Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/22df28e816481e6be70ac3e0255e1d/ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1_2.fastp.fastq.gz
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/0e/da971dc85a9409e006f3372888701f/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/da971dc85a9409e006f3372888701f/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/22df28e816481e6be70ac3e0255e1d/ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/a2781656ad74a73d08d4e2bd56c6c9/ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.56jxr4OFHH/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary
-sample contains 30694500 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir -J /tmp/nxf.56jxr4OFHH/ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.56jxr4OFHH/ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
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[760000], rate=85714.29/min -building interval tree based on /tmp/nxf.56jxr4OFHH/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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[760000], rate=78485.37/min -building interval tree based on /tmp/nxf.56jxr4OFHH/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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[750000], rate=75000.00/min -building interval tree based on /tmp/nxf.56jxr4OFHH/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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[750000], rate=71884.98/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir --filt_file /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
6000000.00 reads per min processed...
12000000.00 reads per min processed...
9000000.00 reads per min processed...
8000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
5400000.00 reads per min processed...
5000000.00 reads per min processed...
5076923.08 reads per min processed...
5142857.14 reads per min processed...
4875000.00 reads per min processed...
4941176.47 reads per min processed...
5000000.00 reads per min processed...
5052631.58 reads per min processed...
5100000.00 reads per min processed...
5142857.14 reads per min processed...
5181818.18 reads per min processed...
5217391.30 reads per min processed...
5040000.00 reads per min processed...
5076923.08 reads per min processed...
5111111.11 reads per min processed...
4965517.24 reads per min processed...
5000000.00 reads per min processed...
5032258.06 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.56jxr4OFHH/ColoN_FFPE_L02_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.56jxr4OFHH/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -44967.404931
EM: Round [1] log likelihood: -44826.249782
EM: Round [2] log likelihood: -44768.775124
EM: Round [3] log likelihood: -44740.176890
EM: Round [4] log likelihood: -44724.699340
EM: Round [5] log likelihood: -44715.965464
EM: Round [6] log likelihood: -44710.869115
EM: Round [7] log likelihood: -44707.790871
EM: Round [8] log likelihood: -44705.864663
EM: Round [9] log likelihood: -44704.617396
EM: Round [10] log likelihood: -44703.783613
EM: Round [11] log likelihood: -44703.209721
EM: Round [12] log likelihood: -44702.804041
EM: Round [13] log likelihood: -44702.510209
EM: Round [14] log likelihood: -44702.292614
EM: Round [15] log likelihood: -44702.128187
EM: Round [16] log likelihood: -44702.001630
EM: Round [17] log likelihood: -44701.902579
EM: Round [18] log likelihood: -44701.823870
EM: Round [19] log likelihood: -44701.760455
EM: Round [20] log likelihood: -44701.708716
EM: Round [21] log likelihood: -44701.666015
EM: Round [22] log likelihood: -44701.630399
EM: Round [23] log likelihood: -44701.600402
