM: Round [35] log likelihood: -227445.291868
EM: Round [36] log likelihood: -227445.279782
EM: Round [37] log likelihood: -227445.268490
EM: Round [38] log likelihood: -227445.257913
EM: Round [39] log likelihood: -227445.247984
EM: Round [40] log likelihood: -227445.238641
EM: Round [41] log likelihood: -227445.229834
EM: Round [42] log likelihood: -227445.221515
EM: Round [43] log likelihood: -227445.213645
EM: Round [44] log likelihood: -227445.206188
EM: Round [45] log likelihood: -227445.199110
EM: Round [46] log likelihood: -227445.192385
EM: Round [47] log likelihood: -227445.185987
EM: Round [48] log likelihood: -227445.179892
EM: Round [49] log likelihood: -227445.174079
EM: Round [50] log likelihood: -227445.168530
EM: Round [51] log likelihood: -227445.163229
EM: Round [52] log likelihood: -227445.158159
EM: Round [53] log likelihood: -227445.153306
EM: Round [54] log likelihood: -227445.148658
EM: Round [55] log likelihood: -227445.144202
EM: Round [56] log likelihood: -227445.139928
EM: Round [57] log likelihood: -227445.135825
EM: Round [58] log likelihood: -227445.131885
EM: Round [59] log likelihood: -227445.128099
EM: Round [60] log likelihood: -227445.124458
EM: Round [61] log likelihood: -227445.120956
EM: Round [62] log likelihood: -227445.117586
EM: Round [63] log likelihood: -227445.114340
EM: Round [64] log likelihood: -227445.111214
EM: Round [65] log likelihood: -227445.108201
EM: Round [66] log likelihood: -227445.105296
EM: Round [67] log likelihood: -227445.102495
EM: Round [68] log likelihood: -227445.099792
EM: Round [69] log likelihood: -227445.097184
EM: Round [70] log likelihood: -227445.094666
EM: Round [71] log likelihood: -227445.092234
EM: Round [72] log likelihood: -227445.089885
EM: Round [73] log likelihood: -227445.087616
EM: Round [74] log likelihood: -227445.085422
EM: Round [75] log likelihood: -227445.083302
EM: Round [76] log likelihood: -227445.081251
EM: Round [77] log likelihood: -227445.079268
EM: Round [78] log likelihood: -227445.077349
EM: Round [79] log likelihood: -227445.075492
EM: Round [80] log likelihood: -227445.073695
EM: Round [81] log likelihood: -227445.071956
EM: Round [82] log likelihood: -227445.070272
EM: Round [83] log likelihood: -227445.068641
EM: Round [84] log likelihood: -227445.067061
EM: Round [85] log likelihood: -227445.065531
EM: Round [86] log likelihood: -227445.064049
EM: Round [87] log likelihood: -227445.062612
EM: Round [88] log likelihood: -227445.061220
EM: Round [89] log likelihood: -227445.059871
EM: Round [90] log likelihood: -227445.058562
EM: Round [91] log likelihood: -227445.057294
EM: Round [92] log likelihood: -227445.056064
EM: Round [93] log likelihood: -227445.054871
EM: Round [94] log likelihood: -227445.053714
EM: Round [95] log likelihood: -227445.052592
EM: Round [96] log likelihood: -227445.051503
EM: Round [97] log likelihood: -227445.050447
EM: Round [98] log likelihood: -227445.049422
EM: Round [99] log likelihood: -227445.048427
EM: Round [100] log likelihood: -227445.047462
EM: Round [101] log likelihood: -227445.046525
EM: Round [102] log likelihood: -227445.045615
EM: Round [103] log likelihood: -227445.044732
EM: Round [104] log likelihood: -227445.043875
EM: Round [105] log likelihood: -227445.043043
EM: Round [106] log likelihood: -227445.042235
EM: Round [107] log likelihood: -227445.041450
EM: Round [108] log likelihood: -227445.040688
EM: Round [109] log likelihood: -227445.039947
EM: Round [110] log likelihood: -227445.039228
EM: Round [111] log likelihood: -227445.038530
EM: Round [112] log likelihood: -227445.037852
EM: Round [113] log likelihood: -227445.037193
EM: Round [114] log likelihood: -227445.036552
