Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/85187f3da8810bad327fba8c7db4d1/HeadNeckN_FFPE_L06_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/52/c8d937ce2bbe717917ff0d2e2487fa/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/c8d937ce2bbe717917ff0d2e2487fa/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/85187f3da8810bad327fba8c7db4d1/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/e67cc2de769685a4f28952ff924403/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
==> STAGING COMPLETE (6 inputs)
-ctat genome lib [/tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.9JQm0xfd57/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary
-sample contains 68408748 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir -J /tmp/nxf.9JQm0xfd57/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction -O /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.9JQm0xfd57/HeadNeckN_FFPE_L06_RNA_01_B23LG7FLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes
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[1130000], rate=49023.86/min -building interval tree based on /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes
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[1120000], rate=47058.82/min -building interval tree based on /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes
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[1130000], rate=45687.33/min -building interval tree based on /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.12 min).
-mapping reads to genes
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[1130000], rate=40501.79/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir --filt_file /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.9JQm0xfd57/./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...
4285714.29 reads per min processed...
4000000.00 reads per min processed...
3818181.82 reads per min processed...
3428571.43 reads per min processed...
3375000.00 reads per min processed...
3157894.74 reads per min processed...
3142857.14 reads per min processed...
2880000.00 reads per min processed...
2689655.17 reads per min processed...
2709677.42 reads per min processed...
2647058.82 reads per min processed...
2666666.67 reads per min processed...
2684210.53 reads per min processed...
2634146.34 reads per min processed...
2651162.79 reads per min processed...
2666666.67 reads per min processed...
2680851.06 reads per min processed...
2693877.55 reads per min processed...
2705882.35 reads per min processed...
2769230.77 reads per min processed...
2830188.68 reads per min processed...
2888888.89 reads per min processed...
2892857.14 reads per min processed...
2847457.63 reads per min processed...
2852459.02 reads per min processed...
2857142.86 reads per min processed...
2861538.46 reads per min processed...
2865671.64 reads per min processed...
2869565.22 reads per min processed...
2833333.33 reads per min processed...
2837837.84 reads per min processed...
2842105.26 reads per min processed...
2846153.85 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.9JQm0xfd57/HeadNeckN_FFPE_L06_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.9JQm0xfd57/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -104943.412917
EM: Round [1] log likelihood: -104749.236454
EM: Round [2] log likelihood: -104673.259221
EM: Round [3] log likelihood: -104636.001163
EM: Round [4] log likelihood: -104615.794743
EM: Round [5] log likelihood: -104604.214798
EM: Round [6] log likelihood: -104597.296525
EM: Round [7] log likelihood: -104592.994605
EM: Round [8] log likelihood: -104590.208956
EM: Round [9] log likelihood: -104588.332501
EM: Round [10] log likelihood: -104587.021552
EM: Round [11] log likelihood: -104586.075623