EM: Round [24] log likelihood: -44701.574907
EM: Round [25] log likelihood: -44701.553053
EM: Round [26] log likelihood: -44701.534171
EM: Round [27] log likelihood: -44701.517731
EM: Round [28] log likelihood: -44701.503315
EM: Round [29] log likelihood: -44701.490586
EM: Round [30] log likelihood: -44701.479271
EM: Round [31] log likelihood: -44701.469150
EM: Round [32] log likelihood: -44701.460042
EM: Round [33] log likelihood: -44701.451797
EM: Round [34] log likelihood: -44701.444293
EM: Round [35] log likelihood: -44701.437427
EM: Round [36] log likelihood: -44701.431114
EM: Round [37] log likelihood: -44701.425282
EM: Round [38] log likelihood: -44701.419871
EM: Round [39] log likelihood: -44701.414831
EM: Round [40] log likelihood: -44701.410117
EM: Round [41] log likelihood: -44701.405694
EM: Round [42] log likelihood: -44701.401531
EM: Round [43] log likelihood: -44701.397600
EM: Round [44] log likelihood: -44701.393879
EM: Round [45] log likelihood: -44701.390349
EM: Round [46] log likelihood: -44701.386992
EM: Round [47] log likelihood: -44701.383793
EM: Round [48] log likelihood: -44701.380740
EM: Round [49] log likelihood: -44701.377822
EM: Round [50] log likelihood: -44701.375028
EM: Round [51] log likelihood: -44701.372350
EM: Round [52] log likelihood: -44701.369780
EM: Round [53] log likelihood: -44701.367312
EM: Round [54] log likelihood: -44701.364939
EM: Round [55] log likelihood: -44701.362655
EM: Round [56] log likelihood: -44701.360457
EM: Round [57] log likelihood: -44701.358339
EM: Round [58] log likelihood: -44701.356297
EM: Round [59] log likelihood: -44701.354328
EM: Round [60] log likelihood: -44701.352428
EM: Round [61] log likelihood: -44701.350594
EM: Round [62] log likelihood: -44701.348823
EM: Round [63] log likelihood: -44701.347113
EM: Round [64] log likelihood: -44701.345461
EM: Round [65] log likelihood: -44701.343865
EM: Round [66] log likelihood: -44701.342321
EM: Round [67] log likelihood: -44701.340830
EM: Round [68] log likelihood: -44701.339387
EM: Round [69] log likelihood: -44701.337992
EM: Round [70] log likelihood: -44701.336643
EM: Round [71] log likelihood: -44701.335338
EM: Round [72] log likelihood: -44701.334075
EM: Round [73] log likelihood: -44701.332853
EM: Round [74] log likelihood: -44701.331671
EM: Round [75] log likelihood: -44701.330527
EM: Round [76] log likelihood: -44701.329419
EM: Round [77] log likelihood: -44701.328347
EM: Round [78] log likelihood: -44701.327309
EM: Round [79] log likelihood: -44701.326305
EM: Round [80] log likelihood: -44701.325332
EM: Round [81] log likelihood: -44701.324390
EM: Round [82] log likelihood: -44701.323477
EM: Round [83] log likelihood: -44701.322594
EM: Round [84] log likelihood: -44701.321738
EM: Round [85] log likelihood: -44701.320909
EM: Round [86] log likelihood: -44701.320106
EM: Round [87] log likelihood: -44701.319328
EM: Round [88] log likelihood: -44701.318574
EM: Round [89] log likelihood: -44701.317844
EM: Round [90] log likelihood: -44701.317136
EM: Round [91] log likelihood: -44701.316450
EM: Round [92] log likelihood: -44701.315785
EM: Round [93] log likelihood: -44701.315140
EM: Round [94] log likelihood: -44701.314516
EM: Round [95] log likelihood: -44701.313910
EM: Round [96] log likelihood: -44701.313322
EM: Round [97] log likelihood: -44701.312753
EM: Round [98] log likelihood: -44701.312201
EM: Round [99] log likelihood: -44701.311665
EM: Round [100] log likelihood: -44701.311145
EM: Round [101] log likelihood: -44701.310641
EM: Round [102] log likelihood: -44701.310152
EM: Round [103] log likelihood: -44701.309678
EM: Round [104] log likelihood: -44701.309218
EM: Round [105] log likelihood: -44701.308771
