Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/33afafac74c3a090289a821c27d944/659_dm4-T1-TRNA-1_B23WHTKLT4_1_1.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/30/e3ef4abfea1ea02d0e7bb6a3018a36/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/0fa1410f6de38afdc58d88b3adedf7/659_dm4-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/e3ef4abfea1ea02d0e7bb6a3018a36/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/33afafac74c3a090289a821c27d944/659_dm4-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.DFis1kKwbz/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary
-sample contains 102160001 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir -J /tmp/nxf.DFis1kKwbz/659_dm4-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction -O /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.DFis1kKwbz/659_dm4-T1-TRNA-1_B23WHTKLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
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[1050000], rate=82245.43/min -building interval tree based on /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
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[1040000], rate=64864.86/min -building interval tree based on /tmp/nxf.DFis1kKwbz/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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[1040000], rate=61356.93/min -building interval tree based on /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.10 min).
-mapping reads to genes
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[1040000], rate=61056.75/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir --filt_file /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.DFis1kKwbz/./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...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
5142857.14 reads per min processed...
4666666.67 reads per min processed...
4800000.00 reads per min processed...
4500000.00 reads per min processed...
4615384.62 reads per min processed...
4714285.71 reads per min processed...
4500000.00 reads per min processed...
4333333.33 reads per min processed...
4200000.00 reads per min processed...
4090909.09 reads per min processed...
4173913.04 reads per min processed...
4080000.00 reads per min processed...
4153846.15 reads per min processed...
4071428.57 reads per min processed...
4137931.03 reads per min processed...
4200000.00 reads per min processed...
4258064.52 reads per min processed...
4312500.00 reads per min processed...
4363636.36 reads per min processed...
4545454.55 reads per min processed...
4457142.86 reads per min processed...
4378378.38 reads per min processed...
4421052.63 reads per min processed...
4350000.00 reads per min processed...
4285714.29 reads per min processed...
4325581.40 reads per min processed...
4266666.67 reads per min processed...
4304347.83 reads per min processed...
4340425.53 reads per min processed...
4285714.29 reads per min processed...
4320000.00 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.DFis1kKwbz/659_dm4-T1-TRNA-1_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.DFis1kKwbz/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -61814.639603
EM: Round [1] log likelihood: -61788.818596
EM: Round [2] log likelihood: -61778.583109
EM: Round [3] log likelihood: -61773.325733
EM: Round [4] log likelihood: -61770.371331
EM: Round [5] log likelihood: -61768.638187
EM: Round [6] log likelihood: -61767.595460
EM: Round [7] log likelihood: -61766.954525
EM: Round [8] log likelihood: -61766.550985
EM: Round [9] log likelihood: -61766.289714
EM: Round [10] log likelihood: -61766.115256
EM: Round [11] log likelihood: -61765.994947
EM: Round [12] log likelihood: -61765.909245
EM: Round [13] log likelihood: -61765.846220
EM: Round [14] log likelihood: -61765.798425
EM: Round [15] log likelihood: -61765.761100
EM: Round [16] log likelihood: -61765.731133
EM: Round [17] log likelihood: -61765.706446
EM: Round [18] log likelihood: -61765.685627