EM: Round [12] log likelihood: -104585.373783
EM: Round [13] log likelihood: -104584.840512
EM: Round [14] log likelihood: -104584.427038
EM: Round [15] log likelihood: -104584.100858
EM: Round [16] log likelihood: -104583.839698
EM: Round [17] log likelihood: -104583.627900
EM: Round [18] log likelihood: -104583.454215
EM: Round [19] log likelihood: -104583.310397
EM: Round [20] log likelihood: -104583.190294
EM: Round [21] log likelihood: -104583.089243
EM: Round [22] log likelihood: -104583.003659
EM: Round [23] log likelihood: -104582.930747
EM: Round [24] log likelihood: -104582.868306
EM: Round [25] log likelihood: -104582.814579
EM: Round [26] log likelihood: -104582.768154
EM: Round [27] log likelihood: -104582.727883
EM: Round [28] log likelihood: -104582.692827
EM: Round [29] log likelihood: -104582.662211
EM: Round [30] log likelihood: -104582.635393
EM: Round [31] log likelihood: -104582.611835
EM: Round [32] log likelihood: -104582.591087
EM: Round [33] log likelihood: -104582.572768
EM: Round [34] log likelihood: -104582.556555
EM: Round [35] log likelihood: -104582.542175
EM: Round [36] log likelihood: -104582.529393
EM: Round [37] log likelihood: -104582.518007
EM: Round [38] log likelihood: -104582.507845
EM: Round [39] log likelihood: -104582.498757
EM: Round [40] log likelihood: -104582.490614
EM: Round [41] log likelihood: -104582.483305
EM: Round [42] log likelihood: -104582.476732
EM: Round [43] log likelihood: -104582.470811
EM: Round [44] log likelihood: -104582.465467
EM: Round [45] log likelihood: -104582.460635
EM: Round [46] log likelihood: -104582.456258
EM: Round [47] log likelihood: -104582.452287
EM: Round [48] log likelihood: -104582.448678
EM: Round [49] log likelihood: -104582.445392
EM: Round [50] log likelihood: -104582.442395
EM: Round [51] log likelihood: -104582.439657
EM: Round [52] log likelihood: -104582.437150
EM: Round [53] log likelihood: -104582.434852
EM: Round [54] log likelihood: -104582.432741
EM: Round [55] log likelihood: -104582.430798
EM: Round [56] log likelihood: -104582.429007
EM: Round [57] log likelihood: -104582.427353
EM: Round [58] log likelihood: -104582.425822
EM: Round [59] log likelihood: -104582.424404
EM: Round [60] log likelihood: -104582.423087
EM: Round [61] log likelihood: -104582.421862
EM: Round [62] log likelihood: -104582.420720
EM: Round [63] log likelihood: -104582.419654
EM: Round [64] log likelihood: -104582.418657
EM: Round [65] log likelihood: -104582.417722
EM: Round [66] log likelihood: -104582.416845
EM: Round [67] log likelihood: -104582.416021
EM: Round [68] log likelihood: -104582.415244
EM: Round [69] log likelihood: -104582.414511
EM: Round [70] log likelihood: -104582.413818
EM: Round [71] log likelihood: -104582.413162
EM: Round [72] log likelihood: -104582.412540
EM: Round [73] log likelihood: -104582.411949
EM: Round [74] log likelihood: -104582.411386
EM: Round [75] log likelihood: -104582.410851
EM: Round [76] log likelihood: -104582.410339
EM: Round [77] log likelihood: -104582.409850
EM: Round [78] log likelihood: -104582.409383
EM: Round [79] log likelihood: -104582.408934
EM: Round [80] log likelihood: -104582.408504
EM: Round [81] log likelihood: -104582.408091
EM: Round [82] log likelihood: -104582.407693
EM: Round [83] log likelihood: -104582.407310
EM: Round [84] log likelihood: -104582.406940
EM: Round [85] log likelihood: -104582.406583
EM: Round [86] log likelihood: -104582.406239
EM: Round [87] log likelihood: -104582.405905
EM: Round [88] log likelihood: -104582.405582
EM: Round [89] log likelihood: -104582.405269
EM: Round [90] log likelihood: -104582.404965
EM: Round [91] log likelihood: -104582.404670
EM: Round [92] log likelihood: -104582.404383
