.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/b7d694903039d315ce6c9b69a22a4b/.command.log
Size: 27.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1)
Attempt
Content

  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/88/6606ea5a2a8fc038b8b36ff231f058/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/b7d694903039d315ce6c9b69a22a4b/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/ea8be5b9c57cb128d61e43fba51e3b/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/b7d694903039d315ce6c9b69a22a4b/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/6606ea5a2a8fc038b8b36ff231f058/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)

-ctat genome lib [/tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.NlSgB6SoGa/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary
-sample contains 16435072 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir  -J /tmp/nxf.NlSgB6SoGa/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  -O /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.NlSgB6SoGa/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=100000.00/min 
[20000], rate=92307.69/min 
[30000], rate=94736.84/min 
[40000], rate=75000.00/min 
[50000], rate=61224.49/min 
[60000], rate=62068.97/min 
[70000], rate=63636.36/min 
[80000], rate=66666.67/min 
[90000], rate=68354.43/min 
[100000], rate=69767.44/min 
[110000], rate=72527.47/min 
[120000], rate=75000.00/min 
[130000], rate=77227.72/min 
[140000], rate=78504.67/min 
[150000], rate=80357.14/min 
[160000], rate=82051.28/min 
[170000], rate=83606.56/min 
[180000], rate=87804.88/min 
[190000], rate=91935.48/min 
[200000], rate=93750.00/min 
[210000], rate=94029.85/min 
[220000], rate=95652.17/min 
[230000], rate=97183.10/min 
[240000], rate=97959.18/min 
[250000], rate=99337.75/min 
[260000], rate=99363.06/min 
[270000], rate=98780.49/min 
[280000], rate=100000.00/min 
[290000], rate=102958.58/min 
[300000], rate=105882.35/min 
[310000], rate=106896.55/min 
[320000], rate=106077.35/min 
[330000], rate=107608.70/min 
[340000], rate=108510.64/min 
[350000], rate=108808.29/min 
[360000], rate=110204.08/min 
[370000], rate=110447.76/min 
[380000], rate=110144.93/min 
[390000], rate=110900.47/min 
[400000], rate=111111.11/min 
[410000], rate=111312.22/min 
[420000], rate=111013.22/min 
[430000], rate=110256.41/min 
[440000], rate=109090.91/min 
[450000], rate=104247.10/min 
[460000], rate=102602.23/min 
[470000], rate=99646.64/min 
[480000], rate=98630.14/min 
[490000], rate=97674.42/min -building interval tree based on /tmp/nxf.NlSgB6SoGa/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=100000.00/min 
[30000], rate=112500.00/min 
[40000], rate=120000.00/min 
[50000], rate=125000.00/min 
[60000], rate=128571.43/min 
[70000], rate=127272.73/min 
[80000], rate=104347.83/min 
[90000], rate=100000.00/min 
[100000], rate=90909.09/min 
[110000], rate=92957.75/min 
[120000], rate=94736.84/min 
[130000], rate=93975.90/min 
[140000], rate=92307.69/min 
[150000], rate=90909.09/min 
[160000], rate=89719.63/min 
[170000], rate=90265.49/min 
[180000], rate=91525.42/min 
[190000], rate=89062.50/min 
[200000], rate=88235.29/min 
[210000], rate=88111.89/min 
[220000], rate=88590.60/min 
[230000], rate=87898.09/min 
[240000], rate=87272.73/min 
[250000], rate=88757.40/min 
[260000], rate=89655.17/min 
[270000], rate=90502.79/min 
[280000], rate=88421.05/min 
[290000], rate=87878.79/min 
[300000], rate=87804.88/min 
[310000], rate=87323.94/min 
[320000], rate=87272.73/min 
[330000], rate=87610.62/min 
[340000], rate=88311.69/min 
[350000], rate=87136.93/min 
[360000], rate=87096.77/min 
[370000], rate=86381.32/min 
[380000], rate=86692.02/min 
[390000], rate=86029.41/min 
[400000], rate=84805.65/min 
[410000], rate=84246.58/min 
[420000], rate=84563.76/min 
[430000], rate=85148.51/min 
[440000], rate=84345.05/min 
[450000], rate=84112.15/min 
[460000], rate=84403.67/min 
[470000], rate=84939.76/min 
[480000], rate=85459.94/min 
[490000], rate=85217.39/min -building interval tree based on /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.08 min).