EM: Round [19] log likelihood: -61765.667696
EM: Round [20] log likelihood: -61765.651967
EM: Round [21] log likelihood: -61765.637947
EM: Round [22] log likelihood: -61765.625284
EM: Round [23] log likelihood: -61765.613718
EM: Round [24] log likelihood: -61765.603056
EM: Round [25] log likelihood: -61765.593155
EM: Round [26] log likelihood: -61765.583903
EM: Round [27] log likelihood: -61765.575217
EM: Round [28] log likelihood: -61765.567030
EM: Round [29] log likelihood: -61765.559288
EM: Round [30] log likelihood: -61765.551950
EM: Round [31] log likelihood: -61765.544978
EM: Round [32] log likelihood: -61765.538345
EM: Round [33] log likelihood: -61765.532025
EM: Round [34] log likelihood: -61765.525996
EM: Round [35] log likelihood: -61765.520239
EM: Round [36] log likelihood: -61765.514739
EM: Round [37] log likelihood: -61765.509480
EM: Round [38] log likelihood: -61765.504449
EM: Round [39] log likelihood: -61765.499633
EM: Round [40] log likelihood: -61765.495021
EM: Round [41] log likelihood: -61765.490604
EM: Round [42] log likelihood: -61765.486371
EM: Round [43] log likelihood: -61765.482314
EM: Round [44] log likelihood: -61765.478425
EM: Round [45] log likelihood: -61765.474695
EM: Round [46] log likelihood: -61765.471117
EM: Round [47] log likelihood: -61765.467684
EM: Round [48] log likelihood: -61765.464391
EM: Round [49] log likelihood: -61765.461230
EM: Round [50] log likelihood: -61765.458196
EM: Round [51] log likelihood: -61765.455284
EM: Round [52] log likelihood: -61765.452487
EM: Round [53] log likelihood: -61765.449802
EM: Round [54] log likelihood: -61765.447224
EM: Round [55] log likelihood: -61765.444747
EM: Round [56] log likelihood: -61765.442368
EM: Round [57] log likelihood: -61765.440082
EM: Round [58] log likelihood: -61765.437886
EM: Round [59] log likelihood: -61765.435776
EM: Round [60] log likelihood: -61765.433748
EM: Round [61] log likelihood: -61765.431800
EM: Round [62] log likelihood: -61765.429927
EM: Round [63] log likelihood: -61765.428127
EM: Round [64] log likelihood: -61765.426397
EM: Round [65] log likelihood: -61765.424733
EM: Round [66] log likelihood: -61765.423134
EM: Round [67] log likelihood: -61765.421597
EM: Round [68] log likelihood: -61765.420118
EM: Round [69] log likelihood: -61765.418697
EM: Round [70] log likelihood: -61765.417330
EM: Round [71] log likelihood: -61765.416015
EM: Round [72] log likelihood: -61765.414751
EM: Round [73] log likelihood: -61765.413535
EM: Round [74] log likelihood: -61765.412366
EM: Round [75] log likelihood: -61765.411241
EM: Round [76] log likelihood: -61765.410159
EM: Round [77] log likelihood: -61765.409118
EM: Round [78] log likelihood: -61765.408117
EM: Round [79] log likelihood: -61765.407154
EM: Round [80] log likelihood: -61765.406227
EM: Round [81] log likelihood: -61765.405336
EM: Round [82] log likelihood: -61765.404478
EM: Round [83] log likelihood: -61765.403653
EM: Round [84] log likelihood: -61765.402858
EM: Round [85] log likelihood: -61765.402094
EM: Round [86] log likelihood: -61765.401359
EM: Round [87] log likelihood: -61765.400652
EM: Round [88] log likelihood: -61765.399971
EM: Round [89] log likelihood: -61765.399316
EM: Round [90] log likelihood: -61765.398685
EM: Round [91] log likelihood: -61765.398079
EM: Round [92] log likelihood: -61765.397495
EM: Round [93] log likelihood: -61765.396933
EM: Round [94] log likelihood: -61765.396392
EM: Round [95] log likelihood: -61765.395871
EM: Round [96] log likelihood: -61765.395370
EM: Round [97] log likelihood: -61765.394888
EM: Round [98] log likelihood: -61765.394424
EM: Round [99] log likelihood: -61765.393977
EM: Round [100] log likelihood: -61765.393547
EM: Round [101] log likelihood: -61765.393133
EM: Round [102] log likelihood: -61765.392735
EM: Round [103] log likelihood: -61765.392351
EM: Round [104] log likelihood: -61765.391982
EM: Round [105] log likelihood: -61765.391627
EM: Round [106] log likelihood: -61765.391285