EM: Round [93] log likelihood: -104582.404104
EM: Round [94] log likelihood: -104582.403833
EM: Round [95] log likelihood: -104582.403568
EM: Round [96] log likelihood: -104582.403311
EM: Round [97] log likelihood: -104582.403060
EM: Round [98] log likelihood: -104582.402815
EM: Round [99] log likelihood: -104582.402575
EM: Round [100] log likelihood: -104582.402341
EM: Round [101] log likelihood: -104582.402113
EM: Round [102] log likelihood: -104582.401890
EM: Round [103] log likelihood: -104582.401671
EM: Round [104] log likelihood: -104582.401457
EM: Round [105] log likelihood: -104582.401248
EM: Round [106] log likelihood: -104582.401043
EM: Round [107] log likelihood: -104582.400842
EM: Round [108] log likelihood: -104582.400645
EM: Round [109] log likelihood: -104582.400452
EM: Round [110] log likelihood: -104582.400263
EM: Round [111] log likelihood: -104582.400077
EM: Round [112] log likelihood: -104582.399895
EM: Round [113] log likelihood: -104582.399716
EM: Round [114] log likelihood: -104582.399541
EM: Round [115] log likelihood: -104582.399369
EM: Round [116] log likelihood: -104582.399200
EM: Round [117] log likelihood: -104582.399033
EM: Round [118] log likelihood: -104582.398870
EM: Round [119] log likelihood: -104582.398710
EM: Round [120] log likelihood: -104582.398552
EM: Round [121] log likelihood: -104582.398397
EM: Round [122] log likelihood: -104582.398245
EM: Round [123] log likelihood: -104582.398095
EM: Round [124] log likelihood: -104582.397948
EM: Round [125] log likelihood: -104582.397804
EM: Round [126] log likelihood: -104582.397661
EM: Round [127] log likelihood: -104582.397521
EM: Round [128] log likelihood: -104582.397384
EM: Round [129] log likelihood: -104582.397248
EM: Round [130] log likelihood: -104582.397115
EM: Round [131] log likelihood: -104582.396984
EM: Round [132] log likelihood: -104582.396855
EM: Round [133] log likelihood: -104582.396729
EM: Round [134] log likelihood: -104582.396604
EM: Round [135] log likelihood: -104582.396481
EM: Round [136] log likelihood: -104582.396361
EM: Round [137] log likelihood: -104582.396242
EM: Round [138] log likelihood: -104582.396125
EM: Round [139] log likelihood: -104582.396010
EM: Round [140] log likelihood: -104582.395897
EM: Round [141] log likelihood: -104582.395786
EM: Round [142] log likelihood: -104582.395676
EM: Round [143] log likelihood: -104582.395568
EM: Round [144] log likelihood: -104582.395462
EM: Round [145] log likelihood: -104582.395358
EM: Round [146] log likelihood: -104582.395255
EM: Round [147] log likelihood: -104582.395154
EM: Round [148] log likelihood: -104582.395054
EM: Stopping iterations at round 148 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -104722.588913
EM: Round [1] log likelihood: -104564.087029
EM: Round [2] log likelihood: -104502.984500
EM: Round [3] log likelihood: -104473.777831
EM: Round [4] log likelihood: -104458.290780
EM: Round [5] log likelihood: -104449.606301
EM: Round [6] log likelihood: -104444.532336
EM: Round [7] log likelihood: -104441.445466
EM: Round [8] log likelihood: -104439.485964
EM: Round [9] log likelihood: -104438.188028
EM: Round [10] log likelihood: -104437.293185
EM: Round [11] log likelihood: -104436.653730
EM: Round [12] log likelihood: -104436.182362
EM: Round [13] log likelihood: -104435.825599
EM: Round [14] log likelihood: -104435.549493
EM: Round [15] log likelihood: -104435.331760
EM: Round [16] log likelihood: -104435.157305
EM: Round [17] log likelihood: -104435.015622
EM: Round [18] log likelihood: -104434.899210
EM: Round [19] log likelihood: -104434.802596
EM: Round [20] log likelihood: -104434.721712
EM: Round [21] log likelihood: -104434.653477
EM: Round [22] log likelihood: -104434.595523