-mapping reads to genes

[10000], rate=150000.00/min 
[20000], rate=171428.57/min 
[30000], rate=150000.00/min 
[40000], rate=141176.47/min 
[50000], rate=157894.74/min 
[60000], rate=144000.00/min 
[70000], rate=144827.59/min 
[80000], rate=141176.47/min 
[90000], rate=145945.95/min 
[100000], rate=142857.14/min 
[110000], rate=140425.53/min 
[120000], rate=138461.54/min 
[130000], rate=139285.71/min 
[140000], rate=137704.92/min 
[150000], rate=140625.00/min 
[160000], rate=141176.47/min 
[170000], rate=139726.03/min 
[180000], rate=142105.26/min 
[190000], rate=140740.74/min 
[200000], rate=141176.47/min 
[210000], rate=143181.82/min 
[220000], rate=140425.53/min 
[230000], rate=138000.00/min 
[240000], rate=139805.83/min 
[250000], rate=129310.34/min 
[260000], rate=107586.21/min 
[270000], rate=96428.57/min 
[280000], rate=88421.05/min 
[290000], rate=84466.02/min 
[300000], rate=82949.31/min 
[310000], rate=81222.71/min 
[320000], rate=80000.00/min 
[330000], rate=78884.46/min 
[340000], rate=78160.92/min 
[350000], rate=77490.77/min 
[360000], rate=76868.33/min 
[370000], rate=75510.20/min 
[380000], rate=74025.97/min 
[390000], rate=73354.23/min 
[400000], rate=73394.50/min 
[410000], rate=71511.63/min 
[420000], rate=69613.26/min 
[430000], rate=69729.73/min 
[440000], rate=70026.53/min 
[450000], rate=69408.74/min 
[460000], rate=68656.72/min 
[470000], rate=68446.60/min 
[480000], rate=68408.55/min 
[490000], rate=68852.46/min -building interval tree based on /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes

[10000], rate=66666.67/min 
[20000], rate=60000.00/min 
[30000], rate=58064.52/min 
[40000], rate=52173.91/min 
[50000], rate=54545.45/min 
[60000], rate=58064.52/min 
[70000], rate=61764.71/min 
[80000], rate=62337.66/min 
[90000], rate=64285.71/min 
[100000], rate=67415.73/min 
[110000], rate=70212.77/min 
[120000], rate=65454.55/min 
[130000], rate=65000.00/min 
[140000], rate=64122.14/min 
[150000], rate=63829.79/min 
[160000], rate=64429.53/min 
[170000], rate=65806.45/min 
[180000], rate=67080.75/min 
[190000], rate=68263.47/min 
[200000], rate=69364.16/min 
[210000], rate=69613.26/min 
[220000], rate=69473.68/min 
[230000], rate=70769.23/min 
[240000], rate=72000.00/min 
[250000], rate=72115.38/min 
[260000], rate=73584.91/min 
[270000], rate=74311.93/min 
[280000], rate=75000.00/min 
[290000], rate=75982.53/min 
[300000], rate=75000.00/min 
[310000], rate=73517.79/min 
[320000], rate=73282.44/min 
[330000], rate=72794.12/min 
[340000], rate=72597.86/min 
[350000], rate=72916.67/min 
[360000], rate=71287.13/min 
[370000], rate=69811.32/min 
[380000], rate=69300.91/min 
[390000], rate=68621.70/min 
[400000], rate=66298.34/min 
[410000], rate=65425.53/min 
[420000], rate=65284.97/min 
[430000], rate=65151.52/min 
[440000], rate=65024.63/min 
[450000], rate=65533.98/min 
[460000], rate=65248.23/min 
[470000], rate=63800.90/min 
[480000], rate=63157.89/min 
[490000], rate=62553.19/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 6000000.00 reads per min processed...  
