.command.err - Workdir - NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-d5fda9-R1_A23YTGFLT4_1)

File Info

Filename: .command.err
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/3c2102d3e3dafc0babc5cce8250211/.command.err
Size: 27.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION (aih-tih-sc-d5fda9-R1_A23YTGFLT4_1)
Attempt
Content

-ctat genome lib [/tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.HNm9yYpVS4/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary
-sample contains 28784902 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes  --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir  -J /tmp/nxf.HNm9yYpVS4/aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.Chimeric.out.junction  -O /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4 
-parsing fusion evidence: /tmp/nxf.HNm9yYpVS4/aih-tih-sc-d5fda9-R1_A23YTGFLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

[10000], rate=31578.95/min 
[20000], rate=34285.71/min 
[30000], rate=38297.87/min 
[40000], rate=42857.14/min 
[50000], rate=47619.05/min 
[60000], rate=52173.91/min 
[70000], rate=49411.76/min 
[80000], rate=47058.82/min 
[90000], rate=47368.42/min 
[100000], rate=47244.09/min 
[110000], rate=48175.18/min 
[120000], rate=48648.65/min 
[130000], rate=50000.00/min 
[140000], rate=51851.85/min 
[150000], rate=53571.43/min 
[160000], rate=54857.14/min 
[170000], rate=56043.96/min 
[180000], rate=57142.86/min 
[190000], rate=58461.54/min 
[200000], rate=60301.51/min 
[210000], rate=61764.71/min 
[220000], rate=63157.89/min 
[230000], rate=64186.05/min 
[240000], rate=64864.86/min 
[250000], rate=66666.67/min 
[260000], rate=67826.09/min 
[270000], rate=69230.77/min 
[280000], rate=69709.54/min 
[290000], rate=70731.71/min 
[300000], rate=71428.57/min 
[310000], rate=72373.54/min 
[320000], rate=72727.27/min 
[330000], rate=73062.73/min 
[340000], rate=73381.29/min 
[350000], rate=73943.66/min 
[360000], rate=73720.14/min 
[370000], rate=72077.92/min 
[380000], rate=70807.45/min 
[390000], rate=70059.88/min 
[400000], rate=69565.22/min 
[410000], rate=69491.53/min 
[420000], rate=70000.00/min -building interval tree based on /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes

[10000], rate=120000.00/min 
[20000], rate=133333.33/min 
[30000], rate=150000.00/min 
[40000], rate=150000.00/min 
[50000], rate=150000.00/min 
[60000], rate=144000.00/min 
[70000], rate=155555.56/min 
[80000], rate=145454.55/min 
[90000], rate=150000.00/min 
[100000], rate=150000.00/min 
[110000], rate=150000.00/min 
[120000], rate=146938.78/min 
[130000], rate=147169.81/min 
[140000], rate=129230.77/min 
[150000], rate=108433.73/min 
[160000], rate=95049.50/min 
[170000], rate=86440.68/min 
[180000], rate=80597.01/min 
[190000], rate=76510.07/min 
[200000], rate=74534.16/min 
[210000], rate=72832.37/min 
[220000], rate=71739.13/min 
[230000], rate=70769.23/min 
[240000], rate=70935.96/min 
[250000], rate=71090.05/min 
[260000], rate=72222.22/min 
[270000], rate=72000.00/min 
[280000], rate=71489.36/min 
[290000], rate=71311.48/min 
[300000], rate=71713.15/min 
[310000], rate=72093.02/min 
[320000], rate=73003.80/min 
[330000], rate=71739.13/min 
[340000], rate=70588.24/min 
[350000], rate=69536.42/min 
[360000], rate=69230.77/min 
[370000], rate=68944.10/min 
[380000], rate=69090.91/min 
[390000], rate=69436.20/min 
[400000], rate=69565.22/min 
[410000], rate=68715.08/min -building interval tree based on /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