EM: Round [23] log likelihood: -104434.546006
EM: Round [24] log likelihood: -104434.503471
EM: Round [25] log likelihood: -104434.466756
EM: Round [26] log likelihood: -104434.434928
EM: Round [27] log likelihood: -104434.407226
EM: Round [28] log likelihood: -104434.383025
EM: Round [29] log likelihood: -104434.361813
EM: Round [30] log likelihood: -104434.343162
EM: Round [31] log likelihood: -104434.326713
EM: Round [32] log likelihood: -104434.312168
EM: Round [33] log likelihood: -104434.299270
EM: Round [34] log likelihood: -104434.287807
EM: Round [35] log likelihood: -104434.277592
EM: Round [36] log likelihood: -104434.268470
EM: Round [37] log likelihood: -104434.260306
EM: Round [38] log likelihood: -104434.252983
EM: Round [39] log likelihood: -104434.246401
EM: Round [40] log likelihood: -104434.240473
EM: Round [41] log likelihood: -104434.235124
EM: Round [42] log likelihood: -104434.230286
EM: Round [43] log likelihood: -104434.225904
EM: Round [44] log likelihood: -104434.221926
EM: Round [45] log likelihood: -104434.218309
EM: Round [46] log likelihood: -104434.215014
EM: Round [47] log likelihood: -104434.212005
EM: Round [48] log likelihood: -104434.209254
EM: Round [49] log likelihood: -104434.206734
EM: Round [50] log likelihood: -104434.204421
EM: Round [51] log likelihood: -104434.202294
EM: Round [52] log likelihood: -104434.200335
EM: Round [53] log likelihood: -104434.198527
EM: Round [54] log likelihood: -104434.196856
EM: Round [55] log likelihood: -104434.195308
EM: Round [56] log likelihood: -104434.193871
EM: Round [57] log likelihood: -104434.192536
EM: Round [58] log likelihood: -104434.191292
EM: Round [59] log likelihood: -104434.190132
EM: Round [60] log likelihood: -104434.189048
EM: Round [61] log likelihood: -104434.188033
EM: Round [62] log likelihood: -104434.187081
EM: Round [63] log likelihood: -104434.186187
EM: Round [64] log likelihood: -104434.185345
EM: Round [65] log likelihood: -104434.184552
EM: Round [66] log likelihood: -104434.183803
EM: Round [67] log likelihood: -104434.183094
EM: Round [68] log likelihood: -104434.182423
EM: Round [69] log likelihood: -104434.181786
EM: Round [70] log likelihood: -104434.181181
EM: Round [71] log likelihood: -104434.180604
EM: Round [72] log likelihood: -104434.180055
EM: Round [73] log likelihood: -104434.179531
EM: Round [74] log likelihood: -104434.179030
EM: Round [75] log likelihood: -104434.178550
EM: Round [76] log likelihood: -104434.178090
EM: Round [77] log likelihood: -104434.177648
EM: Round [78] log likelihood: -104434.177224
EM: Round [79] log likelihood: -104434.176816
EM: Round [80] log likelihood: -104434.176423
EM: Round [81] log likelihood: -104434.176043
EM: Round [82] log likelihood: -104434.175677
EM: Round [83] log likelihood: -104434.175324
EM: Round [84] log likelihood: -104434.174981
EM: Round [85] log likelihood: -104434.174650
EM: Round [86] log likelihood: -104434.174329
EM: Round [87] log likelihood: -104434.174017
EM: Round [88] log likelihood: -104434.173715
EM: Round [89] log likelihood: -104434.173421
EM: Round [90] log likelihood: -104434.173136
EM: Round [91] log likelihood: -104434.172858
EM: Round [92] log likelihood: -104434.172587
EM: Round [93] log likelihood: -104434.172324
EM: Round [94] log likelihood: -104434.172066
EM: Round [95] log likelihood: -104434.171816
EM: Round [96] log likelihood: -104434.171571
EM: Round [97] log likelihood: -104434.171332
EM: Round [98] log likelihood: -104434.171099
EM: Round [99] log likelihood: -104434.170870
EM: Round [100] log likelihood: -104434.170647
EM: Round [101] log likelihood: -104434.170429
EM: Round [102] log likelihood: -104434.170215
EM: Round [103] log likelihood: -104434.170006
EM: Round [104] log likelihood: -104434.169801