EM: Round [107] log likelihood: -61765.390955
EM: Round [108] log likelihood: -61765.390638
EM: Round [109] log likelihood: -61765.390333
EM: Round [110] log likelihood: -61765.390039
EM: Round [111] log likelihood: -61765.389756
EM: Round [112] log likelihood: -61765.389484
EM: Round [113] log likelihood: -61765.389222
EM: Round [114] log likelihood: -61765.388970
EM: Round [115] log likelihood: -61765.388727
EM: Round [116] log likelihood: -61765.388493
EM: Round [117] log likelihood: -61765.388268
EM: Round [118] log likelihood: -61765.388051
EM: Round [119] log likelihood: -61765.387842
EM: Round [120] log likelihood: -61765.387641
EM: Round [121] log likelihood: -61765.387448
EM: Round [122] log likelihood: -61765.387262
EM: Round [123] log likelihood: -61765.387082
EM: Round [124] log likelihood: -61765.386910
EM: Round [125] log likelihood: -61765.386743
EM: Round [126] log likelihood: -61765.386583
EM: Round [127] log likelihood: -61765.386429
EM: Round [128] log likelihood: -61765.386281
EM: Round [129] log likelihood: -61765.386138
EM: Round [130] log likelihood: -61765.386000
EM: Round [131] log likelihood: -61765.385868
EM: Round [132] log likelihood: -61765.385741
EM: Round [133] log likelihood: -61765.385618
EM: Round [134] log likelihood: -61765.385500
EM: Round [135] log likelihood: -61765.385386
EM: Round [136] log likelihood: -61765.385276
EM: Round [137] log likelihood: -61765.385171
EM: Round [138] log likelihood: -61765.385069
EM: Round [139] log likelihood: -61765.384971
EM: Stopping iterations at round 139 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -61791.989118
EM: Round [1] log likelihood: -61767.278932
EM: Round [2] log likelihood: -61757.749841
EM: Round [3] log likelihood: -61752.912570
EM: Round [4] log likelihood: -61750.204722
EM: Round [5] log likelihood: -61748.618820
EM: Round [6] log likelihood: -61747.666651
EM: Round [7] log likelihood: -61747.083111
EM: Round [8] log likelihood: -61746.716909
EM: Round [9] log likelihood: -61746.480450
EM: Round [10] log likelihood: -61746.322763
EM: Round [11] log likelihood: -61746.213948
EM: Round [12] log likelihood: -61746.136214
EM: Round [13] log likelihood: -61746.078767
EM: Round [14] log likelihood: -61746.034907
EM: Round [15] log likelihood: -61746.000379
EM: Round [16] log likelihood: -61745.972412
EM: Round [17] log likelihood: -61745.949165
EM: Round [18] log likelihood: -61745.929386
EM: Round [19] log likelihood: -61745.912211
EM: Round [20] log likelihood: -61745.897032
EM: Round [21] log likelihood: -61745.883417
EM: Round [22] log likelihood: -61745.871051
EM: Round [23] log likelihood: -61745.859703
EM: Round [24] log likelihood: -61745.849204
EM: Round [25] log likelihood: -61745.839423
EM: Round [26] log likelihood: -61745.830261
EM: Round [27] log likelihood: -61745.821642
EM: Round [28] log likelihood: -61745.813505
EM: Round [29] log likelihood: -61745.805801
EM: Round [30] log likelihood: -61745.798491
EM: Round [31] log likelihood: -61745.791541
EM: Round [32] log likelihood: -61745.784923
EM: Round [33] log likelihood: -61745.778615
EM: Round [34] log likelihood: -61745.772596
EM: Round [35] log likelihood: -61745.766847
EM: Round [36] log likelihood: -61745.761352
EM: Round [37] log likelihood: -61745.756097
EM: Round [38] log likelihood: -61745.751069
EM: Round [39] log likelihood: -61745.746255
EM: Round [40] log likelihood: -61745.741646
EM: Round [41] log likelihood: -61745.737230
EM: Round [42] log likelihood: -61745.732999
EM: Round [43] log likelihood: -61745.728943
EM: Round [44] log likelihood: -61745.725054
EM: Round [45] log likelihood: -61745.721324
EM: Round [46] log likelihood: -61745.717747
EM: Round [47] log likelihood: -61745.714315
EM: Round [48] log likelihood: -61745.711022
EM: Round [49] log likelihood: -61745.707861
EM: Round [50] log likelihood: -61745.704827
EM: Round [51] log likelihood: -61745.701915
EM: Round [52] log likelihood: -61745.699119