EM: Round [115] log likelihood: -227445.035930
EM: Round [116] log likelihood: -227445.035326
EM: Round [117] log likelihood: -227445.034738
EM: Round [118] log likelihood: -227445.034168
EM: Round [119] log likelihood: -227445.033613
EM: Round [120] log likelihood: -227445.033074
EM: Round [121] log likelihood: -227445.032550
EM: Round [122] log likelihood: -227445.032041
EM: Round [123] log likelihood: -227445.031546
EM: Round [124] log likelihood: -227445.031065
EM: Round [125] log likelihood: -227445.030598
EM: Round [126] log likelihood: -227445.030143
EM: Round [127] log likelihood: -227445.029701
EM: Round [128] log likelihood: -227445.029272
EM: Round [129] log likelihood: -227445.028854
EM: Round [130] log likelihood: -227445.028448
EM: Round [131] log likelihood: -227445.028053
EM: Round [132] log likelihood: -227445.027669
EM: Round [133] log likelihood: -227445.027296
EM: Round [134] log likelihood: -227445.026933
EM: Round [135] log likelihood: -227445.026581
EM: Round [136] log likelihood: -227445.026237
EM: Round [137] log likelihood: -227445.025904
EM: Round [138] log likelihood: -227445.025579
EM: Round [139] log likelihood: -227445.025264
EM: Round [140] log likelihood: -227445.024957
EM: Round [141] log likelihood: -227445.024658
EM: Round [142] log likelihood: -227445.024368
EM: Round [143] log likelihood: -227445.024086
EM: Round [144] log likelihood: -227445.023811
EM: Round [145] log likelihood: -227445.023544
EM: Round [146] log likelihood: -227445.023284
EM: Round [147] log likelihood: -227445.023031
EM: Round [148] log likelihood: -227445.022785
EM: Round [149] log likelihood: -227445.022546
EM: Round [150] log likelihood: -227445.022314
EM: Round [151] log likelihood: -227445.022087
EM: Round [152] log likelihood: -227445.021867
EM: Round [153] log likelihood: -227445.021653
EM: Round [154] log likelihood: -227445.021445
EM: Round [155] log likelihood: -227445.021242
EM: Round [156] log likelihood: -227445.021045
EM: Round [157] log likelihood: -227445.020853
EM: Round [158] log likelihood: -227445.020666
EM: Round [159] log likelihood: -227445.020484
EM: Round [160] log likelihood: -227445.020308
EM: Round [161] log likelihood: -227445.020136
EM: Round [162] log likelihood: -227445.019968
EM: Round [163] log likelihood: -227445.019806
EM: Round [164] log likelihood: -227445.019647
EM: Round [165] log likelihood: -227445.019493
EM: Round [166] log likelihood: -227445.019343
EM: Round [167] log likelihood: -227445.019197
EM: Round [168] log likelihood: -227445.019055
EM: Round [169] log likelihood: -227445.018917
EM: Round [170] log likelihood: -227445.018782
EM: Round [171] log likelihood: -227445.018651
EM: Round [172] log likelihood: -227445.018524
EM: Round [173] log likelihood: -227445.018400
EM: Round [174] log likelihood: -227445.018279
EM: Round [175] log likelihood: -227445.018161
EM: Round [176] log likelihood: -227445.018047
EM: Round [177] log likelihood: -227445.017936
EM: Round [178] log likelihood: -227445.017828
EM: Round [179] log likelihood: -227445.017722
EM: Round [180] log likelihood: -227445.017620
EM: Round [181] log likelihood: -227445.017520
EM: Stopping iterations at round 181 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -227474.762531
EM: Round [1] log likelihood: -227343.026748
EM: Round [2] log likelihood: -227297.224276
EM: Round [3] log likelihood: -227276.257985
EM: Round [4] log likelihood: -227265.404375
EM: Round [5] log likelihood: -227259.417173
EM: Round [6] log likelihood: -227255.958074
EM: Round [7] log likelihood: -227253.869951
EM: Round [8] log likelihood: -227252.552156
EM: Round [9] log likelihood: -227251.683203