EM: Round [105] log likelihood: -104434.169601
EM: Round [106] log likelihood: -104434.169404
EM: Round [107] log likelihood: -104434.169211
EM: Round [108] log likelihood: -104434.169022
EM: Round [109] log likelihood: -104434.168836
EM: Round [110] log likelihood: -104434.168654
EM: Round [111] log likelihood: -104434.168475
EM: Round [112] log likelihood: -104434.168300
EM: Round [113] log likelihood: -104434.168128
EM: Round [114] log likelihood: -104434.167959
EM: Round [115] log likelihood: -104434.167793
EM: Round [116] log likelihood: -104434.167630
EM: Round [117] log likelihood: -104434.167469
EM: Round [118] log likelihood: -104434.167312
EM: Round [119] log likelihood: -104434.167157
EM: Round [120] log likelihood: -104434.167005
EM: Round [121] log likelihood: -104434.166856
EM: Round [122] log likelihood: -104434.166709
EM: Round [123] log likelihood: -104434.166564
EM: Round [124] log likelihood: -104434.166422
EM: Round [125] log likelihood: -104434.166282
EM: Round [126] log likelihood: -104434.166145
EM: Round [127] log likelihood: -104434.166010
EM: Round [128] log likelihood: -104434.165877
EM: Round [129] log likelihood: -104434.165746
EM: Round [130] log likelihood: -104434.165617
EM: Round [131] log likelihood: -104434.165491
EM: Round [132] log likelihood: -104434.165366
EM: Round [133] log likelihood: -104434.165244
EM: Round [134] log likelihood: -104434.165123
EM: Round [135] log likelihood: -104434.165005
EM: Round [136] log likelihood: -104434.164888
EM: Round [137] log likelihood: -104434.164773
EM: Round [138] log likelihood: -104434.164660
EM: Round [139] log likelihood: -104434.164549
EM: Round [140] log likelihood: -104434.164440
EM: Round [141] log likelihood: -104434.164332
EM: Round [142] log likelihood: -104434.164226
EM: Round [143] log likelihood: -104434.164122
EM: Round [144] log likelihood: -104434.164020
EM: Round [145] log likelihood: -104434.163919
EM: Round [146] log likelihood: -104434.163819
EM: Stopping iterations at round 146 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.9JQm0xfd57/./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.9JQm0xfd57/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.9JQm0xfd57/./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.9JQm0xfd57/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 68408748 > /tmp/nxf.9JQm0xfd57/./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.9JQm0xfd57/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir > /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir --annotate /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.9JQm0xfd57/./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.9JQm0xfd57/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir
-done, see /tmp/nxf.9JQm0xfd57/./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.9JQm0xfd57/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.9JQm0xfd57/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 715, filtered: 6169)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.9JQm0xfd57/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.9JQm0xfd57/./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.9JQm0xfd57/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000229739.4]
WARNING, no entry stored in dbm for [ENSG00000225594.1]
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 [ENSG00000128438.10]
WARNING, no entry stored in dbm for [ENSG00000238276.6]
WARNING, no entry stored in dbm for [ENSG00000230559.1]
WARNING, no entry stored in dbm for [ENSG00000239899.3]
WARNING, no entry stored in dbm for [ENSG00000241175.3]
WARNING, no entry stored in dbm for [ENSG00000227632.2]
WARNING, no entry stored in dbm for [ENSG00000287721.1]
