-ctat genome lib [/tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir] validates.
CMD: mkdir -p /tmp/nxf.rYzp0iHBGp/./_starF_checkpoints
CMD: mkdir -p /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary
-sample contains 201017995 rnaseq fragments
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.map_chimeric_reads_to_genes --genome_lib_dir /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir -J /tmp/nxf.rYzp0iHBGp/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction -O /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --CPU 4
-parsing fusion evidence: /tmp/nxf.rYzp0iHBGp/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_1.Chimeric.out.junction
-building interval tree based on /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes
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[1740000], rate=72299.17/min -building interval tree based on /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes
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[1740000], rate=71165.64/min -building interval tree based on /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.07 min).
-mapping reads to genes
[10000], rate=85714.29/min
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[1740000], rate=69879.52/min -building interval tree based on /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu
-done building interval tree (0.05 min).
-mapping reads to genes
[10000], rate=100000.00/min
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[160000], rate=129729.73/min
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[180000], rate=131707.32/min
[190000], rate=131034.48/min
[200000], rate=129032.26/min
[210000], rate=131250.00/min
[220000], rate=132000.00/min
[230000], rate=131428.57/min
[240000], rate=130909.09/min
[250000], rate=122950.82/min
[260000], rate=111428.57/min
[270000], rate=103184.71/min
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[300000], rate=87378.64/min
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[320000], rate=81012.66/min
[330000], rate=78571.43/min
[340000], rate=76404.49/min
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[370000], rate=70476.19/min
[380000], rate=68882.18/min
[390000], rate=67435.16/min
[400000], rate=66298.34/min
[410000], rate=65079.37/min
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[430000], rate=63235.29/min
[440000], rate=62411.35/min
[450000], rate=61503.42/min
[460000], rate=60526.32/min
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[490000], rate=58565.74/min
[500000], rate=58027.08/min
[510000], rate=57627.12/min
[520000], rate=57142.86/min
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[540000], rate=56347.83/min
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[580000], rate=55325.91/min
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[1420000], rate=60468.42/min
[1430000], rate=60507.76/min
[1440000], rate=60589.06/min
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[1480000], rate=61030.93/min
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[1540000], rate=60909.69/min
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[1610000], rate=60792.95/min
[1620000], rate=60750.00/min
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[1720000], rate=61246.29/min
[1730000], rate=61347.52/min
[1740000], rate=61447.91/min * Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.handle_multimapping_reads -J /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt --genome_lib_dir /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir --filt_file /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.fail -M 50 > /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-parsing /tmp/nxf.rYzp0iHBGp/./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...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
6000000.00 reads per min processed...
5142857.14 reads per min processed...
5250000.00 reads per min processed...
5333333.33 reads per min processed...
5400000.00 reads per min processed...
5000000.00 reads per min processed...
5076923.08 reads per min processed...
5142857.14 reads per min processed...
4875000.00 reads per min processed...
4941176.47 reads per min processed...
5000000.00 reads per min processed...
4800000.00 reads per min processed...
4857142.86 reads per min processed...
4909090.91 reads per min processed...
4750000.00 reads per min processed...
4800000.00 reads per min processed...
4846153.85 reads per min processed...
4714285.71 reads per min processed...
4758620.69 reads per min processed...
4800000.00 reads per min processed...
4838709.68 reads per min processed...
4875000.00 reads per min processed...
4764705.88 reads per min processed...
4800000.00 reads per min processed...
4833333.33 reads per min processed...
5000000.00 reads per min processed...
5027027.03 reads per min processed...
5052631.58 reads per min processed...
5076923.08 reads per min processed...
4975609.76 reads per min processed...
5000000.00 reads per min processed...
5023255.81 reads per min processed...
5045454.55 reads per min processed...
5066666.67 reads per min processed...
5086956.52 reads per min processed...
5000000.00 reads per min processed...
5020408.16 reads per min processed...
5040000.00 reads per min processed...
5058823.53 reads per min processed...
5076923.08 reads per min processed...
5094339.62 reads per min processed...
5111111.11 reads per min processed...
5035714.29 reads per min processed...
5052631.58 reads per min processed...
done.