[10000], rate=42857.14/min 
[20000], rate=38709.68/min 
[30000], rate=41860.47/min 
[40000], rate=48979.59/min 
[50000], rate=49180.33/min 
[60000], rate=48648.65/min 
[70000], rate=50000.00/min 
[80000], rate=51612.90/min 
[90000], rate=54000.00/min 
[100000], rate=56074.77/min 
[110000], rate=56896.55/min 
[120000], rate=56250.00/min 
[130000], rate=55714.29/min 
[140000], rate=56000.00/min 
[150000], rate=56603.77/min 
[160000], rate=58181.82/min 
[170000], rate=59649.12/min 
[180000], rate=59016.39/min 
[190000], rate=58461.54/min 
[200000], rate=58252.43/min 
[210000], rate=58333.33/min 
[220000], rate=58407.08/min 
[230000], rate=58974.36/min 
[240000], rate=59504.13/min 
[250000], rate=60728.74/min 
[260000], rate=61417.32/min 
[270000], rate=60902.26/min 
[280000], rate=60649.82/min 
[290000], rate=61052.63/min 
[300000], rate=62283.74/min 
[310000], rate=63481.23/min 
[320000], rate=63157.89/min 
[330000], rate=63057.32/min 
[340000], rate=63157.89/min 
[350000], rate=63444.11/min 
[360000], rate=64670.66/min 
[370000], rate=65294.12/min 
[380000], rate=65142.86/min 
[390000], rate=65000.00/min 
[400000], rate=65217.39/min 
[410000], rate=65951.74/min -building interval tree based on /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes

[10000], rate=33333.33/min 
[20000], rate=38709.68/min 
[30000], rate=45000.00/min 
[40000], rate=54545.45/min 
[50000], rate=58823.53/min 
[60000], rate=62068.97/min 
[70000], rate=62686.57/min 
[80000], rate=64000.00/min 
[90000], rate=64285.71/min 
[100000], rate=66666.67/min 
[110000], rate=68041.24/min 
[120000], rate=67289.72/min 
[130000], rate=67241.38/min 
[140000], rate=68292.68/min 
[150000], rate=68702.29/min 
[160000], rate=67605.63/min 
[170000], rate=66666.67/min 
[180000], rate=65853.66/min 
[190000], rate=65142.86/min 
[200000], rate=64864.86/min 
[210000], rate=64615.38/min 
[220000], rate=64705.88/min 
[230000], rate=65094.34/min 
[240000], rate=64864.86/min 
[250000], rate=64935.06/min 
[260000], rate=65271.97/min 
[270000], rate=66122.45/min 
[280000], rate=64864.86/min 
[290000], rate=63736.26/min 
[300000], rate=62937.06/min 
[310000], rate=62416.11/min 
[320000], rate=62337.66/min 
[330000], rate=62264.15/min 
[340000], rate=62006.08/min 
[350000], rate=62314.54/min 
[360000], rate=62790.70/min 
[370000], rate=63247.86/min 
[380000], rate=64044.94/min 
[390000], rate=64462.81/min 
[400000], rate=63324.54/min 
[410000], rate=62436.55/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads  -J /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt  --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir  --filt_file /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail  -M 50  > /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass 
-parsing /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.

 0.00 reads per min processed...  
 6000000.00 reads per min processed...  
 4500000.00 reads per min processed...  
 4000000.00 reads per min processed...  
 3750000.00 reads per min processed...  
 3272727.27 reads per min processed...  
 3230769.23 reads per min processed...  
 3200000.00 reads per min processed...  
 3375000.00 reads per min processed...  
 3529411.76 reads per min processed...  
 3473684.21 reads per min processed...  
 3428571.43 reads per min processed...  
 3545454.55 reads per min processed...  
 3500000.00 reads per min processed...  
done.

* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict  -J /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass  -O /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion 
-parsing fusion evidence: /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter  --fusion_preds /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary  -J /tmp/nxf.HNm9yYpVS4/aih-tih-sc-d5fda9-R1_A23YTGFLT4_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.HNm9yYpVS4/ctat_genome_lib_build_dir  --out_prefix /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -41134.964754
EM: Round [1] log likelihood: -41099.337213
EM: Round [2] log likelihood: -41083.299978
EM: Round [3] log likelihood: -41074.977764
EM: Round [4] log likelihood: -41070.414868
EM: Round [5] log likelihood: -41067.860660
EM: Round [6] log likelihood: -41066.406034
EM: Round [7] log likelihood: -41065.556822
EM: Round [8] log likelihood: -41065.044744
EM: Round [9] log likelihood: -41064.724484
EM: Round [10] log likelihood: -41064.516530
EM: Round [11] log likelihood: -41064.376468
EM: Round [12] log likelihood: -41064.278809
EM: Round [13] log likelihood: -41064.208489
EM: Round [14] log likelihood: -41064.156335
EM: Round [15] log likelihood: -41064.116597
EM: Round [16] log likelihood: -41064.085572
EM: Round [17] log likelihood: -41064.060813
EM: Round [18] log likelihood: -41064.040661
EM: Round [19] log likelihood: -41064.023972
EM: Round [20] log likelihood: -41064.009936
EM: Round [21] log likelihood: -41063.997970
EM: Round [22] log likelihood: -41063.987649
EM: Round [23] log likelihood: -41063.978652
EM: Round [24] log likelihood: -41063.970741
EM: Round [25] log likelihood: -41063.963729
EM: Round [26] log likelihood: -41063.957470
EM: Round [27] log likelihood: -41063.951851
EM: Round [28] log likelihood: -41063.946780
EM: Round [29] log likelihood: -41063.942181
EM: Round [30] log likelihood: -41063.937994
EM: Round [31] log likelihood: -41063.934168
EM: Round [32] log likelihood: -41063.930660
EM: Round [33] log likelihood: -41063.927434
EM: Round [34] log likelihood: -41063.924460
EM: Round [35] log likelihood: -41063.921711
EM: Round [36] log likelihood: -41063.919165
EM: Round [37] log likelihood: -41063.916803
EM: Round [38] log likelihood: -41063.914607
EM: Round [39] log likelihood: -41063.912562
EM: Round [40] log likelihood: -41063.910655
EM: Round [41] log likelihood: -41063.908874
EM: Round [42] log likelihood: -41063.907209
EM: Round [43] log likelihood: -41063.905651
EM: Round [44] log likelihood: -41063.904190
EM: Round [45] log likelihood: -41063.902820
EM: Round [46] log likelihood: -41063.901534
EM: Round [47] log likelihood: -41063.900326
EM: Round [48] log likelihood: -41063.899189
EM: Round [49] log likelihood: -41063.898120
EM: Round [50] log likelihood: -41063.897113
EM: Round [51] log likelihood: -41063.896164
EM: Round [52] log likelihood: -41063.895269
EM: Round [53] log likelihood: -41063.894425
EM: Round [54] log likelihood: -41063.893629
EM: Round [55] log likelihood: -41063.892877
EM: Round [56] log likelihood: -41063.892166
EM: Round [57] log likelihood: -41063.891494
EM: Round [58] log likelihood: -41063.890859
EM: Round [59] log likelihood: -41063.890258
EM: Round [60] log likelihood: -41063.889690
EM: Round [61] log likelihood: -41063.889151
EM: Round [62] log likelihood: -41063.888642
EM: Round [63] log likelihood: -41063.888159
EM: Round [64] log likelihood: -41063.887701
EM: Round [65] log likelihood: -41063.887267
EM: Round [66] log likelihood: -41063.886856
EM: Round [67] log likelihood: -41063.886466
EM: Round [68] log likelihood: -41063.886096
EM: Round [69] log likelihood: -41063.885745
EM: Round [70] log likelihood: -41063.885412
EM: Round [71] log likelihood: -41063.885095
EM: Round [72] log likelihood: -41063.884794
EM: Round [73] log likelihood: -41063.884509
EM: Round [74] log likelihood: -41063.884237