EM: Round [10] log likelihood: -227251.085994
EM: Round [11] log likelihood: -227250.659887
EM: Round [12] log likelihood: -227250.345731
EM: Round [13] log likelihood: -227250.107502
EM: Round [14] log likelihood: -227249.922468
EM: Round [15] log likelihood: -227249.775777
EM: Round [16] log likelihood: -227249.657411
EM: Round [17] log likelihood: -227249.560410
EM: Round [18] log likelihood: -227249.479821
EM: Round [19] log likelihood: -227249.412035
EM: Round [20] log likelihood: -227249.354375
EM: Round [21] log likelihood: -227249.304824
EM: Round [22] log likelihood: -227249.261840
EM: Round [23] log likelihood: -227249.224226
EM: Round [24] log likelihood: -227249.191048
EM: Round [25] log likelihood: -227249.161567
EM: Round [26] log likelihood: -227249.135192
EM: Round [27] log likelihood: -227249.111449
EM: Round [28] log likelihood: -227249.089951
EM: Round [29] log likelihood: -227249.070383
EM: Round [30] log likelihood: -227249.052486
EM: Round [31] log likelihood: -227249.036044
EM: Round [32] log likelihood: -227249.020878
EM: Round [33] log likelihood: -227249.006836
EM: Round [34] log likelihood: -227248.993790
EM: Round [35] log likelihood: -227248.981632
EM: Round [36] log likelihood: -227248.970269
EM: Round [37] log likelihood: -227248.959622
EM: Round [38] log likelihood: -227248.949621
EM: Round [39] log likelihood: -227248.940206
EM: Round [40] log likelihood: -227248.931325
EM: Round [41] log likelihood: -227248.922932
EM: Round [42] log likelihood: -227248.914987
EM: Round [43] log likelihood: -227248.907454
EM: Round [44] log likelihood: -227248.900301
EM: Round [45] log likelihood: -227248.893500
EM: Round [46] log likelihood: -227248.887026
EM: Round [47] log likelihood: -227248.880855
EM: Round [48] log likelihood: -227248.874968
EM: Round [49] log likelihood: -227248.869346
EM: Round [50] log likelihood: -227248.863971
EM: Round [51] log likelihood: -227248.858829
EM: Round [52] log likelihood: -227248.853905
EM: Round [53] log likelihood: -227248.849187
EM: Round [54] log likelihood: -227248.844663
EM: Round [55] log likelihood: -227248.840322
EM: Round [56] log likelihood: -227248.836154
EM: Round [57] log likelihood: -227248.832150
EM: Round [58] log likelihood: -227248.828301
EM: Round [59] log likelihood: -227248.824599
EM: Round [60] log likelihood: -227248.821037
EM: Round [61] log likelihood: -227248.817608
EM: Round [62] log likelihood: -227248.814306
EM: Round [63] log likelihood: -227248.811124
EM: Round [64] log likelihood: -227248.808057
EM: Round [65] log likelihood: -227248.805100
EM: Round [66] log likelihood: -227248.802247
EM: Round [67] log likelihood: -227248.799495
EM: Round [68] log likelihood: -227248.796838
EM: Round [69] log likelihood: -227248.794273
EM: Round [70] log likelihood: -227248.791795
EM: Round [71] log likelihood: -227248.789402
EM: Round [72] log likelihood: -227248.787088
EM: Round [73] log likelihood: -227248.784852
EM: Round [74] log likelihood: -227248.782690
EM: Round [75] log likelihood: -227248.780599
EM: Round [76] log likelihood: -227248.778577
EM: Round [77] log likelihood: -227248.776620
EM: Round [78] log likelihood: -227248.774726
EM: Round [79] log likelihood: -227248.772893
EM: Round [80] log likelihood: -227248.771118
EM: Round [81] log likelihood: -227248.769399
EM: Round [82] log likelihood: -227248.767735
EM: Round [83] log likelihood: -227248.766122
EM: Round [84] log likelihood: -227248.764560
EM: Round [85] log likelihood: -227248.763047
EM: Round [86] log likelihood: -227248.761580
EM: Round [87] log likelihood: -227248.760158
EM: Round [88] log likelihood: -227248.758779
EM: Round [89] log likelihood: -227248.757443
EM: Round [90] log likelihood: -227248.756147