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.predict -J /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass -O /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion
-parsing fusion evidence: /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.junction_breakpts_to_genes.txt.pass
-outputting fusion candidates to file: /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary
* Running CMD: /usr/local/src/STAR-Fusion/util/STAR-Fusion.filter --fusion_preds /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary -J /tmp/nxf.rYzp0iHBGp/1173_N5V_T1_RNA_SLD_01_A23T55JLT4_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.rYzp0iHBGp/ctat_genome_lib_build_dir --out_prefix /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion
CMD: mkdir -p /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir
EM: Starting log likelihood: -1186180.228324
EM: Round [1] log likelihood: -1185865.190100
EM: Round [2] log likelihood: -1185756.623251
EM: Round [3] log likelihood: -1185705.995810
EM: Round [4] log likelihood: -1185678.698163
EM: Round [5] log likelihood: -1185662.729407
EM: Round [6] log likelihood: -1185652.820133
EM: Round [7] log likelihood: -1185646.354893
EM: Round [8] log likelihood: -1185641.946241
EM: Round [9] log likelihood: -1185638.822389
EM: Round [10] log likelihood: -1185636.535392
EM: Round [11] log likelihood: -1185634.814464
EM: Round [12] log likelihood: -1185633.489441
EM: Round [13] log likelihood: -1185632.449460
EM: Round [14] log likelihood: -1185631.619886
EM: Round [15] log likelihood: -1185630.948978
EM: Round [16] log likelihood: -1185630.399937
EM: Round [17] log likelihood: -1185629.945991
EM: Round [18] log likelihood: -1185629.567280
EM: Round [19] log likelihood: -1185629.248818
EM: Round [20] log likelihood: -1185628.979122
EM: Round [21] log likelihood: -1185628.749277
EM: Round [22] log likelihood: -1185628.552278
EM: Round [23] log likelihood: -1185628.382560
EM: Round [24] log likelihood: -1185628.235660
EM: Round [25] log likelihood: -1185628.107967
EM: Round [26] log likelihood: -1185627.996533
EM: Round [27] log likelihood: -1185627.898936
EM: Round [28] log likelihood: -1185627.813173
EM: Round [29] log likelihood: -1185627.737573
EM: Round [30] log likelihood: -1185627.670737
EM: Round [31] log likelihood: -1185627.611490
EM: Round [32] log likelihood: -1185627.558832
EM: Round [33] log likelihood: -1185627.511919
EM: Round [34] log likelihood: -1185627.470025
EM: Round [35] log likelihood: -1185627.432531
EM: Round [36] log likelihood: -1185627.398904
EM: Round [37] log likelihood: -1185627.368683
EM: Round [38] log likelihood: -1185627.341469
EM: Round [39] log likelihood: -1185627.316917
EM: Round [40] log likelihood: -1185627.294726
EM: Round [41] log likelihood: -1185627.274632
EM: Round [42] log likelihood: -1185627.256405
EM: Round [43] log likelihood: -1185627.239843
EM: Round [44] log likelihood: -1185627.224770
EM: Round [45] log likelihood: -1185627.211028
EM: Round [46] log likelihood: -1185627.198481
EM: Round [47] log likelihood: -1185627.187006
EM: Round [48] log likelihood: -1185627.176495
EM: Round [49] log likelihood: -1185627.166854
EM: Round [50] log likelihood: -1185627.157996
EM: Round [51] log likelihood: -1185627.149847
EM: Round [52] log likelihood: -1185627.142339
EM: Round [53] log likelihood: -1185627.135412
EM: Round [54] log likelihood: -1185627.129012
EM: Round [55] log likelihood: -1185627.123092
EM: Round [56] log likelihood: -1185627.117607
EM: Round [57] log likelihood: -1185627.112521
EM: Round [58] log likelihood: -1185627.107797
EM: Round [59] log likelihood: -1185627.103405
EM: Round [60] log likelihood: -1185627.099317
EM: Round [61] log likelihood: -1185627.095507
EM: Round [62] log likelihood: -1185627.091952
EM: Round [63] log likelihood: -1185627.088632
EM: Round [64] log likelihood: -1185627.085528
EM: Round [65] log likelihood: -1185627.082622
EM: Round [66] log likelihood: -1185627.079900
EM: Round [67] log likelihood: -1185627.077347
EM: Round [68] log likelihood: -1185627.074952
EM: Round [69] log likelihood: -1185627.072701
EM: Round [70] log likelihood: -1185627.070584
EM: Round [71] log likelihood: -1185627.068593
EM: Round [72] log likelihood: -1185627.066717
EM: Round [73] log likelihood: -1185627.064949
EM: Round [74] log likelihood: -1185627.063281
EM: Round [75] log likelihood: -1185627.061707