WARNING, no entry stored in dbm for [ENSG00000272142.4]
WARNING, no entry stored in dbm for [ENSG00000181126.13]
WARNING, no entry stored in dbm for [ENSG00000260298.2]
WARNING, no entry stored in dbm for [ENSG00000188460.4]
WARNING, no entry stored in dbm for [ENSG00000225205.5]
WARNING, no entry stored in dbm for [ENSG00000217289.3]
WARNING, no entry stored in dbm for [ENSG00000257343.1]
WARNING, no entry stored in dbm for [ENSG00000264920.2]
WARNING, no entry stored in dbm for [ENSG00000287664.1]
WARNING, no entry stored in dbm for [ENSG00000234420.7]
WARNING, no entry stored in dbm for [ENSG00000237992.3]
WARNING, no entry stored in dbm for [ENSG00000220949.2]
WARNING, no entry stored in dbm for [ENSG00000282458.1]
WARNING, no entry stored in dbm for [ENSG00000234769.7]
WARNING, no entry stored in dbm for [ENSG00000225292.2]
WARNING, no entry stored in dbm for [ENSG00000286694.1]
WARNING, no entry stored in dbm for [ENSG00000277739.1]
WARNING, no entry stored in dbm for [ENSG00000283568.1]
WARNING, no entry stored in dbm for [ENSG00000199568.1]
WARNING, no entry stored in dbm for [ENSG00000238040.1]
WARNING, no entry stored in dbm for [ENSG00000227195.11]
WARNING, no entry stored in dbm for [ENSG00000235904.3]
WARNING, no entry stored in dbm for [ENSG00000170919.16]
WARNING, no entry stored in dbm for [ENSG00000260072.1]
WARNING, no entry stored in dbm for [ENSG00000266733.7]
WARNING, no entry stored in dbm for [ENSG00000228862.4]
WARNING, no entry stored in dbm for [ENSG00000253642.6]
WARNING, no entry stored in dbm for [ENSG00000270890.1]
WARNING, no entry stored in dbm for [ENSG00000228695.10]
WARNING, no entry stored in dbm for [ENSG00000288535.1]
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 [ENSG00000242207.1]
WARNING, no entry stored in dbm for [ENSG00000283795.1]
WARNING, no entry stored in dbm for [ENSG00000245556.3]
WARNING, no entry stored in dbm for [ENSG00000279159.1]
WARNING, no entry stored in dbm for [ENSG00000230629.2]
WARNING, no entry stored in dbm for [ENSG00000175886.10]
WARNING, no entry stored in dbm for [ENSG00000231562.1]
WARNING, no entry stored in dbm for [ENSG00000251474.6]
WARNING, no entry stored in dbm for [ENSG00000242993.1]
WARNING, no entry stored in dbm for [ENSG00000213295.3]
WARNING, no entry stored in dbm for [ENSG00000241129.3]
WARNING, no entry stored in dbm for [ENSG00000206975.1]
WARNING, no entry stored in dbm for [ENSG00000121089.4]
WARNING, no entry stored in dbm for [ENSG00000222177.1]
WARNING, no entry stored in dbm for [ENSG00000201342.1]
WARNING, no entry stored in dbm for [ENSG00000200296.1]
WARNING, no entry stored in dbm for [ENSG00000276047.1]
WARNING, no entry stored in dbm for [ENSG00000241529.3]
WARNING, no entry stored in dbm for [ENSG00000244056.3]
WARNING, no entry stored in dbm for [ENSG00000239437.3]
WARNING, no entry stored in dbm for [ENSG00000201758.1]
WARNING, no entry stored in dbm for [ENSG00000222240.1]
WARNING, no entry stored in dbm for [ENSG00000201315.1]
WARNING, no entry stored in dbm for [ENSG00000222240.1]
WARNING, no entry stored in dbm for [ENSG00000131401.11]
WARNING, no entry stored in dbm for [ENSG00000280219.1]
WARNING, no entry stored in dbm for [ENSG00000242894.3]
WARNING, no entry stored in dbm for [ENSG00000281128.2]
WARNING, no entry stored in dbm for [ENSG00000249859.12]
WARNING, no entry stored in dbm for [ENSG00000204434.6]
WARNING, no entry stored in dbm for [ENSG00000269350.1]
WARNING, no entry stored in dbm for [ENSG00000273125.2]
WARNING, no entry stored in dbm for [ENSG00000281649.2]
WARNING, no entry stored in dbm for [ENSG00000287901.1]
WARNING, no entry stored in dbm for [ENSG00000214465.3]
WARNING, no entry stored in dbm for [ENSG00000258853.1]
WARNING, no entry stored in dbm for [ENSG00000265802.2]
