-ctat genome lib [/tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.tUjwmqx8LY/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary
-sample contains 121082139 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir -J /tmp/nxf.tUjwmqx8LY/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_2.Chimeric.out.junction -O /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.tUjwmqx8LY/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_2.Chimeric.out.junction
-building interval tree based on /tmp/nxf.tUjwmqx8LY/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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[2270000], rate=47924.00/min -building interval tree based on /tmp/nxf.tUjwmqx8LY/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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[2250000], rate=44628.10/min -building interval tree based on /tmp/nxf.tUjwmqx8LY/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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[2260000], rate=35816.16/min -building interval tree based on /tmp/nxf.tUjwmqx8LY/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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[2260000], rate=29255.66/min
[2270000], rate=29240.02/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir --filt_file /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt, organizing read mapping info.
6000000.00 reads per min processed...
6000000.00 reads per min processed...
9000000.00 reads per min processed...
8000000.00 reads per min processed...
7500000.00 reads per min processed...
7200000.00 reads per min processed...
7000000.00 reads per min processed...
6857142.86 reads per min processed...
6000000.00 reads per min processed...
5454545.45 reads per min processed...
5076923.08 reads per min processed...
4500000.00 reads per min processed...
4105263.16 reads per min processed...
4200000.00 reads per min processed...
4090909.09 reads per min processed...
4000000.00 reads per min processed...
3777777.78 reads per min processed...
3724137.93 reads per min processed...
3562500.00 reads per min processed...
3428571.43 reads per min processed...
3405405.41 reads per min processed...
3300000.00 reads per min processed...
3209302.33 reads per min processed...
3200000.00 reads per min processed...
3125000.00 reads per min processed...
3058823.53 reads per min processed...
3056603.77 reads per min processed...
3054545.45 reads per min processed...
3052631.58 reads per min processed...
3050847.46 reads per min processed...
3049180.33 reads per min processed...
3047619.05 reads per min processed...
3046153.85 reads per min processed...
3090909.09 reads per min processed...
3088235.29 reads per min processed...
3130434.78 reads per min processed...
3171428.57 reads per min processed...
3166666.67 reads per min processed...
3162162.16 reads per min processed...
3157894.74 reads per min processed...
3194805.19 reads per min processed...
3189873.42 reads per min processed...
3225000.00 reads per min processed...
3259259.26 reads per min processed...
3253012.05 reads per min processed...
3247058.82 reads per min processed...
3241379.31 reads per min processed...
3235955.06 reads per min processed...
3266666.67 reads per min processed...
3260869.57 reads per min processed...
3255319.15 reads per min processed...
3250000.00 reads per min processed...
3278350.52 reads per min processed...
3340206.19 reads per min processed...
3367346.94 reads per min processed...
3393939.39 reads per min processed...
3420000.00 reads per min processed...
3445544.55 reads per min processed...
3470588.24 reads per min processed...
3495145.63 reads per min processed...
3485714.29 reads per min processed...
3476635.51 reads per min processed...
3500000.00 reads per min processed...
3459459.46 reads per min processed...
3451327.43 reads per min processed...
3473684.21 reads per min processed...
3465517.24 reads per min processed...
3487179.49 reads per min processed...
3478991.60 reads per min processed...
3471074.38 reads per min processed...
3520661.16 reads per min processed...
3512195.12 reads per min processed...
3532258.06 reads per min processed...
3552000.00 reads per min processed...
3571428.57 reads per min processed...
3562500.00 reads per min processed...
3581395.35 reads per min processed...
3600000.00 reads per min processed...
3618320.61 reads per min processed...