EM: Round [53] log likelihood: -61745.696434
EM: Round [54] log likelihood: -61745.693855
EM: Round [55] log likelihood: -61745.691378
EM: Round [56] log likelihood: -61745.688999
EM: Round [57] log likelihood: -61745.686713
EM: Round [58] log likelihood: -61745.684518
EM: Round [59] log likelihood: -61745.682408
EM: Round [60] log likelihood: -61745.680380
EM: Round [61] log likelihood: -61745.678431
EM: Round [62] log likelihood: -61745.676559
EM: Round [63] log likelihood: -61745.674759
EM: Round [64] log likelihood: -61745.673028
EM: Round [65] log likelihood: -61745.671365
EM: Round [66] log likelihood: -61745.669766
EM: Round [67] log likelihood: -61745.668228
EM: Round [68] log likelihood: -61745.666750
EM: Round [69] log likelihood: -61745.665328
EM: Round [70] log likelihood: -61745.663961
EM: Round [71] log likelihood: -61745.662647
EM: Round [72] log likelihood: -61745.661383
EM: Round [73] log likelihood: -61745.660167
EM: Round [74] log likelihood: -61745.658997
EM: Round [75] log likelihood: -61745.657873
EM: Round [76] log likelihood: -61745.656791
EM: Round [77] log likelihood: -61745.655750
EM: Round [78] log likelihood: -61745.654749
EM: Round [79] log likelihood: -61745.653785
EM: Round [80] log likelihood: -61745.652859
EM: Round [81] log likelihood: -61745.651967
EM: Round [82] log likelihood: -61745.651109
EM: Round [83] log likelihood: -61745.650284
EM: Round [84] log likelihood: -61745.649490
EM: Round [85] log likelihood: -61745.648726
EM: Round [86] log likelihood: -61745.647991
EM: Round [87] log likelihood: -61745.647283
EM: Round [88] log likelihood: -61745.646603
EM: Round [89] log likelihood: -61745.645947
EM: Round [90] log likelihood: -61745.645317
EM: Round [91] log likelihood: -61745.644710
EM: Round [92] log likelihood: -61745.644126
EM: Round [93] log likelihood: -61745.643564
EM: Round [94] log likelihood: -61745.643023
EM: Round [95] log likelihood: -61745.642503
EM: Round [96] log likelihood: -61745.642002
EM: Round [97] log likelihood: -61745.641520
EM: Round [98] log likelihood: -61745.641056
EM: Round [99] log likelihood: -61745.640609
EM: Round [100] log likelihood: -61745.640179
EM: Round [101] log likelihood: -61745.639765
EM: Round [102] log likelihood: -61745.639366
EM: Round [103] log likelihood: -61745.638983
EM: Round [104] log likelihood: -61745.638614
EM: Round [105] log likelihood: -61745.638258
EM: Round [106] log likelihood: -61745.637916
EM: Round [107] log likelihood: -61745.637587
EM: Round [108] log likelihood: -61745.637270
EM: Round [109] log likelihood: -61745.636965
EM: Round [110] log likelihood: -61745.636671
EM: Round [111] log likelihood: -61745.636388
EM: Round [112] log likelihood: -61745.636116
EM: Round [113] log likelihood: -61745.635854
EM: Round [114] log likelihood: -61745.635601
EM: Round [115] log likelihood: -61745.635358
EM: Round [116] log likelihood: -61745.635125
EM: Round [117] log likelihood: -61745.634899
EM: Round [118] log likelihood: -61745.634683
EM: Round [119] log likelihood: -61745.634474
EM: Round [120] log likelihood: -61745.634273
EM: Round [121] log likelihood: -61745.634080
EM: Round [122] log likelihood: -61745.633893
EM: Round [123] log likelihood: -61745.633714
EM: Round [124] log likelihood: -61745.633541
EM: Round [125] log likelihood: -61745.633375
EM: Round [126] log likelihood: -61745.633215
EM: Round [127] log likelihood: -61745.633061
EM: Round [128] log likelihood: -61745.632913
EM: Round [129] log likelihood: -61745.632770
EM: Round [130] log likelihood: -61745.632632
EM: Round [131] log likelihood: -61745.632500
EM: Round [132] log likelihood: -61745.632372
EM: Round [133] log likelihood: -61745.632249
EM: Round [134] log likelihood: -61745.632131
EM: Round [135] log likelihood: -61745.632017
EM: Round [136] log likelihood: -61745.631908
EM: Round [137] log likelihood: -61745.631802
EM: Round [138] log likelihood: -61745.631701
EM: Round [139] log likelihood: -61745.631603