 6000000.00 reads per min processed...  
 4500000.00 reads per min processed...  
 4000000.00 reads per min processed...  
 3333333.33 reads per min processed...  
 3272727.27 reads per min processed...  
 3230769.23 reads per min processed...  
 3000000.00 reads per min processed...  
 3000000.00 reads per min processed...  
 3000000.00 reads per min processed...  
 3142857.14 reads per min processed...  
 3272727.27 reads per min processed...  
 3391304.35 reads per min processed...  
 3230769.23 reads per min processed...  
 3214285.71 reads per min processed...  
 3200000.00 reads per min processed...  
 3290322.58 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.NlSgB6SoGa/HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.Chimeric.out.junction  --tmpdir /tmp  --min_junction_reads 0  --min_sum_frags 1  --require_LDAS 0  --max_promiscuity 10  --min_pct_dom_promiscuity 20  --min_novel_junction_support 1  --min_alt_pct_junction 10  --aggregate_novel_junction_dist 5  --min_spanning_frags_only 1  --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -27857.159511
EM: Round [1] log likelihood: -27792.352912
EM: Round [2] log likelihood: -27764.188172
EM: Round [3] log likelihood: -27749.535879
EM: Round [4] log likelihood: -27741.282262
EM: Round [5] log likelihood: -27736.493021
EM: Round [6] log likelihood: -27733.670168
EM: Round [7] log likelihood: -27731.973654
EM: Round [8] log likelihood: -27730.925200
EM: Round [9] log likelihood: -27730.254914
EM: Round [10] log likelihood: -27729.810826
EM: Round [11] log likelihood: -27729.506356
EM: Round [12] log likelihood: -27729.291039
EM: Round [13] log likelihood: -27729.134582
EM: Round [14] log likelihood: -27729.018206
EM: Round [15] log likelihood: -27728.929891
EM: Round [16] log likelihood: -27728.861701
EM: Round [17] log likelihood: -27728.808252
EM: Round [18] log likelihood: -27728.765794
EM: Round [19] log likelihood: -27728.731665
EM: Round [20] log likelihood: -27728.703933
EM: Round [21] log likelihood: -27728.681174
EM: Round [22] log likelihood: -27728.662325
EM: Round [23] log likelihood: -27728.646579
EM: Round [24] log likelihood: -27728.633318
EM: Round [25] log likelihood: -27728.622063
EM: Round [26] log likelihood: -27728.612441
EM: Round [27] log likelihood: -27728.604155
EM: Round [28] log likelihood: -27728.596969
EM: Round [29] log likelihood: -27728.590697
EM: Round [30] log likelihood: -27728.585185
EM: Round [31] log likelihood: -27728.580310
EM: Round [32] log likelihood: -27728.575972
EM: Round [33] log likelihood: -27728.572088
EM: Round [34] log likelihood: -27728.568589
EM: Round [35] log likelihood: -27728.565419
EM: Round [36] log likelihood: -27728.562532
EM: Round [37] log likelihood: -27728.559889
EM: Round [38] log likelihood: -27728.557456
EM: Round [39] log likelihood: -27728.555206
EM: Round [40] log likelihood: -27728.553116
EM: Round [41] log likelihood: -27728.551167
EM: Round [42] log likelihood: -27728.549342
EM: Round [43] log likelihood: -27728.547628
EM: Round [44] log likelihood: -27728.546012
EM: Round [45] log likelihood: -27728.544485
EM: Round [46] log likelihood: -27728.543037
EM: Round [47] log likelihood: -27728.541662
EM: Round [48] log likelihood: -27728.540353
EM: Round [49] log likelihood: -27728.539104
EM: Round [50] log likelihood: -27728.537911
EM: Round [51] log likelihood: -27728.536771
EM: Round [52] log likelihood: -27728.535678
EM: Round [53] log likelihood: -27728.534631
EM: Round [54] log likelihood: -27728.533626
EM: Round [55] log likelihood: -27728.532661