EM: Round [75] log likelihood: -41063.883979
EM: Round [76] log likelihood: -41063.883734
EM: Round [77] log likelihood: -41063.883501
EM: Round [78] log likelihood: -41063.883279
EM: Round [79] log likelihood: -41063.883068
EM: Round [80] log likelihood: -41063.882867
EM: Round [81] log likelihood: -41063.882676
EM: Round [82] log likelihood: -41063.882494
EM: Round [83] log likelihood: -41063.882321
EM: Round [84] log likelihood: -41063.882156
EM: Round [85] log likelihood: -41063.881999
EM: Round [86] log likelihood: -41063.881849
EM: Round [87] log likelihood: -41063.881706
EM: Round [88] log likelihood: -41063.881570
EM: Round [89] log likelihood: -41063.881441
EM: Round [90] log likelihood: -41063.881317
EM: Round [91] log likelihood: -41063.881199
EM: Round [92] log likelihood: -41063.881087
EM: Round [93] log likelihood: -41063.880979
EM: Round [94] log likelihood: -41063.880877
EM: Round [95] log likelihood: -41063.880779
EM: Stopping iterations at round 95 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -41125.554447
EM: Round [1] log likelihood: -41094.311658
EM: Round [2] log likelihood: -41080.583487
EM: Round [3] log likelihood: -41073.477730
EM: Round [4] log likelihood: -41069.573208
EM: Round [5] log likelihood: -41067.376626
EM: Round [6] log likelihood: -41066.117163
EM: Round [7] log likelihood: -41065.376343
EM: Round [8] log likelihood: -41064.926256
EM: Round [9] log likelihood: -41064.642726
EM: Round [10] log likelihood: -41064.457347
EM: Round [11] log likelihood: -41064.331655
EM: Round [12] log likelihood: -41064.243447
EM: Round [13] log likelihood: -41064.179535
EM: Round [14] log likelihood: -41064.131853
EM: Round [15] log likelihood: -41064.095325
EM: Round [16] log likelihood: -41064.066669
EM: Round [17] log likelihood: -41064.043706
EM: Round [18] log likelihood: -41064.024957
EM: Round [19] log likelihood: -41064.009393
EM: Round [20] log likelihood: -41063.996285
EM: Round [21] log likelihood: -41063.985106
EM: Round [22] log likelihood: -41063.975466
EM: Round [23] log likelihood: -41063.967074
EM: Round [24] log likelihood: -41063.959709
EM: Round [25] log likelihood: -41063.953196
EM: Round [26] log likelihood: -41063.947403
EM: Round [27] log likelihood: -41063.942220
EM: Round [28] log likelihood: -41063.937560
EM: Round [29] log likelihood: -41063.933353
EM: Round [30] log likelihood: -41063.929540
EM: Round [31] log likelihood: -41063.926073
EM: Round [32] log likelihood: -41063.922909
EM: Round [33] log likelihood: -41063.920015
EM: Round [34] log likelihood: -41063.917360
EM: Round [35] log likelihood: -41063.914919
EM: Round [36] log likelihood: -41063.912670
EM: Round [37] log likelihood: -41063.910594
EM: Round [38] log likelihood: -41063.908673
EM: Round [39] log likelihood: -41063.906894
EM: Round [40] log likelihood: -41063.905243
EM: Round [41] log likelihood: -41063.903708
EM: Round [42] log likelihood: -41063.902280
EM: Round [43] log likelihood: -41063.900949
EM: Round [44] log likelihood: -41063.899707
EM: Round [45] log likelihood: -41063.898547
EM: Round [46] log likelihood: -41063.897463
EM: Round [47] log likelihood: -41063.896448
EM: Round [48] log likelihood: -41063.895497
EM: Round [49] log likelihood: -41063.894605
EM: Round [50] log likelihood: -41063.893768
EM: Round [51] log likelihood: -41063.892981
EM: Round [52] log likelihood: -41063.892242
EM: Round [53] log likelihood: -41063.891547
EM: Round [54] log likelihood: -41063.890892
EM: Round [55] log likelihood: -41063.890276
EM: Round [56] log likelihood: -41063.889694
EM: Round [57] log likelihood: -41063.889146
EM: Round [58] log likelihood: -41063.888629
EM: Round [59] log likelihood: -41063.888140
EM: Round [60] log likelihood: -41063.887678
EM: Round [61] log likelihood: -41063.887242
EM: Round [62] log likelihood: -41063.886829
EM: Round [63] log likelihood: -41063.886438
EM: Round [64] log likelihood: -41063.886069