EM: Round [91] log likelihood: -227248.754890
EM: Round [92] log likelihood: -227248.753671
EM: Round [93] log likelihood: -227248.752488
EM: Round [94] log likelihood: -227248.751341
EM: Round [95] log likelihood: -227248.750228
EM: Round [96] log likelihood: -227248.749148
EM: Round [97] log likelihood: -227248.748099
EM: Round [98] log likelihood: -227248.747082
EM: Round [99] log likelihood: -227248.746094
EM: Round [100] log likelihood: -227248.745135
EM: Round [101] log likelihood: -227248.744205
EM: Round [102] log likelihood: -227248.743301
EM: Round [103] log likelihood: -227248.742423
EM: Round [104] log likelihood: -227248.741571
EM: Round [105] log likelihood: -227248.740744
EM: Round [106] log likelihood: -227248.739940
EM: Round [107] log likelihood: -227248.739159
EM: Round [108] log likelihood: -227248.738401
EM: Round [109] log likelihood: -227248.737664
EM: Round [110] log likelihood: -227248.736948
EM: Round [111] log likelihood: -227248.736253
EM: Round [112] log likelihood: -227248.735577
EM: Round [113] log likelihood: -227248.734921
EM: Round [114] log likelihood: -227248.734283
EM: Round [115] log likelihood: -227248.733663
EM: Round [116] log likelihood: -227248.733061
EM: Round [117] log likelihood: -227248.732475
EM: Round [118] log likelihood: -227248.731906
EM: Round [119] log likelihood: -227248.731353
EM: Round [120] log likelihood: -227248.730815
EM: Round [121] log likelihood: -227248.730293
EM: Round [122] log likelihood: -227248.729785
EM: Round [123] log likelihood: -227248.729291
EM: Round [124] log likelihood: -227248.728810
EM: Round [125] log likelihood: -227248.728344
EM: Round [126] log likelihood: -227248.727890
EM: Round [127] log likelihood: -227248.727448
EM: Round [128] log likelihood: -227248.727019
EM: Round [129] log likelihood: -227248.726602
EM: Round [130] log likelihood: -227248.726196
EM: Round [131] log likelihood: -227248.725801
EM: Round [132] log likelihood: -227248.725418
EM: Round [133] log likelihood: -227248.725044
EM: Round [134] log likelihood: -227248.724681
EM: Round [135] log likelihood: -227248.724328
EM: Round [136] log likelihood: -227248.723985
EM: Round [137] log likelihood: -227248.723651
EM: Round [138] log likelihood: -227248.723326
EM: Round [139] log likelihood: -227248.723010
EM: Round [140] log likelihood: -227248.722703
EM: Round [141] log likelihood: -227248.722404
EM: Round [142] log likelihood: -227248.722113
EM: Round [143] log likelihood: -227248.721830
EM: Round [144] log likelihood: -227248.721555
EM: Round [145] log likelihood: -227248.721287
EM: Round [146] log likelihood: -227248.721027
EM: Round [147] log likelihood: -227248.720773
EM: Round [148] log likelihood: -227248.720527
EM: Round [149] log likelihood: -227248.720287
EM: Round [150] log likelihood: -227248.720053
EM: Round [151] log likelihood: -227248.719826
EM: Round [152] log likelihood: -227248.719605
EM: Round [153] log likelihood: -227248.719390
EM: Round [154] log likelihood: -227248.719181
EM: Round [155] log likelihood: -227248.718978
EM: Round [156] log likelihood: -227248.718779
EM: Round [157] log likelihood: -227248.718587
EM: Round [158] log likelihood: -227248.718399
EM: Round [159] log likelihood: -227248.718216
EM: Round [160] log likelihood: -227248.718039
EM: Round [161] log likelihood: -227248.717866
EM: Round [162] log likelihood: -227248.717698
EM: Round [163] log likelihood: -227248.717534
EM: Round [164] log likelihood: -227248.717374
EM: Round [165] log likelihood: -227248.717219
EM: Round [166] log likelihood: -227248.717068
EM: Round [167] log likelihood: -227248.716921
EM: Round [168] log likelihood: -227248.716778