EM: Round [56] log likelihood: -27728.531734
EM: Round [57] log likelihood: -27728.530842
EM: Round [58] log likelihood: -27728.529985
EM: Round [59] log likelihood: -27728.529161
EM: Round [60] log likelihood: -27728.528368
EM: Round [61] log likelihood: -27728.527605
EM: Round [62] log likelihood: -27728.526871
EM: Round [63] log likelihood: -27728.526164
EM: Round [64] log likelihood: -27728.525484
EM: Round [65] log likelihood: -27728.524830
EM: Round [66] log likelihood: -27728.524200
EM: Round [67] log likelihood: -27728.523595
EM: Round [68] log likelihood: -27728.523012
EM: Round [69] log likelihood: -27728.522451
EM: Round [70] log likelihood: -27728.521912
EM: Round [71] log likelihood: -27728.521394
EM: Round [72] log likelihood: -27728.520895
EM: Round [73] log likelihood: -27728.520416
EM: Round [74] log likelihood: -27728.519956
EM: Round [75] log likelihood: -27728.519514
EM: Round [76] log likelihood: -27728.519089
EM: Round [77] log likelihood: -27728.518680
EM: Round [78] log likelihood: -27728.518288
EM: Round [79] log likelihood: -27728.517912
EM: Round [80] log likelihood: -27728.517551
EM: Round [81] log likelihood: -27728.517204
EM: Round [82] log likelihood: -27728.516871
EM: Round [83] log likelihood: -27728.516552
EM: Round [84] log likelihood: -27728.516245
EM: Round [85] log likelihood: -27728.515951
EM: Round [86] log likelihood: -27728.515669
EM: Round [87] log likelihood: -27728.515399
EM: Round [88] log likelihood: -27728.515140
EM: Round [89] log likelihood: -27728.514892
EM: Round [90] log likelihood: -27728.514653
EM: Round [91] log likelihood: -27728.514425
EM: Round [92] log likelihood: -27728.514206
EM: Round [93] log likelihood: -27728.513997
EM: Round [94] log likelihood: -27728.513796
EM: Round [95] log likelihood: -27728.513604
EM: Round [96] log likelihood: -27728.513419
EM: Round [97] log likelihood: -27728.513243
EM: Round [98] log likelihood: -27728.513074
EM: Round [99] log likelihood: -27728.512912
EM: Round [100] log likelihood: -27728.512756
EM: Round [101] log likelihood: -27728.512608
EM: Round [102] log likelihood: -27728.512465
EM: Round [103] log likelihood: -27728.512329
EM: Round [104] log likelihood: -27728.512199
EM: Round [105] log likelihood: -27728.512074
EM: Round [106] log likelihood: -27728.511954
EM: Round [107] log likelihood: -27728.511840
EM: Round [108] log likelihood: -27728.511730
EM: Round [109] log likelihood: -27728.511625
EM: Round [110] log likelihood: -27728.511524
EM: Round [111] log likelihood: -27728.511428
EM: Stopping iterations at round 111 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -27841.924843
EM: Round [1] log likelihood: -27783.441666
EM: Round [2] log likelihood: -27758.713878
EM: Round [3] log likelihood: -27746.074209
EM: Round [4] log likelihood: -27739.049465
EM: Round [5] log likelihood: -27735.024583
EM: Round [6] log likelihood: -27732.683635
EM: Round [7] log likelihood: -27731.295428
EM: Round [8] log likelihood: -27730.448220
EM: Round [9] log likelihood: -27729.912509
EM: Round [10] log likelihood: -27729.560644
EM: Round [11] log likelihood: -27729.320787
EM: Round [12] log likelihood: -27729.151595
EM: Round [13] log likelihood: -27729.028577
EM: Round [14] log likelihood: -27728.936756
EM: Round [15] log likelihood: -27728.866663
EM: Round [16] log likelihood: -27728.812120
EM: Round [17] log likelihood: -27728.768974
EM: Round [18] log likelihood: -27728.734354
EM: Round [19] log likelihood: -27728.706228
EM: Round [20] log likelihood: -27728.683124
EM: Round [21] log likelihood: -27728.663960