3636363.64 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.tUjwmqx8LY/ColoN_FFPE_L06_RNA_01_B23LG7FLT4_2.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.tUjwmqx8LY/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -119379.617768
EM: Round [1] log likelihood: -119090.142061
EM: Round [2] log likelihood: -118979.179547
EM: Round [3] log likelihood: -118924.637266
EM: Round [4] log likelihood: -118894.785301
EM: Round [5] log likelihood: -118877.600704
EM: Round [6] log likelihood: -118867.329798
EM: Round [7] log likelihood: -118860.947462
EM: Round [8] log likelihood: -118856.814667
EM: Round [9] log likelihood: -118854.027455
EM: Round [10] log likelihood: -118852.075868
EM: Round [11] log likelihood: -118850.663658
EM: Round [12] log likelihood: -118849.612788
EM: Round [13] log likelihood: -118848.812350
EM: Round [14] log likelihood: -118848.190742
EM: Round [15] log likelihood: -118847.700150
EM: Round [16] log likelihood: -118847.307650
EM: Round [17] log likelihood: -118846.989946
EM: Round [18] log likelihood: -118846.730164
EM: Round [19] log likelihood: -118846.515831
EM: Round [20] log likelihood: -118846.337568
EM: Round [21] log likelihood: -118846.188221
EM: Round [22] log likelihood: -118846.062258
EM: Round [23] log likelihood: -118845.955358
EM: Round [24] log likelihood: -118845.864110
EM: Round [25] log likelihood: -118845.785800
EM: Round [26] log likelihood: -118845.718251
EM: Round [27] log likelihood: -118845.659702
EM: Round [28] log likelihood: -118845.608723
EM: Round [29] log likelihood: -118845.564142
EM: Round [30] log likelihood: -118845.524995
EM: Round [31] log likelihood: -118845.490485
EM: Round [32] log likelihood: -118845.459948
EM: Round [33] log likelihood: -118845.432831
EM: Round [34] log likelihood: -118845.408668
EM: Round [35] log likelihood: -118845.387067
EM: Round [36] log likelihood: -118845.367696
EM: Round [37] log likelihood: -118845.350274
EM: Round [38] log likelihood: -118845.334560
EM: Round [39] log likelihood: -118845.320347
EM: Round [40] log likelihood: -118845.307459
EM: Round [41] log likelihood: -118845.295742
EM: Round [42] log likelihood: -118845.285066
EM: Round [43] log likelihood: -118845.275315
EM: Round [44] log likelihood: -118845.266390
EM: Round [45] log likelihood: -118845.258203
EM: Round [46] log likelihood: -118845.250678
EM: Round [47] log likelihood: -118845.243749
EM: Round [48] log likelihood: -118845.237355
EM: Round [49] log likelihood: -118845.231446
EM: Round [50] log likelihood: -118845.225975
EM: Round [51] log likelihood: -118845.220901
EM: Round [52] log likelihood: -118845.216188
EM: Round [53] log likelihood: -118845.211804
EM: Round [54] log likelihood: -118845.207719
EM: Round [55] log likelihood: -118845.203907
EM: Round [56] log likelihood: -118845.200347
EM: Round [57] log likelihood: -118845.197016
EM: Round [58] log likelihood: -118845.193895
EM: Round [59] log likelihood: -118845.190969
EM: Round [60] log likelihood: -118845.188221
EM: Round [61] log likelihood: -118845.185638
EM: Round [62] log likelihood: -118845.183208
EM: Round [63] log likelihood: -118845.180918
EM: Round [64] log likelihood: -118845.178758
EM: Round [65] log likelihood: -118845.176719
EM: Round [66] log likelihood: -118845.174793
EM: Round [67] log likelihood: -118845.172971
EM: Round [68] log likelihood: -118845.171246
EM: Round [69] log likelihood: -118845.169612
EM: Round [70] log likelihood: -118845.168063
EM: Round [71] log likelihood: -118845.166592
EM: Round [72] log likelihood: -118845.165196
EM: Round [73] log likelihood: -118845.163868
EM: Round [74] log likelihood: -118845.162606
EM: Round [75] log likelihood: -118845.161404
EM: Round [76] log likelihood: -118845.160259
EM: Round [77] log likelihood: -118845.159167
EM: Round [78] log likelihood: -118845.158126
EM: Round [79] log likelihood: -118845.157133
EM: Round [80] log likelihood: -118845.156184
EM: Round [81] log likelihood: -118845.155277
EM: Round [82] log likelihood: -118845.154410
EM: Round [83] log likelihood: -118845.153581
EM: Round [84] log likelihood: -118845.152787
EM: Round [85] log likelihood: -118845.152027
EM: Round [86] log likelihood: -118845.151299
EM: Round [87] log likelihood: -118845.150600
EM: Round [88] log likelihood: -118845.149931
EM: Round [89] log likelihood: -118845.149288
EM: Round [90] log likelihood: -118845.148671
EM: Round [91] log likelihood: -118845.148079
EM: Round [92] log likelihood: -118845.147509