EM: Round [106] log likelihood: -44701.308338
EM: Round [107] log likelihood: -44701.307917
EM: Round [108] log likelihood: -44701.307508
EM: Round [109] log likelihood: -44701.307112
EM: Round [110] log likelihood: -44701.306727
EM: Round [111] log likelihood: -44701.306353
EM: Round [112] log likelihood: -44701.305990
EM: Round [113] log likelihood: -44701.305638
EM: Round [114] log likelihood: -44701.305295
EM: Round [115] log likelihood: -44701.304962
EM: Round [116] log likelihood: -44701.304639
EM: Round [117] log likelihood: -44701.304325
EM: Round [118] log likelihood: -44701.304020
EM: Round [119] log likelihood: -44701.303724
EM: Round [120] log likelihood: -44701.303436
EM: Round [121] log likelihood: -44701.303156
EM: Round [122] log likelihood: -44701.302884
EM: Round [123] log likelihood: -44701.302619
EM: Round [124] log likelihood: -44701.302362
EM: Round [125] log likelihood: -44701.302112
EM: Round [126] log likelihood: -44701.301868
EM: Round [127] log likelihood: -44701.301632
EM: Round [128] log likelihood: -44701.301402
EM: Round [129] log likelihood: -44701.301178
EM: Round [130] log likelihood: -44701.300960
EM: Round [131] log likelihood: -44701.300748
EM: Round [132] log likelihood: -44701.300542
EM: Round [133] log likelihood: -44701.300341
EM: Round [134] log likelihood: -44701.300146
EM: Round [135] log likelihood: -44701.299956
EM: Round [136] log likelihood: -44701.299771
EM: Round [137] log likelihood: -44701.299591
EM: Round [138] log likelihood: -44701.299416
EM: Round [139] log likelihood: -44701.299245
EM: Round [140] log likelihood: -44701.299079
EM: Round [141] log likelihood: -44701.298918
EM: Round [142] log likelihood: -44701.298760
EM: Round [143] log likelihood: -44701.298606
EM: Round [144] log likelihood: -44701.298457
EM: Round [145] log likelihood: -44701.298311
EM: Round [146] log likelihood: -44701.298170
EM: Round [147] log likelihood: -44701.298031
EM: Round [148] log likelihood: -44701.297897
EM: Round [149] log likelihood: -44701.297765
EM: Round [150] log likelihood: -44701.297637
EM: Round [151] log likelihood: -44701.297513
EM: Round [152] log likelihood: -44701.297391
EM: Round [153] log likelihood: -44701.297273
EM: Round [154] log likelihood: -44701.297157
EM: Round [155] log likelihood: -44701.297045
EM: Round [156] log likelihood: -44701.296935
EM: Round [157] log likelihood: -44701.296828
EM: Round [158] log likelihood: -44701.296723
EM: Round [159] log likelihood: -44701.296622
EM: Round [160] log likelihood: -44701.296522
EM: Stopping iterations at round 160 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -44927.931917
EM: Round [1] log likelihood: -44804.785007
EM: Round [2] log likelihood: -44756.408030
EM: Round [3] log likelihood: -44732.773174
EM: Round [4] log likelihood: -44720.144920
EM: Round [5] log likelihood: -44713.081896
EM: Round [6] log likelihood: -44708.984019
EM: Round [7] log likelihood: -44706.517778
EM: Round [8] log likelihood: -44704.978264
EM: Round [9] log likelihood: -44703.983181
EM: Round [10] log likelihood: -44703.318910
EM: Round [11] log likelihood: -44702.862149
EM: Round [12] log likelihood: -44702.539427
EM: Round [13] log likelihood: -44702.305640
EM: Round [14] log likelihood: -44702.132343
EM: Round [15] log likelihood: -44702.001143
EM: Round [16] log likelihood: -44701.899873
EM: Round [17] log likelihood: -44701.820311
EM: Round [18] log likelihood: -44701.756786
EM: Round [19] log likelihood: -44701.705316
EM: Round [20] log likelihood: -44701.663051
EM: Round [21] log likelihood: -44701.627918
EM: Round [22] log likelihood: -44701.598385
EM: Round [23] log likelihood: -44701.573304
EM: Round [24] log likelihood: -44701.551801