EM: Stopping iterations at round 139 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.DFis1kKwbz/./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.DFis1kKwbz/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.DFis1kKwbz/./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.DFis1kKwbz/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 102160001 > /tmp/nxf.DFis1kKwbz/./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.DFis1kKwbz/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir > /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir --annotate /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.DFis1kKwbz/./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.DFis1kKwbz/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir
-done, see /tmp/nxf.DFis1kKwbz/./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.DFis1kKwbz/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.DFis1kKwbz/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 756, filtered: 5626)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.DFis1kKwbz/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.DFis1kKwbz/./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.DFis1kKwbz/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000239268.3]
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WARNING, no entry stored in dbm for [ENSG00000241291.3]
WARNING, no entry stored in dbm for [ENSG00000278771.1]
WARNING, no entry stored in dbm for [ENSG00000240772.3]
WARNING, no entry stored in dbm for [ENSG00000239437.3]
WARNING, no entry stored in dbm for [ENSG00000240772.3]
WARNING, no entry stored in dbm for [ENSG00000278771.1]
WARNING, no entry stored in dbm for [ENSG00000241229.3]
WARNING, no entry stored in dbm for [ENSG00000239437.3]
WARNING, no entry stored in dbm for [ENSG00000241229.3]
WARNING, no entry stored in dbm for [ENSG00000278771.1]
WARNING, no entry stored in dbm for [ENSG00000249201.2]
WARNING, no entry stored in dbm for [ENSG00000214176.9]
WARNING, no entry stored in dbm for [ENSG00000258888.1]
WARNING, no entry stored in dbm for [ENSG00000223575.2]
WARNING, no entry stored in dbm for [ENSG00000248215.6]
WARNING, no entry stored in dbm for [ENSG00000204055.5]
WARNING, no entry stored in dbm for [ENSG00000281128.2]
WARNING, no entry stored in dbm for [ENSG00000231165.3]
WARNING, no entry stored in dbm for [ENSG00000237984.3]
WARNING, no entry stored in dbm for [ENSG00000234690.7]
WARNING, no entry stored in dbm for [ENSG00000258584.2]
WARNING, no entry stored in dbm for [ENSG00000229105.1]
WARNING, no entry stored in dbm for [ENSG00000226985.7]
WARNING, no entry stored in dbm for [ENSG00000272767.1]
WARNING, no entry stored in dbm for [ENSG00000285993.1]
WARNING, no entry stored in dbm for [ENSG00000287998.1]
WARNING, no entry stored in dbm for [ENSG00000233184.7]
WARNING, no entry stored in dbm for [ENSG00000232117.2]
WARNING, no entry stored in dbm for [ENSG00000273125.2]
WARNING, no entry stored in dbm for [ENSG00000282012.1]
WARNING, no entry stored in dbm for [ENSG00000265369.3]
WARNING, no entry stored in dbm for [ENSG00000225638.1]
WARNING, no entry stored in dbm for [ENSG00000230673.3]
WARNING, no entry stored in dbm for [ENSG00000230364.1]
WARNING, no entry stored in dbm for [ENSG00000230834.1]
WARNING, no entry stored in dbm for [ENSG00000251485.1]
WARNING, no entry stored in dbm for [ENSG00000214807.2]
WARNING, no entry stored in dbm for [ENSG00000226703.1]
WARNING, no entry stored in dbm for [ENSG00000269904.2]
WARNING, no entry stored in dbm for [ENSG00000235703.6]
WARNING, no entry stored in dbm for [ENSG00000235703.6]
WARNING, no entry stored in dbm for [ENSG00000235703.6]
WARNING, no entry stored in dbm for [ENSG00000235703.6]
WARNING, no entry stored in dbm for [ENSG00000223881.1]
WARNING, no entry stored in dbm for [ENSG00000227632.2]
WARNING, no entry stored in dbm for [ENSG00000224078.15]
WARNING, no entry stored in dbm for [ENSG00000250731.1]
WARNING, no entry stored in dbm for [ENSG00000229091.3]