EM: Round [93] log likelihood: -118845.146962
EM: Round [94] log likelihood: -118845.146436
EM: Round [95] log likelihood: -118845.145930
EM: Round [96] log likelihood: -118845.145443
EM: Round [97] log likelihood: -118845.144974
EM: Round [98] log likelihood: -118845.144522
EM: Round [99] log likelihood: -118845.144087
EM: Round [100] log likelihood: -118845.143667
EM: Round [101] log likelihood: -118845.143263
EM: Round [102] log likelihood: -118845.142873
EM: Round [103] log likelihood: -118845.142496
EM: Round [104] log likelihood: -118845.142133
EM: Round [105] log likelihood: -118845.141783
EM: Round [106] log likelihood: -118845.141444
EM: Round [107] log likelihood: -118845.141117
EM: Round [108] log likelihood: -118845.140801
EM: Round [109] log likelihood: -118845.140496
EM: Round [110] log likelihood: -118845.140201
EM: Round [111] log likelihood: -118845.139916
EM: Round [112] log likelihood: -118845.139640
EM: Round [113] log likelihood: -118845.139373
EM: Round [114] log likelihood: -118845.139114
EM: Round [115] log likelihood: -118845.138864
EM: Round [116] log likelihood: -118845.138622
EM: Round [117] log likelihood: -118845.138387
EM: Round [118] log likelihood: -118845.138160
EM: Round [119] log likelihood: -118845.137940
EM: Round [120] log likelihood: -118845.137727
EM: Round [121] log likelihood: -118845.137520
EM: Round [122] log likelihood: -118845.137320
EM: Round [123] log likelihood: -118845.137125
EM: Round [124] log likelihood: -118845.136937
EM: Round [125] log likelihood: -118845.136754
EM: Round [126] log likelihood: -118845.136576
EM: Round [127] log likelihood: -118845.136404
EM: Round [128] log likelihood: -118845.136237
EM: Round [129] log likelihood: -118845.136075
EM: Round [130] log likelihood: -118845.135917
EM: Round [131] log likelihood: -118845.135764
EM: Round [132] log likelihood: -118845.135615
EM: Round [133] log likelihood: -118845.135471
EM: Round [134] log likelihood: -118845.135331
EM: Round [135] log likelihood: -118845.135194
EM: Round [136] log likelihood: -118845.135062
EM: Round [137] log likelihood: -118845.134933
EM: Round [138] log likelihood: -118845.134808
EM: Round [139] log likelihood: -118845.134686
EM: Round [140] log likelihood: -118845.134567
EM: Round [141] log likelihood: -118845.134452
EM: Round [142] log likelihood: -118845.134340
EM: Round [143] log likelihood: -118845.134230
EM: Round [144] log likelihood: -118845.134124
EM: Round [145] log likelihood: -118845.134021
EM: Round [146] log likelihood: -118845.133920
EM: Round [147] log likelihood: -118845.133822
EM: Stopping iterations at round 147 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -119204.966701
EM: Round [1] log likelihood: -118963.632546
EM: Round [2] log likelihood: -118874.637723
EM: Round [3] log likelihood: -118832.023686
EM: Round [4] log likelihood: -118809.223566
EM: Round [5] log likelihood: -118796.353801
EM: Round [6] log likelihood: -118788.789409
EM: Round [7] log likelihood: -118784.155873
EM: Round [8] log likelihood: -118781.192638
EM: Round [9] log likelihood: -118779.215806
EM: Round [10] log likelihood: -118777.844739
EM: Round [11] log likelihood: -118776.860845
EM: Round [12] log likelihood: -118776.134066
EM: Round [13] log likelihood: -118775.584097
EM: Round [14] log likelihood: -118775.159497
EM: Round [15] log likelihood: -118774.826153
EM: Round [16] log likelihood: -118774.560726
EM: Round [17] log likelihood: -118774.346797
EM: Round [18] log likelihood: -118774.172539
EM: Round [19] log likelihood: -118774.029255
EM: Round [20] log likelihood: -118773.910440
EM: Round [21] log likelihood: -118773.811157
EM: Round [22] log likelihood: -118773.727604
EM: Round [23] log likelihood: -118773.656828
EM: Round [24] log likelihood: -118773.596506
EM: Round [25] log likelihood: -118773.544799
EM: Round [26] log likelihood: -118773.500236
EM: Round [27] log likelihood: -118773.461632
EM: Round [28] log likelihood: -118773.428029
EM: Round [29] log likelihood: -118773.398643
EM: Round [30] log likelihood: -118773.372833
EM: Round [31] log likelihood: -118773.350070
EM: Round [32] log likelihood: -118773.329913
EM: Round [33] log likelihood: -118773.311996
EM: Round [34] log likelihood: -118773.296014
EM: Round [35] log likelihood: -118773.281708
EM: Round [36] log likelihood: -118773.268860
EM: Round [37] log likelihood: -118773.257287
EM: Round [38] log likelihood: -118773.246830