WARNING, no entry stored in dbm for [ENSG00000281692.2]
WARNING, no entry stored in dbm for [ENSG00000203709.12]
WARNING, no entry stored in dbm for [ENSG00000229167.2]
WARNING, no entry stored in dbm for [ENSG00000237296.9]
WARNING, no entry stored in dbm for [ENSG00000235644.1]
WARNING, no entry stored in dbm for [ENSG00000260793.2]
WARNING, no entry stored in dbm for [ENSG00000251562.8]
WARNING, no entry stored in dbm for [ENSG00000232527.8]
WARNING, no entry stored in dbm for [ENSG00000212719.13]
WARNING, no entry stored in dbm for [ENSG00000251129.2]
WARNING, no entry stored in dbm for [ENSG00000238837.3]
WARNING, no entry stored in dbm for [ENSG00000236720.2]
WARNING, no entry stored in dbm for [ENSG00000236052.2]
WARNING, no entry stored in dbm for [ENSG00000235437.8]
WARNING, no entry stored in dbm for [ENSG00000266256.3]
WARNING, no entry stored in dbm for [ENSG00000236790.6]
WARNING, no entry stored in dbm for [ENSG00000231028.9]
WARNING, no entry stored in dbm for [ENSG00000203809.7]
WARNING, no entry stored in dbm for [ENSG00000249641.2]
WARNING, no entry stored in dbm for [ENSG00000259388.1]
WARNING, no entry stored in dbm for [ENSG00000253218.1]
WARNING, no entry stored in dbm for [ENSG00000254452.1]
WARNING, no entry stored in dbm for [ENSG00000234929.2]
WARNING, no entry stored in dbm for [ENSG00000251347.2]
WARNING, no entry stored in dbm for [ENSG00000231156.1]
WARNING, no entry stored in dbm for [ENSG00000286675.1]
WARNING, no entry stored in dbm for [ENSG00000253158.1]
WARNING, no entry stored in dbm for [ENSG00000271375.1]
WARNING, no entry stored in dbm for [ENSG00000271620.1]
WARNING, no entry stored in dbm for [ENSG00000261834.2]
WARNING, no entry stored in dbm for [ENSG00000270864.1]
WARNING, no entry stored in dbm for [ENSG00000223931.2]
WARNING, no entry stored in dbm for [ENSG00000260464.1]
WARNING, no entry stored in dbm for [ENSG00000204622.11]
WARNING, no entry stored in dbm for [ENSG00000235290.1]
WARNING, no entry stored in dbm for [ENSG00000206341.7]
WARNING, no entry stored in dbm for [ENSG00000176318.8]
WARNING, no entry stored in dbm for [ENSG00000270255.1]
WARNING, no entry stored in dbm for [ENSG00000237781.3]
WARNING, no entry stored in dbm for [ENSG00000279036.1]
WARNING, no entry stored in dbm for [ENSG00000285108.1]
WARNING, no entry stored in dbm for [ENSG00000253438.4]
WARNING, no entry stored in dbm for [ENSG00000281103.2]
WARNING, no entry stored in dbm for [ENSG00000224165.6]
WARNING, no entry stored in dbm for [ENSG00000261195.1]
WARNING, no entry stored in dbm for [ENSG00000285108.1]
WARNING, no entry stored in dbm for [ENSG00000204623.9]
WARNING, no entry stored in dbm for [ENSG00000280890.1]
WARNING, no entry stored in dbm for [ENSG00000263883.1]
WARNING, no entry stored in dbm for [ENSG00000281649.2]
WARNING, no entry stored in dbm for [ENSG00000227288.3]
WARNING, no entry stored in dbm for [ENSG00000186704.9]
WARNING, no entry stored in dbm for [ENSG00000235192.1]
WARNING, no entry stored in dbm for [ENSG00000245532.9]
WARNING, no entry stored in dbm for [ENSG00000245384.2]
WARNING, no entry stored in dbm for [ENSG00000270352.1]
WARNING, no entry stored in dbm for [ENSG00000235673.1]
WARNING, no entry stored in dbm for [ENSG00000249047.2]
WARNING, no entry stored in dbm for [ENSG00000287774.1]
WARNING, no entry stored in dbm for [ENSG00000207691.1]
WARNING, no entry stored in dbm for [ENSG00000224287.2]
WARNING, no entry stored in dbm for [ENSG00000233652.1]
WARNING, no entry stored in dbm for [ENSG00000259755.1]
WARNING, no entry stored in dbm for [ENSG00000226937.9]
WARNING, no entry stored in dbm for [ENSG00000230681.1]
WARNING, no entry stored in dbm for [ENSG00000224660.2]