EM: Round [65] log likelihood: -41063.885718
EM: Round [66] log likelihood: -41063.885386
EM: Round [67] log likelihood: -41063.885072
EM: Round [68] log likelihood: -41063.884774
EM: Round [69] log likelihood: -41063.884491
EM: Round [70] log likelihood: -41063.884222
EM: Round [71] log likelihood: -41063.883967
EM: Round [72] log likelihood: -41063.883725
EM: Round [73] log likelihood: -41063.883494
EM: Round [74] log likelihood: -41063.883276
EM: Round [75] log likelihood: -41063.883068
EM: Round [76] log likelihood: -41063.882870
EM: Round [77] log likelihood: -41063.882682
EM: Round [78] log likelihood: -41063.882502
EM: Round [79] log likelihood: -41063.882332
EM: Round [80] log likelihood: -41063.882169
EM: Round [81] log likelihood: -41063.882015
EM: Round [82] log likelihood: -41063.881867
EM: Round [83] log likelihood: -41063.881727
EM: Round [84] log likelihood: -41063.881593
EM: Round [85] log likelihood: -41063.881465
EM: Round [86] log likelihood: -41063.881343
EM: Round [87] log likelihood: -41063.881227
EM: Round [88] log likelihood: -41063.881116
EM: Round [89] log likelihood: -41063.881010
EM: Round [90] log likelihood: -41063.880909
EM: Round [91] log likelihood: -41063.880812
EM: Stopping iterations at round 91 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20  --fusion_preds /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir 
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter  --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 20 
CMD: cp /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 28784902 > /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir > /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir --annotate /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir
-done, see /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.HNm9yYpVS4/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 346, filtered: 3803)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.HNm9yYpVS4/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.HNm9yYpVS4/./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.HNm9yYpVS4/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000158482.10]
WARNING, no entry stored in dbm for [ENSG00000276721.1]
WARNING, no entry stored in dbm for [ENSG00000237390.1]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000225465.10]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000213643.3]
WARNING, no entry stored in dbm for [ENSG00000275374.1]
WARNING, no entry stored in dbm for [ENSG00000286356.1]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000274343.1]
WARNING, no entry stored in dbm for [ENSG00000287356.1]
WARNING, no entry stored in dbm for [ENSG00000203709.12]
WARNING, no entry stored in dbm for [ENSG00000287920.1]
WARNING, no entry stored in dbm for [ENSG00000283426.1]
WARNING, no entry stored in dbm for [ENSG00000225689.2]
WARNING, no entry stored in dbm for [ENSG00000286630.1]
WARNING, no entry stored in dbm for [ENSG00000230423.3]
WARNING, no entry stored in dbm for [ENSG00000230937.12]
WARNING, no entry stored in dbm for [ENSG00000239881.1]
WARNING, no entry stored in dbm for [ENSG00000228665.2]
WARNING, no entry stored in dbm for [ENSG00000223508.5]
WARNING, no entry stored in dbm for [ENSG00000265735.2]
WARNING, no entry stored in dbm for [ENSG00000244112.3]
WARNING, no entry stored in dbm for [ENSG00000202058.1]
WARNING, no entry stored in dbm for [ENSG00000202406.1]
WARNING, no entry stored in dbm for [ENSG00000222982.1]
WARNING, no entry stored in dbm for [ENSG00000201078.1]
WARNING, no entry stored in dbm for [ENSG00000199640.1]
WARNING, no entry stored in dbm for [ENSG00000199622.1]
WARNING, no entry stored in dbm for [ENSG00000199640.1]
WARNING, no entry stored in dbm for [ENSG00000199622.1]
WARNING, no entry stored in dbm for [ENSG00000202344.1]
WARNING, no entry stored in dbm for [ENSG00000222385.1]