EM: Round [25] log likelihood: -44701.533203
EM: Round [26] log likelihood: -44701.516985
EM: Round [27] log likelihood: -44701.502734
EM: Round [28] log likelihood: -44701.490120
EM: Round [29] log likelihood: -44701.478879
EM: Round [30] log likelihood: -44701.468798
EM: Round [31] log likelihood: -44701.459701
EM: Round [32] log likelihood: -44701.451446
EM: Round [33] log likelihood: -44701.443913
EM: Round [34] log likelihood: -44701.437006
EM: Round [35] log likelihood: -44701.430641
EM: Round [36] log likelihood: -44701.424751
EM: Round [37] log likelihood: -44701.419277
EM: Round [38] log likelihood: -44701.414170
EM: Round [39] log likelihood: -44701.409388
EM: Round [40] log likelihood: -44701.404898
EM: Round [41] log likelihood: -44701.400667
EM: Round [42] log likelihood: -44701.396671
EM: Round [43] log likelihood: -44701.392887
EM: Round [44] log likelihood: -44701.389295
EM: Round [45] log likelihood: -44701.385880
EM: Round [46] log likelihood: -44701.382625
EM: Round [47] log likelihood: -44701.379520
EM: Round [48] log likelihood: -44701.376552
EM: Round [49] log likelihood: -44701.373711
EM: Round [50] log likelihood: -44701.370989
EM: Round [51] log likelihood: -44701.368379
EM: Round [52] log likelihood: -44701.365872
EM: Round [53] log likelihood: -44701.363464
EM: Round [54] log likelihood: -44701.361148
EM: Round [55] log likelihood: -44701.358920
EM: Round [56] log likelihood: -44701.356774
EM: Round [57] log likelihood: -44701.354708
EM: Round [58] log likelihood: -44701.352716
EM: Round [59] log likelihood: -44701.350796
EM: Round [60] log likelihood: -44701.348943
EM: Round [61] log likelihood: -44701.347156
EM: Round [62] log likelihood: -44701.345432
EM: Round [63] log likelihood: -44701.343767
EM: Round [64] log likelihood: -44701.342159
EM: Round [65] log likelihood: -44701.340607
EM: Round [66] log likelihood: -44701.339107
EM: Round [67] log likelihood: -44701.337658
EM: Round [68] log likelihood: -44701.336258
EM: Round [69] log likelihood: -44701.334905
EM: Round [70] log likelihood: -44701.333598
EM: Round [71] log likelihood: -44701.332334
EM: Round [72] log likelihood: -44701.331112
EM: Round [73] log likelihood: -44701.329931
EM: Round [74] log likelihood: -44701.328789
EM: Round [75] log likelihood: -44701.327684
EM: Round [76] log likelihood: -44701.326616
EM: Round [77] log likelihood: -44701.325583
EM: Round [78] log likelihood: -44701.324584
EM: Round [79] log likelihood: -44701.323617
EM: Round [80] log likelihood: -44701.322682
EM: Round [81] log likelihood: -44701.321778
EM: Round [82] log likelihood: -44701.320903
EM: Round [83] log likelihood: -44701.320056
EM: Round [84] log likelihood: -44701.319237
EM: Round [85] log likelihood: -44701.318444
EM: Round [86] log likelihood: -44701.317677
EM: Round [87] log likelihood: -44701.316935
EM: Round [88] log likelihood: -44701.316216
EM: Round [89] log likelihood: -44701.315520
EM: Round [90] log likelihood: -44701.314847
EM: Round [91] log likelihood: -44701.314195
EM: Round [92] log likelihood: -44701.313564
EM: Round [93] log likelihood: -44701.312953
EM: Round [94] log likelihood: -44701.312361
EM: Round [95] log likelihood: -44701.311788
EM: Round [96] log likelihood: -44701.311233
EM: Round [97] log likelihood: -44701.310696
EM: Round [98] log likelihood: -44701.310175
EM: Round [99] log likelihood: -44701.309671
EM: Round [100] log likelihood: -44701.309182
EM: Round [101] log likelihood: -44701.308709
EM: Round [102] log likelihood: -44701.308250
EM: Round [103] log likelihood: -44701.307806
EM: Round [104] log likelihood: -44701.307375
EM: Round [105] log likelihood: -44701.306958
EM: Round [106] log likelihood: -44701.306553