EM: Round [39] log likelihood: -118773.237355
EM: Round [40] log likelihood: -118773.228746
EM: Round [41] log likelihood: -118773.220905
EM: Round [42] log likelihood: -118773.213745
EM: Round [43] log likelihood: -118773.207193
EM: Round [44] log likelihood: -118773.201182
EM: Round [45] log likelihood: -118773.195657
EM: Round [46] log likelihood: -118773.190569
EM: Round [47] log likelihood: -118773.185873
EM: Round [48] log likelihood: -118773.181532
EM: Round [49] log likelihood: -118773.177511
EM: Round [50] log likelihood: -118773.173781
EM: Round [51] log likelihood: -118773.170316
EM: Round [52] log likelihood: -118773.167091
EM: Round [53] log likelihood: -118773.164086
EM: Round [54] log likelihood: -118773.161281
EM: Round [55] log likelihood: -118773.158660
EM: Round [56] log likelihood: -118773.156208
EM: Round [57] log likelihood: -118773.153910
EM: Round [58] log likelihood: -118773.151755
EM: Round [59] log likelihood: -118773.149732
EM: Round [60] log likelihood: -118773.147830
EM: Round [61] log likelihood: -118773.146040
EM: Round [62] log likelihood: -118773.144354
EM: Round [63] log likelihood: -118773.142764
EM: Round [64] log likelihood: -118773.141263
EM: Round [65] log likelihood: -118773.139846
EM: Round [66] log likelihood: -118773.138506
EM: Round [67] log likelihood: -118773.137237
EM: Round [68] log likelihood: -118773.136036
EM: Round [69] log likelihood: -118773.134898
EM: Round [70] log likelihood: -118773.133818
EM: Round [71] log likelihood: -118773.132793
EM: Round [72] log likelihood: -118773.131819
EM: Round [73] log likelihood: -118773.130893
EM: Round [74] log likelihood: -118773.130012
EM: Round [75] log likelihood: -118773.129173
EM: Round [76] log likelihood: -118773.128374
EM: Round [77] log likelihood: -118773.127613
EM: Round [78] log likelihood: -118773.126887
EM: Round [79] log likelihood: -118773.126194
EM: Round [80] log likelihood: -118773.125532
EM: Round [81] log likelihood: -118773.124899
EM: Round [82] log likelihood: -118773.124295
EM: Round [83] log likelihood: -118773.123716
EM: Round [84] log likelihood: -118773.123163
EM: Round [85] log likelihood: -118773.122633
EM: Round [86] log likelihood: -118773.122125
EM: Round [87] log likelihood: -118773.121638
EM: Round [88] log likelihood: -118773.121172
EM: Round [89] log likelihood: -118773.120724
EM: Round [90] log likelihood: -118773.120294
EM: Round [91] log likelihood: -118773.119881
EM: Round [92] log likelihood: -118773.119485
EM: Round [93] log likelihood: -118773.119103
EM: Round [94] log likelihood: -118773.118737
EM: Round [95] log likelihood: -118773.118384
EM: Round [96] log likelihood: -118773.118045
EM: Round [97] log likelihood: -118773.117718
EM: Round [98] log likelihood: -118773.117404
EM: Round [99] log likelihood: -118773.117100
EM: Round [100] log likelihood: -118773.116808
EM: Round [101] log likelihood: -118773.116526
EM: Round [102] log likelihood: -118773.116255
EM: Round [103] log likelihood: -118773.115992
EM: Round [104] log likelihood: -118773.115739
EM: Round [105] log likelihood: -118773.115495
EM: Round [106] log likelihood: -118773.115259
EM: Round [107] log likelihood: -118773.115030
EM: Round [108] log likelihood: -118773.114810
EM: Round [109] log likelihood: -118773.114597
EM: Round [110] log likelihood: -118773.114391
EM: Round [111] log likelihood: -118773.114191
EM: Round [112] log likelihood: -118773.113998
EM: Round [113] log likelihood: -118773.113811
EM: Round [114] log likelihood: -118773.113630
EM: Round [115] log likelihood: -118773.113455
EM: Round [116] log likelihood: -118773.113285
EM: Round [117] log likelihood: -118773.113121
EM: Round [118] log likelihood: -118773.112962
EM: Round [119] log likelihood: -118773.112807
EM: Round [120] log likelihood: -118773.112657
EM: Round [121] log likelihood: -118773.112512
EM: Round [122] log likelihood: -118773.112370
EM: Round [123] log likelihood: -118773.112233
EM: Round [124] log likelihood: -118773.112100
EM: Round [125] log likelihood: -118773.111971
EM: Round [126] log likelihood: -118773.111846
EM: Round [127] log likelihood: -118773.111724
EM: Round [128] log likelihood: -118773.111606
EM: Round [129] log likelihood: -118773.111491
EM: Round [130] log likelihood: -118773.111379
EM: Round [131] log likelihood: -118773.111270
EM: Round [132] log likelihood: -118773.111164
EM: Round [133] log likelihood: -118773.111061
EM: Round [134] log likelihood: -118773.110961