EM: Round [22] log likelihood: -27728.647920
EM: Round [23] log likelihood: -27728.634385
EM: Round [24] log likelihood: -27728.622877
EM: Round [25] log likelihood: -27728.613022
EM: Round [26] log likelihood: -27728.604526
EM: Round [27] log likelihood: -27728.597152
EM: Round [28] log likelihood: -27728.590713
EM: Round [29] log likelihood: -27728.585055
EM: Round [30] log likelihood: -27728.580053
EM: Round [31] log likelihood: -27728.575606
EM: Round [32] log likelihood: -27728.571629
EM: Round [33] log likelihood: -27728.568052
EM: Round [34] log likelihood: -27728.564817
EM: Round [35] log likelihood: -27728.561877
EM: Round [36] log likelihood: -27728.559190
EM: Round [37] log likelihood: -27728.556723
EM: Round [38] log likelihood: -27728.554446
EM: Round [39] log likelihood: -27728.552337
EM: Round [40] log likelihood: -27728.550374
EM: Round [41] log likelihood: -27728.548540
EM: Round [42] log likelihood: -27728.546821
EM: Round [43] log likelihood: -27728.545203
EM: Round [44] log likelihood: -27728.543678
EM: Round [45] log likelihood: -27728.542234
EM: Round [46] log likelihood: -27728.540865
EM: Round [47] log likelihood: -27728.539564
EM: Round [48] log likelihood: -27728.538325
EM: Round [49] log likelihood: -27728.537143
EM: Round [50] log likelihood: -27728.536013
EM: Round [51] log likelihood: -27728.534933
EM: Round [52] log likelihood: -27728.533898
EM: Round [53] log likelihood: -27728.532907
EM: Round [54] log likelihood: -27728.531956
EM: Round [55] log likelihood: -27728.531042
EM: Round [56] log likelihood: -27728.530165
EM: Round [57] log likelihood: -27728.529323
EM: Round [58] log likelihood: -27728.528513
EM: Round [59] log likelihood: -27728.527734
EM: Round [60] log likelihood: -27728.526985
EM: Round [61] log likelihood: -27728.526264
EM: Round [62] log likelihood: -27728.525572
EM: Round [63] log likelihood: -27728.524905
EM: Round [64] log likelihood: -27728.524264
EM: Round [65] log likelihood: -27728.523648
EM: Round [66] log likelihood: -27728.523055
EM: Round [67] log likelihood: -27728.522485
EM: Round [68] log likelihood: -27728.521937
EM: Round [69] log likelihood: -27728.521410
EM: Round [70] log likelihood: -27728.520903
EM: Round [71] log likelihood: -27728.520417
EM: Round [72] log likelihood: -27728.519949
EM: Round [73] log likelihood: -27728.519500
EM: Round [74] log likelihood: -27728.519068
EM: Round [75] log likelihood: -27728.518654
EM: Round [76] log likelihood: -27728.518256
EM: Round [77] log likelihood: -27728.517874
EM: Round [78] log likelihood: -27728.517507
EM: Round [79] log likelihood: -27728.517155
EM: Round [80] log likelihood: -27728.516817
EM: Round [81] log likelihood: -27728.516493
EM: Round [82] log likelihood: -27728.516183
EM: Round [83] log likelihood: -27728.515885
EM: Round [84] log likelihood: -27728.515599
EM: Round [85] log likelihood: -27728.515325
EM: Round [86] log likelihood: -27728.515062
EM: Round [87] log likelihood: -27728.514811
EM: Round [88] log likelihood: -27728.514570
EM: Round [89] log likelihood: -27728.514339
EM: Round [90] log likelihood: -27728.514117
EM: Round [91] log likelihood: -27728.513905
EM: Round [92] log likelihood: -27728.513702
EM: Round [93] log likelihood: -27728.513507
EM: Round [94] log likelihood: -27728.513321
EM: Round [95] log likelihood: -27728.513142
EM: Round [96] log likelihood: -27728.512972
EM: Round [97] log likelihood: -27728.512808
EM: Round [98] log likelihood: -27728.512651
EM: Round [99] log likelihood: -27728.512501
EM: Round [100] log likelihood: -27728.512358
EM: Round [101] log likelihood: -27728.512220