EM: Round [169] log likelihood: -227248.716639
EM: Round [170] log likelihood: -227248.716504
EM: Round [171] log likelihood: -227248.716372
EM: Round [172] log likelihood: -227248.716243
EM: Round [173] log likelihood: -227248.716118
EM: Round [174] log likelihood: -227248.715996
EM: Round [175] log likelihood: -227248.715878
EM: Round [176] log likelihood: -227248.715763
EM: Round [177] log likelihood: -227248.715650
EM: Round [178] log likelihood: -227248.715541
EM: Round [179] log likelihood: -227248.715435
EM: Round [180] log likelihood: -227248.715331
EM: Round [181] log likelihood: -227248.715230
EM: Round [182] log likelihood: -227248.715132
EM: Stopping iterations at round 182 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.6Db6Qmi4oP/./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.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.6Db6Qmi4oP/./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.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 247274493 > /tmp/nxf.6Db6Qmi4oP/./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.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir > /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir --annotate /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.6Db6Qmi4oP/./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.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir
-done, see /tmp/nxf.6Db6Qmi4oP/./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.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.6Db6Qmi4oP/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1543, filtered: 10397)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.6Db6Qmi4oP/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.6Db6Qmi4oP/./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.6Db6Qmi4oP/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 [ENSG00000226121.2]
WARNING, no entry stored in dbm for [ENSG00000250698.1]
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WARNING, no entry stored in dbm for [ENSG00000215908.10]
WARNING, no entry stored in dbm for [ENSG00000183666.17]
WARNING, no entry stored in dbm for [ENSG00000283541.1]
WARNING, no entry stored in dbm for [ENSG00000260416.1]
WARNING, no entry stored in dbm for [ENSG00000267493.4]
WARNING, no entry stored in dbm for [ENSG00000276717.2]
WARNING, no entry stored in dbm for [ENSG00000259755.1]
WARNING, no entry stored in dbm for [ENSG00000234715.2]
WARNING, no entry stored in dbm for [ENSG00000237986.4]
WARNING, no entry stored in dbm for [ENSG00000267024.1]
WARNING, no entry stored in dbm for [ENSG00000237447.1]
WARNING, no entry stored in dbm for [ENSG00000286277.1]
WARNING, no entry stored in dbm for [ENSG00000218426.5]
WARNING, no entry stored in dbm for [ENSG00000230860.1]
WARNING, no entry stored in dbm for [ENSG00000245750.10]
WARNING, no entry stored in dbm for [ENSG00000218565.2]
WARNING, no entry stored in dbm for [ENSG00000261402.1]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000228544.1]
WARNING, no entry stored in dbm for [ENSG00000233766.7]
WARNING, no entry stored in dbm for [ENSG00000258383.1]
WARNING, no entry stored in dbm for [ENSG00000233662.1]
WARNING, no entry stored in dbm for [ENSG00000255618.2]
WARNING, no entry stored in dbm for [ENSG00000229807.12]
WARNING, no entry stored in dbm for [ENSG00000232841.1]
WARNING, no entry stored in dbm for [ENSG00000205534.6]
WARNING, no entry stored in dbm for [ENSG00000261556.10]
WARNING, no entry stored in dbm for [ENSG00000267439.1]
WARNING, no entry stored in dbm for [ENSG00000253130.2]
WARNING, no entry stored in dbm for [ENSG00000224346.1]
WARNING, no entry stored in dbm for [ENSG00000233967.7]