WARNING, no entry stored in dbm for [ENSG00000202344.1]
WARNING, no entry stored in dbm for [ENSG00000255857.6]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000288588.1]
WARNING, no entry stored in dbm for [ENSG00000203799.13]
WARNING, no entry stored in dbm for [ENSG00000258090.1]
WARNING, no entry stored in dbm for [ENSG00000186960.12]
WARNING, no entry stored in dbm for [ENSG00000263740.2]
WARNING, no entry stored in dbm for [ENSG00000215154.6]
WARNING, no entry stored in dbm for [ENSG00000203825.4]
WARNING, no entry stored in dbm for [ENSG00000203825.4]
WARNING, no entry stored in dbm for [ENSG00000203825.4]
WARNING, no entry stored in dbm for [ENSG00000203825.4]
WARNING, no entry stored in dbm for [ENSG00000203825.4]
WARNING, no entry stored in dbm for [ENSG00000281026.1]
WARNING, no entry stored in dbm for [ENSG00000277047.5]
WARNING, no entry stored in dbm for [ENSG00000214955.5]
WARNING, no entry stored in dbm for [ENSG00000226320.6]
WARNING, no entry stored in dbm for [ENSG00000235687.9]
WARNING, no entry stored in dbm for [ENSG00000227060.7]
WARNING, no entry stored in dbm for [ENSG00000135477.11]
WARNING, no entry stored in dbm for [ENSG00000269821.1]
WARNING, no entry stored in dbm for [ENSG00000236679.2]
WARNING, no entry stored in dbm for [ENSG00000249768.2]
WARNING, no entry stored in dbm for [ENSG00000261395.3]
WARNING, no entry stored in dbm for [ENSG00000272620.2]
WARNING, no entry stored in dbm for [ENSG00000272595.2]
WARNING, no entry stored in dbm for [ENSG00000234741.8]
WARNING, no entry stored in dbm for [ENSG00000248360.7]
WARNING, no entry stored in dbm for [ENSG00000223652.2]
WARNING, no entry stored in dbm for [ENSG00000235768.1]
WARNING, no entry stored in dbm for [ENSG00000228887.3]
WARNING, no entry stored in dbm for [ENSG00000186704.9]
WARNING, no entry stored in dbm for [ENSG00000233514.1]
WARNING, no entry stored in dbm for [ENSG00000214659.4]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000223745.8]
WARNING, no entry stored in dbm for [ENSG00000214548.18]
WARNING, no entry stored in dbm for [ENSG00000220267.1]
WARNING, no entry stored in dbm for [ENSG00000254290.1]
WARNING, no entry stored in dbm for [ENSG00000279367.1]
WARNING, no entry stored in dbm for [ENSG00000287285.1]
WARNING, no entry stored in dbm for [ENSG00000234353.2]
WARNING, no entry stored in dbm for [ENSG00000267419.2]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000236627.1]
WARNING, no entry stored in dbm for [ENSG00000225096.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
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 [ENSG00000237788.1]
WARNING, no entry stored in dbm for [ENSG00000241354.2]
WARNING, no entry stored in dbm for [ENSG00000214535.3]
WARNING, no entry stored in dbm for [ENSG00000203413.3]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000231160.10]
WARNING, no entry stored in dbm for [ENSG00000250696.5]
WARNING, no entry stored in dbm for [ENSG00000224218.1]
WARNING, no entry stored in dbm for [ENSG00000282375.1]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000286436.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000228303.1]
WARNING, no entry stored in dbm for [ENSG00000252765.1]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000254485.5]
WARNING, no entry stored in dbm for [ENSG00000264666.1]
WARNING, no entry stored in dbm for [ENSG00000286982.1]
WARNING, no entry stored in dbm for [ENSG00000279249.3]
WARNING, no entry stored in dbm for [ENSG00000279317.2]
WARNING, no entry stored in dbm for [ENSG00000267469.1]
WARNING, no entry stored in dbm for [ENSG00000230305.2]
WARNING, no entry stored in dbm for [ENSG00000231139.1]
WARNING, no entry stored in dbm for [ENSG00000242737.1]
WARNING, no entry stored in dbm for [ENSG00000277739.1]


	* STAR-Fusion complete.  See output: /tmp/nxf.HNm9yYpVS4/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)