EM: Round [102] log likelihood: -27728.512089
EM: Round [103] log likelihood: -27728.511963
EM: Round [104] log likelihood: -27728.511843
EM: Round [105] log likelihood: -27728.511727
EM: Round [106] log likelihood: -27728.511617
EM: Round [107] log likelihood: -27728.511512
EM: Round [108] log likelihood: -27728.511411
EM: Round [109] log likelihood: -27728.511314
EM: Stopping iterations at round 109 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 16435072 > /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir > /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir --annotate /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir
-done, see /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.NlSgB6SoGa/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 146, filtered: 2126)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.NlSgB6SoGa/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.NlSgB6SoGa/./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.NlSgB6SoGa/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000205634.7]
WARNING, no entry stored in dbm for [ENSG00000279910.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000219491.7]
WARNING, no entry stored in dbm for [ENSG00000234782.3]
WARNING, no entry stored in dbm for [ENSG00000224271.7]
WARNING, no entry stored in dbm for [ENSG00000224437.2]
WARNING, no entry stored in dbm for [ENSG00000214559.3]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000228948.2]
WARNING, no entry stored in dbm for [ENSG00000171101.13]
WARNING, no entry stored in dbm for [ENSG00000236190.1]
WARNING, no entry stored in dbm for [ENSG00000236047.1]
WARNING, no entry stored in dbm for [ENSG00000236047.1]
WARNING, no entry stored in dbm for [ENSG00000236047.1]
WARNING, no entry stored in dbm for [ENSG00000278771.1]
WARNING, no entry stored in dbm for [ENSG00000240877.3]
WARNING, no entry stored in dbm for [ENSG00000278771.1]
WARNING, no entry stored in dbm for [ENSG00000244112.3]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000221817.10]
WARNING, no entry stored in dbm for [ENSG00000261393.1]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000231367.6]
WARNING, no entry stored in dbm for [ENSG00000204792.2]
WARNING, no entry stored in dbm for [ENSG00000260807.7]
WARNING, no entry stored in dbm for [ENSG00000270761.1]
WARNING, no entry stored in dbm for [ENSG00000230202.1]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000233101.10]
WARNING, no entry stored in dbm for [ENSG00000231367.6]
WARNING, no entry stored in dbm for [ENSG00000260807.7]
WARNING, no entry stored in dbm for [ENSG00000250662.1]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000283849.1]
WARNING, no entry stored in dbm for [ENSG00000223896.2]
WARNING, no entry stored in dbm for [ENSG00000241104.5]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000264958.2]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000287991.1]
WARNING, no entry stored in dbm for [ENSG00000211459.2]
WARNING, no entry stored in dbm for [ENSG00000276850.5]
WARNING, no entry stored in dbm for [ENSG00000246596.7]
WARNING, no entry stored in dbm for [IGL-.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000260757.1]
WARNING, no entry stored in dbm for [ENSG00000260757.1]
WARNING, no entry stored in dbm for [ENSG00000286176.2]
WARNING, no entry stored in dbm for [ENSG00000282033.1]
WARNING, no entry stored in dbm for [ENSG00000257167.2]


	* STAR-Fusion complete.  See output: /tmp/nxf.NlSgB6SoGa/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)