EM: Round [135] log likelihood: -118773.110864
EM: Stopping iterations at round 135 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.tUjwmqx8LY/./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.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.tUjwmqx8LY/./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.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 121082139 > /tmp/nxf.tUjwmqx8LY/./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.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir > /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir --annotate /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.tUjwmqx8LY/./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.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir
-done, see /tmp/nxf.tUjwmqx8LY/./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.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.tUjwmqx8LY/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 480, filtered: 5293)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.tUjwmqx8LY/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.tUjwmqx8LY/./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.tUjwmqx8LY/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [ENSG00000286907.1]
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WARNING, no entry stored in dbm for [IGH.g@-ext]
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WARNING, no entry stored in dbm for [IGH.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000281128.2]
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WARNING, no entry stored in dbm for [ENSG00000263731.1]
WARNING, no entry stored in dbm for [ENSG00000237773.7]
WARNING, no entry stored in dbm for [ENSG00000286389.1]
WARNING, no entry stored in dbm for [ENSG00000232496.2]
WARNING, no entry stored in dbm for [ENSG00000226312.7]
WARNING, no entry stored in dbm for [ENSG00000197099.8]
WARNING, no entry stored in dbm for [ENSG00000241684.6]
WARNING, no entry stored in dbm for [ENSG00000250961.2]
WARNING, no entry stored in dbm for [ENSG00000213736.2]
WARNING, no entry stored in dbm for [ENSG00000288049.1]
WARNING, no entry stored in dbm for [ENSG00000250922.1]
WARNING, no entry stored in dbm for [ENSG00000255931.2]
WARNING, no entry stored in dbm for [ENSG00000259605.3]
WARNING, no entry stored in dbm for [ENSG00000287917.1]
WARNING, no entry stored in dbm for [ENSG00000285799.1]
WARNING, no entry stored in dbm for [ENSG00000254741.1]
WARNING, no entry stored in dbm for [ENSG00000225075.1]
WARNING, no entry stored in dbm for [ENSG00000238232.1]
WARNING, no entry stored in dbm for [ENSG00000236358.1]
WARNING, no entry stored in dbm for [ENSG00000286870.1]
WARNING, no entry stored in dbm for [ENSG00000232310.8]
WARNING, no entry stored in dbm for [ENSG00000285407.1]
WARNING, no entry stored in dbm for [ENSG00000213107.2]
WARNING, no entry stored in dbm for [ENSG00000224078.15]
WARNING, no entry stored in dbm for [ENSG00000258730.1]
WARNING, no entry stored in dbm for [ENSG00000229930.1]
WARNING, no entry stored in dbm for [ENSG00000229930.1]
WARNING, no entry stored in dbm for [ENSG00000282508.2]
WARNING, no entry stored in dbm for [ENSG00000259993.1]
WARNING, no entry stored in dbm for [ENSG00000259191.2]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000186704.9]
WARNING, no entry stored in dbm for [ENSG00000280285.1]
WARNING, no entry stored in dbm for [ENSG00000260236.1]
WARNING, no entry stored in dbm for [ENSG00000205976.4]
WARNING, no entry stored in dbm for [ENSG00000240519.1]
WARNING, no entry stored in dbm for [ENSG00000264151.6]
WARNING, no entry stored in dbm for [ENSG00000277837.1]
WARNING, no entry stored in dbm for [ENSG00000277837.1]
WARNING, no entry stored in dbm for [ENSG00000254485.5]
WARNING, no entry stored in dbm for [ENSG00000288070.1]
WARNING, no entry stored in dbm for [ENSG00000257453.1]
WARNING, no entry stored in dbm for [ENSG00000229914.1]
WARNING, no entry stored in dbm for [ENSG00000287170.1]
WARNING, no entry stored in dbm for [ENSG00000277458.1]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000278975.1]
WARNING, no entry stored in dbm for [ENSG00000268460.2]
WARNING, no entry stored in dbm for [ENSG00000223544.1]
WARNING, no entry stored in dbm for [ENSG00000286923.1]
WARNING, no entry stored in dbm for [ENSG00000225722.1]
* STAR-Fusion complete. See output: /tmp/nxf.tUjwmqx8LY/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)