EM: Round [107] log likelihood: -44701.306161
EM: Round [108] log likelihood: -44701.305781
EM: Round [109] log likelihood: -44701.305412
EM: Round [110] log likelihood: -44701.305055
EM: Round [111] log likelihood: -44701.304708
EM: Round [112] log likelihood: -44701.304372
EM: Round [113] log likelihood: -44701.304046
EM: Round [114] log likelihood: -44701.303730
EM: Round [115] log likelihood: -44701.303423
EM: Round [116] log likelihood: -44701.303126
EM: Round [117] log likelihood: -44701.302837
EM: Round [118] log likelihood: -44701.302557
EM: Round [119] log likelihood: -44701.302285
EM: Round [120] log likelihood: -44701.302021
EM: Round [121] log likelihood: -44701.301765
EM: Round [122] log likelihood: -44701.301516
EM: Round [123] log likelihood: -44701.301275
EM: Round [124] log likelihood: -44701.301041
EM: Round [125] log likelihood: -44701.300813
EM: Round [126] log likelihood: -44701.300592
EM: Round [127] log likelihood: -44701.300378
EM: Round [128] log likelihood: -44701.300169
EM: Round [129] log likelihood: -44701.299967
EM: Round [130] log likelihood: -44701.299770
EM: Round [131] log likelihood: -44701.299579
EM: Round [132] log likelihood: -44701.299393
EM: Round [133] log likelihood: -44701.299213
EM: Round [134] log likelihood: -44701.299037
EM: Round [135] log likelihood: -44701.298867
EM: Round [136] log likelihood: -44701.298701
EM: Round [137] log likelihood: -44701.298540
EM: Round [138] log likelihood: -44701.298384
EM: Round [139] log likelihood: -44701.298232
EM: Round [140] log likelihood: -44701.298084
EM: Round [141] log likelihood: -44701.297940
EM: Round [142] log likelihood: -44701.297800
EM: Round [143] log likelihood: -44701.297663
EM: Round [144] log likelihood: -44701.297531
EM: Round [145] log likelihood: -44701.297402
EM: Round [146] log likelihood: -44701.297277
EM: Round [147] log likelihood: -44701.297155
EM: Round [148] log likelihood: -44701.297036
EM: Round [149] log likelihood: -44701.296920
EM: Round [150] log likelihood: -44701.296808
EM: Round [151] log likelihood: -44701.296698
EM: Round [152] log likelihood: -44701.296592
EM: Round [153] log likelihood: -44701.296488
EM: Round [154] log likelihood: -44701.296387
EM: Round [155] log likelihood: -44701.296288
EM: Stopping iterations at round 155 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 30694500 > /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir > /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir --annotate /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir
-done, see /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.56jxr4OFHH/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 200, filtered: 2935)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.56jxr4OFHH/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.56jxr4OFHH/./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.56jxr4OFHH/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000181577.16]
WARNING, no entry stored in dbm for [ENSG00000247809.9]
WARNING, no entry stored in dbm for [ENSG00000230202.1]
WARNING, no entry stored in dbm for [ENSG00000181126.13]
WARNING, no entry stored in dbm for [ENSG00000258537.5]
WARNING, no entry stored in dbm for [ENSG00000250802.7]
WARNING, no entry stored in dbm for [ENSG00000255319.5]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000285367.1]
WARNING, no entry stored in dbm for [ENSG00000240549.2]
WARNING, no entry stored in dbm for [ENSG00000258313.1]
WARNING, no entry stored in dbm for [ENSG00000272447.1]
WARNING, no entry stored in dbm for [ENSG00000267433.1]
WARNING, no entry stored in dbm for [ENSG00000185986.12]
WARNING, no entry stored in dbm for [ENSG00000214135.8]