WARNING, no entry stored in dbm for [ENSG00000274292.1]
WARNING, no entry stored in dbm for [ENSG00000197595.4]
WARNING, no entry stored in dbm for [ENSG00000227881.1]
WARNING, no entry stored in dbm for [ENSG00000231183.4]
WARNING, no entry stored in dbm for [ENSG00000206772.1]
WARNING, no entry stored in dbm for [ENSG00000202089.1]
WARNING, no entry stored in dbm for [ENSG00000213962.2]
WARNING, no entry stored in dbm for [ENSG00000266961.1]
WARNING, no entry stored in dbm for [ENSG00000234509.1]
WARNING, no entry stored in dbm for [ENSG00000261019.1]
WARNING, no entry stored in dbm for [ENSG00000215067.10]
WARNING, no entry stored in dbm for [ENSG00000229257.2]
WARNING, no entry stored in dbm for [ENSG00000215835.2]
WARNING, no entry stored in dbm for [ENSG00000270780.1]
WARNING, no entry stored in dbm for [ENSG00000234589.4]
WARNING, no entry stored in dbm for [ENSG00000284744.1]
WARNING, no entry stored in dbm for [ENSG00000218426.5]
WARNING, no entry stored in dbm for [ENSG00000227619.3]
WARNING, no entry stored in dbm for [ENSG00000277047.5]
WARNING, no entry stored in dbm for [ENSG00000235020.5]
WARNING, no entry stored in dbm for [ENSG00000240122.1]
WARNING, no entry stored in dbm for [ENSG00000232347.1]
WARNING, no entry stored in dbm for [ENSG00000228685.1]
WARNING, no entry stored in dbm for [ENSG00000234851.4]
WARNING, no entry stored in dbm for [ENSG00000213087.3]
WARNING, no entry stored in dbm for [ENSG00000286740.1]
WARNING, no entry stored in dbm for [ENSG00000258634.3]
WARNING, no entry stored in dbm for [ENSG00000233968.7]
WARNING, no entry stored in dbm for [ENSG00000274691.1]
WARNING, no entry stored in dbm for [ENSG00000230490.3]
WARNING, no entry stored in dbm for [ENSG00000232098.3]
WARNING, no entry stored in dbm for [ENSG00000231881.2]
WARNING, no entry stored in dbm for [ENSG00000283142.1]
WARNING, no entry stored in dbm for [ENSG00000280434.1]
WARNING, no entry stored in dbm for [ENSG00000284646.1]
WARNING, no entry stored in dbm for [ENSG00000286933.1]
WARNING, no entry stored in dbm for [ENSG00000282572.2]
WARNING, no entry stored in dbm for [ENSG00000279440.1]
WARNING, no entry stored in dbm for [ENSG00000213107.2]
WARNING, no entry stored in dbm for [ENSG00000224966.4]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000223959.8]
WARNING, no entry stored in dbm for [ENSG00000286681.1]
WARNING, no entry stored in dbm for [ENSG00000276216.1]
WARNING, no entry stored in dbm for [ENSG00000277089.4]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000229930.1]
WARNING, no entry stored in dbm for [ENSG00000259813.1]
WARNING, no entry stored in dbm for [ENSG00000223509.8]
WARNING, no entry stored in dbm for [ENSG00000270055.1]
WARNING, no entry stored in dbm for [ENSG00000278212.2]
WARNING, no entry stored in dbm for [ENSG00000260670.1]
WARNING, no entry stored in dbm for [ENSG00000257951.2]
WARNING, no entry stored in dbm for [ENSG00000250899.3]
WARNING, no entry stored in dbm for [ENSG00000233031.1]
WARNING, no entry stored in dbm for [ENSG00000280117.1]
WARNING, no entry stored in dbm for [ENSG00000249244.1]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000288075.1]
WARNING, no entry stored in dbm for [ENSG00000277332.1]
WARNING, no entry stored in dbm for [ENSG00000253836.1]
WARNING, no entry stored in dbm for [ENSG00000254035.1]
WARNING, no entry stored in dbm for [ENSG00000253557.6]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000226097.6]
WARNING, no entry stored in dbm for [ENSG00000249125.2]
WARNING, no entry stored in dbm for [ENSG00000287919.1]
WARNING, no entry stored in dbm for [ENSG00000284428.1]
WARNING, no entry stored in dbm for [ENSG00000288620.1]