WARNING, no entry stored in dbm for [ENSG00000235142.10]
WARNING, no entry stored in dbm for [ENSG00000270960.1]
WARNING, no entry stored in dbm for [ENSG00000203392.3]
WARNING, no entry stored in dbm for [ENSG00000232527.8]
WARNING, no entry stored in dbm for [ENSG00000272779.1]
WARNING, no entry stored in dbm for [ENSG00000255008.3]
WARNING, no entry stored in dbm for [ENSG00000259448.3]
WARNING, no entry stored in dbm for [ENSG00000260433.3]
WARNING, no entry stored in dbm for [ENSG00000234928.1]
WARNING, no entry stored in dbm for [ENSG00000227755.1]
WARNING, no entry stored in dbm for [ENSG00000226917.6]
WARNING, no entry stored in dbm for [ENSG00000227036.8]
WARNING, no entry stored in dbm for [ENSG00000237854.3]
WARNING, no entry stored in dbm for [ENSG00000230710.2]
WARNING, no entry stored in dbm for [ENSG00000216817.1]
WARNING, no entry stored in dbm for [ENSG00000215838.4]
WARNING, no entry stored in dbm for [ENSG00000264177.1]
WARNING, no entry stored in dbm for [ENSG00000203709.12]
WARNING, no entry stored in dbm for [ENSG00000229976.2]
WARNING, no entry stored in dbm for [ENSG00000264823.3]
WARNING, no entry stored in dbm for [ENSG00000254034.2]
WARNING, no entry stored in dbm for [ENSG00000244652.1]
WARNING, no entry stored in dbm for [ENSG00000242337.5]
WARNING, no entry stored in dbm for [ENSG00000261275.1]
WARNING, no entry stored in dbm for [ENSG00000229979.1]
WARNING, no entry stored in dbm for [ENSG00000227259.2]
WARNING, no entry stored in dbm for [ENSG00000237380.7]
WARNING, no entry stored in dbm for [ENSG00000266602.2]
WARNING, no entry stored in dbm for [ENSG00000228223.3]
WARNING, no entry stored in dbm for [ENSG00000198237.8]
WARNING, no entry stored in dbm for [ENSG00000251451.1]
WARNING, no entry stored in dbm for [ENSG00000229180.7]
WARNING, no entry stored in dbm for [ENSG00000241838.3]
WARNING, no entry stored in dbm for [ENSG00000281103.2]
WARNING, no entry stored in dbm for [ENSG00000285763.1]
WARNING, no entry stored in dbm for [ENSG00000245954.8]
WARNING, no entry stored in dbm for [ENSG00000258535.1]
WARNING, no entry stored in dbm for [ENSG00000280441.3]
WARNING, no entry stored in dbm for [ENSG00000203801.8]
WARNING, no entry stored in dbm for [ENSG00000215063.3]
WARNING, no entry stored in dbm for [ENSG00000255052.5]
WARNING, no entry stored in dbm for [ENSG00000254016.3]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000277083.1]
WARNING, no entry stored in dbm for [ENSG00000235338.1]
WARNING, no entry stored in dbm for [ENSG00000235338.1]
WARNING, no entry stored in dbm for [ENSG00000251584.2]
WARNING, no entry stored in dbm for [ENSG00000284523.2]
WARNING, no entry stored in dbm for [ENSG00000231672.8]
WARNING, no entry stored in dbm for [ENSG00000187185.4]
WARNING, no entry stored in dbm for [ENSG00000212282.1]
WARNING, no entry stored in dbm for [ENSG00000264070.1]
WARNING, no entry stored in dbm for [ENSG00000233871.2]
WARNING, no entry stored in dbm for [ENSG00000225005.1]
WARNING, no entry stored in dbm for [ENSG00000239944.1]
WARNING, no entry stored in dbm for [ENSG00000204790.9]
WARNING, no entry stored in dbm for [ENSG00000255438.2]
WARNING, no entry stored in dbm for [ENSG00000234715.2]
WARNING, no entry stored in dbm for [ENSG00000272888.7]
WARNING, no entry stored in dbm for [ENSG00000163098.6]
WARNING, no entry stored in dbm for [ENSG00000235501.6]
WARNING, no entry stored in dbm for [ENSG00000228775.8]
WARNING, no entry stored in dbm for [ENSG00000268601.1]
WARNING, no entry stored in dbm for [ENSG00000167747.15]
WARNING, no entry stored in dbm for [ENSG00000236105.1]
WARNING, no entry stored in dbm for [ENSG00000258780.1]
WARNING, no entry stored in dbm for [ENSG00000271138.1]
WARNING, no entry stored in dbm for [ENSG00000158482.10]
WARNING, no entry stored in dbm for [ENSG00000272692.2]
WARNING, no entry stored in dbm for [ENSG00000273986.1]
WARNING, no entry stored in dbm for [ENSG00000257252.6]
WARNING, no entry stored in dbm for [ENSG00000238021.6]