WARNING, no entry stored in dbm for [ENSG00000246889.2]
WARNING, no entry stored in dbm for [ENSG00000270111.3]
WARNING, no entry stored in dbm for [ENSG00000196183.5]
WARNING, no entry stored in dbm for [ENSG00000202441.2]
WARNING, no entry stored in dbm for [ENSG00000202124.1]
WARNING, no entry stored in dbm for [ENSG00000202441.2]
WARNING, no entry stored in dbm for [ENSG00000238711.1]
WARNING, no entry stored in dbm for [ENSG00000202441.2]
WARNING, no entry stored in dbm for [ENSG00000201377.1]
WARNING, no entry stored in dbm for [ENSG00000202441.2]
WARNING, no entry stored in dbm for [ENSG00000199400.1]
WARNING, no entry stored in dbm for [ENSG00000202441.2]
WARNING, no entry stored in dbm for [ENSG00000267482.1]
WARNING, no entry stored in dbm for [ENSG00000207357.1]
WARNING, no entry stored in dbm for [ENSG00000263934.5]
WARNING, no entry stored in dbm for [ENSG00000278525.1]
WARNING, no entry stored in dbm for [ENSG00000263740.2]
WARNING, no entry stored in dbm for [ENSG00000278525.1]
WARNING, no entry stored in dbm for [ENSG00000244642.3]
WARNING, no entry stored in dbm for [ENSG00000202058.1]
WARNING, no entry stored in dbm for [ENSG00000200794.1]
WARNING, no entry stored in dbm for [ENSG00000269900.3]
WARNING, no entry stored in dbm for [ENSG00000127957.18]
WARNING, no entry stored in dbm for [ENSG00000271538.6]
WARNING, no entry stored in dbm for [IGL.g@-ext]
WARNING, no entry stored in dbm for [ENSG00000232610.1]
WARNING, no entry stored in dbm for [ENSG00000261610.1]
WARNING, no entry stored in dbm for [ENSG00000228666.1]
WARNING, no entry stored in dbm for [ENSG00000280927.1]
WARNING, no entry stored in dbm for [ENSG00000257137.7]
WARNING, no entry stored in dbm for [ENSG00000226581.2]
WARNING, no entry stored in dbm for [ENSG00000261863.1]
WARNING, no entry stored in dbm for [ENSG00000283103.3]
WARNING, no entry stored in dbm for [ENSG00000270926.1]
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 [ENSG00000240477.1]
WARNING, no entry stored in dbm for [ENSG00000232022.7]
WARNING, no entry stored in dbm for [ENSG00000270482.1]
WARNING, no entry stored in dbm for [ENSG00000267328.1]
WARNING, no entry stored in dbm for [ENSG00000173077.16]
WARNING, no entry stored in dbm for [ENSG00000255136.3]
WARNING, no entry stored in dbm for [ENSG00000242186.2]
WARNING, no entry stored in dbm for [ENSG00000266522.1]
WARNING, no entry stored in dbm for [ENSG00000254590.1]
WARNING, no entry stored in dbm for [ENSG00000196312.15]
WARNING, no entry stored in dbm for [ENSG00000272106.1]
WARNING, no entry stored in dbm for [ENSG00000235582.2]
WARNING, no entry stored in dbm for [ENSG00000280285.1]
WARNING, no entry stored in dbm for [ENSG00000279406.1]
WARNING, no entry stored in dbm for [ENSG00000279738.1]
WARNING, no entry stored in dbm for [ENSG00000271519.1]
WARNING, no entry stored in dbm for [ENSG00000232855.7]
WARNING, no entry stored in dbm for [ENSG00000229930.1]
WARNING, no entry stored in dbm for [ENSG00000284675.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000283849.1]
WARNING, no entry stored in dbm for [ENSG00000239268.3]
WARNING, no entry stored in dbm for [ENSG00000276538.1]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000257337.7]
WARNING, no entry stored in dbm for [ENSG00000185641.6]
WARNING, no entry stored in dbm for [ENSG00000235725.1]
WARNING, no entry stored in dbm for [ENSG00000284052.1]
WARNING, no entry stored in dbm for [ENSG00000271163.1]
WARNING, no entry stored in dbm for [ENSG00000271394.1]
WARNING, no entry stored in dbm for [ENSG00000200794.1]
* STAR-Fusion complete. See output: /tmp/nxf.56jxr4OFHH/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)