WARNING, no entry stored in dbm for [ENSG00000250033.5]
WARNING, no entry stored in dbm for [ENSG00000250437.1]
WARNING, no entry stored in dbm for [ENSG00000213671.3]
WARNING, no entry stored in dbm for [ENSG00000182352.8]
WARNING, no entry stored in dbm for [ENSG00000182352.8]
WARNING, no entry stored in dbm for [ENSG00000262413.1]
WARNING, no entry stored in dbm for [ENSG00000204177.10]
WARNING, no entry stored in dbm for [ENSG00000243289.1]
WARNING, no entry stored in dbm for [ENSG00000240205.3]
WARNING, no entry stored in dbm for [ENSG00000257252.6]
WARNING, no entry stored in dbm for [ENSG00000261187.1]
WARNING, no entry stored in dbm for [ENSG00000231991.4]
WARNING, no entry stored in dbm for [ENSG00000230006.7]
WARNING, no entry stored in dbm for [ENSG00000232576.2]
WARNING, no entry stored in dbm for [ENSG00000227619.3]
WARNING, no entry stored in dbm for [ENSG00000285280.2]
WARNING, no entry stored in dbm for [ENSG00000235582.2]
WARNING, no entry stored in dbm for [ENSG00000215016.2]
WARNING, no entry stored in dbm for [ENSG00000231703.2]
WARNING, no entry stored in dbm for [ENSG00000274090.1]
WARNING, no entry stored in dbm for [ENSG00000268628.2]
WARNING, no entry stored in dbm for [ENSG00000244756.1]
WARNING, no entry stored in dbm for [ENSG00000243423.1]
WARNING, no entry stored in dbm for [ENSG00000280395.1]
WARNING, no entry stored in dbm for [ENSG00000215022.7]
WARNING, no entry stored in dbm for [ENSG00000233955.1]
WARNING, no entry stored in dbm for [ENSG00000230869.1]
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 [ENSG00000250421.5]
WARNING, no entry stored in dbm for [ENSG00000218052.5]
WARNING, no entry stored in dbm for [ENSG00000223804.5]
WARNING, no entry stored in dbm for [ENSG00000263590.2]
WARNING, no entry stored in dbm for [ENSG00000223612.3]
WARNING, no entry stored in dbm for [ENSG00000223931.2]
WARNING, no entry stored in dbm for [ENSG00000224585.1]
WARNING, no entry stored in dbm for [ENSG00000229930.1]
WARNING, no entry stored in dbm for [ENSG00000243596.1]
WARNING, no entry stored in dbm for [ENSG00000273156.2]
WARNING, no entry stored in dbm for [ENSG00000260235.1]
WARNING, no entry stored in dbm for [ENSG00000253284.2]
WARNING, no entry stored in dbm for [ENSG00000267749.1]
WARNING, no entry stored in dbm for [ENSG00000250643.1]
WARNING, no entry stored in dbm for [ENSG00000287893.1]
WARNING, no entry stored in dbm for [ENSG00000258324.2]
WARNING, no entry stored in dbm for [ENSG00000232053.7]
WARNING, no entry stored in dbm for [ENSG00000288077.1]
WARNING, no entry stored in dbm for [ENSG00000257817.2]
WARNING, no entry stored in dbm for [ENSG00000260693.1]
WARNING, no entry stored in dbm for [ENSG00000250764.1]
WARNING, no entry stored in dbm for [ENSG00000254668.1]
WARNING, no entry stored in dbm for [ENSG00000260276.2]
WARNING, no entry stored in dbm for [ENSG00000285106.2]
WARNING, no entry stored in dbm for [ENSG00000270776.1]
WARNING, no entry stored in dbm for [ENSG00000280394.1]
WARNING, no entry stored in dbm for [ENSG00000284649.1]
WARNING, no entry stored in dbm for [ENSG00000261273.1]
WARNING, no entry stored in dbm for [ENSG00000267207.1]
WARNING, no entry stored in dbm for [ENSG00000268650.3]
WARNING, no entry stored in dbm for [ENSG00000274712.2]
WARNING, no entry stored in dbm for [ENSG00000286045.1]
WARNING, no entry stored in dbm for [ENSG00000248278.1]
WARNING, no entry stored in dbm for [ENSG00000254610.3]
WARNING, no entry stored in dbm for [ENSG00000241278.1]
WARNING, no entry stored in dbm for [ENSG00000253507.5]
WARNING, no entry stored in dbm for [ENSG00000271394.1]
WARNING, no entry stored in dbm for [ENSG00000222240.1]
* STAR-Fusion complete. See output: /tmp/nxf.9JQm0xfd57/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)