WARNING, no entry stored in dbm for [ENSG00000288620.1]
WARNING, no entry stored in dbm for [ENSG00000259655.1]
WARNING, no entry stored in dbm for [ENSG00000280828.1]
WARNING, no entry stored in dbm for [ENSG00000279259.1]
WARNING, no entry stored in dbm for [ENSG00000267558.2]
WARNING, no entry stored in dbm for [ENSG00000224094.1]
WARNING, no entry stored in dbm for [ENSG00000259722.2]
WARNING, no entry stored in dbm for [ENSG00000266208.1]
WARNING, no entry stored in dbm for [ENSG00000230979.3]
WARNING, no entry stored in dbm for [ENSG00000258088.1]
WARNING, no entry stored in dbm for [ENSG00000288663.1]
WARNING, no entry stored in dbm for [ENSG00000288663.1]
WARNING, no entry stored in dbm for [ENSG00000275223.1]
WARNING, no entry stored in dbm for [ENSG00000234129.8]
WARNING, no entry stored in dbm for [ENSG00000189229.11]
WARNING, no entry stored in dbm for [ENSG00000275929.1]
WARNING, no entry stored in dbm for [ENSG00000259200.2]
WARNING, no entry stored in dbm for [ENSG00000247765.2]
WARNING, no entry stored in dbm for [ENSG00000258590.5]
WARNING, no entry stored in dbm for [ENSG00000145063.15]
WARNING, no entry stored in dbm for [ENSG00000254951.7]
WARNING, no entry stored in dbm for [ENSG00000267040.6]
WARNING, no entry stored in dbm for [ENSG00000257817.2]
WARNING, no entry stored in dbm for [ENSG00000188002.10]
WARNING, no entry stored in dbm for [ENSG00000259234.6]
WARNING, no entry stored in dbm for [ENSG00000287677.2]
WARNING, no entry stored in dbm for [ENSG00000259702.3]
WARNING, no entry stored in dbm for [ENSG00000274461.2]
WARNING, no entry stored in dbm for [ENSG00000288538.1]
WARNING, no entry stored in dbm for [ENSG00000259407.1]
WARNING, no entry stored in dbm for [ENSG00000287537.1]
WARNING, no entry stored in dbm for [ENSG00000233223.3]
WARNING, no entry stored in dbm for [ENSG00000285106.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000278911.1]
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 [ENSG00000267723.1]
WARNING, no entry stored in dbm for [ENSG00000255106.1]
WARNING, no entry stored in dbm for [ENSG00000241741.1]
WARNING, no entry stored in dbm for [ENSG00000269439.6]
WARNING, no entry stored in dbm for [ENSG00000255399.4]
WARNING, no entry stored in dbm for [ENSG00000268119.6]
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 [ENSG00000229689.3]
WARNING, no entry stored in dbm for [ENSG00000278058.1]
WARNING, no entry stored in dbm for [ENSG00000238045.9]
WARNING, no entry stored in dbm for [ENSG00000260905.1]
WARNING, no entry stored in dbm for [ENSG00000284671.1]
WARNING, no entry stored in dbm for [ENSG00000276548.1]
WARNING, no entry stored in dbm for [ENSG00000271699.5]
WARNING, no entry stored in dbm for [ENSG00000279108.1]
WARNING, no entry stored in dbm for [ENSG00000250258.1]
WARNING, no entry stored in dbm for [ENSG00000259124.1]
WARNING, no entry stored in dbm for [ENSG00000260249.3]
WARNING, no entry stored in dbm for [ENSG00000260249.3]
WARNING, no entry stored in dbm for [ENSG00000277458.1]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000233891.8]
WARNING, no entry stored in dbm for [ENSG00000278959.1]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000267623.3]
WARNING, no entry stored in dbm for [ENSG00000232756.1]
WARNING, no entry stored in dbm for [ENSG00000214243.3]
WARNING, no entry stored in dbm for [ENSG00000225792.2]
WARNING, no entry stored in dbm for [ENSG00000274177.1]
WARNING, no entry stored in dbm for [ENSG00000229533.1]
WARNING, no entry stored in dbm for [ENSG00000223838.2]
WARNING, no entry stored in dbm for [ENSG00000287952.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.6Db6Qmi4oP/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)