WARNING, no entry stored in dbm for [ENSG00000223602.2]
WARNING, no entry stored in dbm for [ENSG00000204790.9]
WARNING, no entry stored in dbm for [ENSG00000238045.9]
WARNING, no entry stored in dbm for [ENSG00000239415.1]
WARNING, no entry stored in dbm for [ENSG00000237187.9]
WARNING, no entry stored in dbm for [ENSG00000261019.1]
WARNING, no entry stored in dbm for [ENSG00000237037.9]
WARNING, no entry stored in dbm for [ENSG00000224839.1]
WARNING, no entry stored in dbm for [ENSG00000286974.1]
WARNING, no entry stored in dbm for [ENSG00000279575.1]
WARNING, no entry stored in dbm for [ENSG00000276888.1]
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 [ENSG00000237356.7]
WARNING, no entry stored in dbm for [ENSG00000258731.1]
WARNING, no entry stored in dbm for [ENSG00000235804.2]
WARNING, no entry stored in dbm for [ENSG00000286439.1]
WARNING, no entry stored in dbm for [ENSG00000286439.1]
WARNING, no entry stored in dbm for [ENSG00000286439.1]
WARNING, no entry stored in dbm for [ENSG00000228436.3]
WARNING, no entry stored in dbm for [ENSG00000220685.3]
WARNING, no entry stored in dbm for [ENSG00000278231.1]
WARNING, no entry stored in dbm for [ENSG00000273619.1]
WARNING, no entry stored in dbm for [ENSG00000287920.1]
WARNING, no entry stored in dbm for [ENSG00000282740.1]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000258458.8]
WARNING, no entry stored in dbm for [ENSG00000272734.1]
WARNING, no entry stored in dbm for [ENSG00000281731.3]
WARNING, no entry stored in dbm for [ENSG00000226755.2]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000228223.3]
WARNING, no entry stored in dbm for [ENSG00000242142.1]
WARNING, no entry stored in dbm for [ENSG00000223804.5]
WARNING, no entry stored in dbm for [ENSG00000230937.12]
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 [ENSG00000232729.8]
WARNING, no entry stored in dbm for [ENSG00000229930.1]
WARNING, no entry stored in dbm for [ENSG00000266717.1]
WARNING, no entry stored in dbm for [ENSG00000248752.3]
WARNING, no entry stored in dbm for [ENSG00000188850.9]
WARNING, no entry stored in dbm for [ENSG00000260037.5]
WARNING, no entry stored in dbm for [ENSG00000247193.3]
WARNING, no entry stored in dbm for [ENSG00000285788.1]
WARNING, no entry stored in dbm for [ENSG00000271943.2]
WARNING, no entry stored in dbm for [ENSG00000286596.1]
WARNING, no entry stored in dbm for [ENSG00000287129.1]
WARNING, no entry stored in dbm for [ENSG00000231646.6]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
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 [ENSG00000187953.10]
WARNING, no entry stored in dbm for [ENSG00000257337.7]
WARNING, no entry stored in dbm for [ENSG00000283674.3]
WARNING, no entry stored in dbm for [ENSG00000283674.3]
WARNING, no entry stored in dbm for [ENSG00000248618.1]
WARNING, no entry stored in dbm for [ENSG00000254339.5]
WARNING, no entry stored in dbm for [ENSG00000267648.1]
WARNING, no entry stored in dbm for [ENSG00000267040.6]
WARNING, no entry stored in dbm for [ENSG00000260693.1]
WARNING, no entry stored in dbm for [ENSG00000287677.2]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000242338.6]
WARNING, no entry stored in dbm for [ENSG00000267075.1]
WARNING, no entry stored in dbm for [ENSG00000269321.1]
WARNING, no entry stored in dbm for [ENSG00000272622.2]
WARNING, no entry stored in dbm for [ENSG00000250360.1]
WARNING, no entry stored in dbm for [ENSG00000235583.2]
WARNING, no entry stored in dbm for [ENSG00000255595.5]
WARNING, no entry stored in dbm for [ENSG00000267623.3]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000205485.13]
WARNING, no entry stored in dbm for [ENSG00000254610.3]
WARNING, no entry stored in dbm for [ENSG00000248498.4]
WARNING, no entry stored in dbm for [ENSG00000231749.3]
WARNING, no entry stored in dbm for [ENSG00000286063.1]
* STAR-Fusion complete. See output: /tmp/nxf.DFis1kKwbz/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)