EM: Round [76] log likelihood: -1185627.060221
EM: Round [77] log likelihood: -1185627.058816
EM: Round [78] log likelihood: -1185627.057487
EM: Round [79] log likelihood: -1185627.056229
EM: Round [80] log likelihood: -1185627.055038
EM: Round [81] log likelihood: -1185627.053910
EM: Round [82] log likelihood: -1185627.052841
EM: Round [83] log likelihood: -1185627.051827
EM: Round [84] log likelihood: -1185627.050865
EM: Round [85] log likelihood: -1185627.049951
EM: Round [86] log likelihood: -1185627.049084
EM: Round [87] log likelihood: -1185627.048260
EM: Round [88] log likelihood: -1185627.047476
EM: Round [89] log likelihood: -1185627.046731
EM: Round [90] log likelihood: -1185627.046023
EM: Round [91] log likelihood: -1185627.045349
EM: Round [92] log likelihood: -1185627.044707
EM: Round [93] log likelihood: -1185627.044096
EM: Round [94] log likelihood: -1185627.043514
EM: Round [95] log likelihood: -1185627.042959
EM: Round [96] log likelihood: -1185627.042430
EM: Round [97] log likelihood: -1185627.041927
EM: Round [98] log likelihood: -1185627.041446
EM: Round [99] log likelihood: -1185627.040988
EM: Round [100] log likelihood: -1185627.040550
EM: Round [101] log likelihood: -1185627.040133
EM: Round [102] log likelihood: -1185627.039735
EM: Round [103] log likelihood: -1185627.039355
EM: Round [104] log likelihood: -1185627.038991
EM: Round [105] log likelihood: -1185627.038645
EM: Round [106] log likelihood: -1185627.038313
EM: Round [107] log likelihood: -1185627.037997
EM: Round [108] log likelihood: -1185627.037694
EM: Round [109] log likelihood: -1185627.037405
EM: Round [110] log likelihood: -1185627.037128
EM: Round [111] log likelihood: -1185627.036864
EM: Round [112] log likelihood: -1185627.036611
EM: Round [113] log likelihood: -1185627.036370
EM: Round [114] log likelihood: -1185627.036138
EM: Round [115] log likelihood: -1185627.035917
EM: Round [116] log likelihood: -1185627.035705
EM: Round [117] log likelihood: -1185627.035502
EM: Round [118] log likelihood: -1185627.035308
EM: Round [119] log likelihood: -1185627.035123
EM: Round [120] log likelihood: -1185627.034945
EM: Round [121] log likelihood: -1185627.034774
EM: Round [122] log likelihood: -1185627.034611
EM: Round [123] log likelihood: -1185627.034455
EM: Round [124] log likelihood: -1185627.034305
EM: Round [125] log likelihood: -1185627.034162
EM: Round [126] log likelihood: -1185627.034024
EM: Round [127] log likelihood: -1185627.033893
EM: Round [128] log likelihood: -1185627.033767
EM: Round [129] log likelihood: -1185627.033646
EM: Round [130] log likelihood: -1185627.033530
EM: Round [131] log likelihood: -1185627.033418
EM: Round [132] log likelihood: -1185627.033312
EM: Round [133] log likelihood: -1185627.033209
EM: Round [134] log likelihood: -1185627.033111
EM: Stopping iterations at round 134 due to insufficient improvement in likelihood.
EM: Starting log likelihood: -1184237.670278
EM: Round [1] log likelihood: -1184000.721752
EM: Round [2] log likelihood: -1183923.666913
EM: Round [3] log likelihood: -1183888.940565
EM: Round [4] log likelihood: -1183870.547318
EM: Round [5] log likelihood: -1183859.888095
EM: Round [6] log likelihood: -1183853.309218
EM: Round [7] log likelihood: -1183849.030559
EM: Round [8] log likelihood: -1183846.117439
EM: Round [9] log likelihood: -1183844.053541
EM: Round [10] log likelihood: -1183842.541011
EM: Round [11] log likelihood: -1183841.400804
EM: Round [12] log likelihood: -1183840.520941
EM: Round [13] log likelihood: -1183839.828711
EM: Round [14] log likelihood: -1183839.275244
EM: Round [15] log likelihood: -1183838.826662
EM: Round [16] log likelihood: -1183838.458838
EM: Round [17] log likelihood: -1183838.154179
EM: Round [18] log likelihood: -1183837.899600
EM: Round [19] log likelihood: -1183837.685196
EM: Round [20] log likelihood: -1183837.503359
EM: Round [21] log likelihood: -1183837.348166
EM: Round [22] log likelihood: -1183837.214954
EM: Round [23] log likelihood: -1183837.100014
EM: Round [24] log likelihood: -1183837.000366
EM: Round [25] log likelihood: -1183836.913598
EM: Round [26] log likelihood: -1183836.837740
EM: Round [27] log likelihood: -1183836.771175
EM: Round [28] log likelihood: -1183836.712562
EM: Round [29] log likelihood: -1183836.660786
EM: Round [30] log likelihood: -1183836.614911
EM: Round [31] log likelihood: -1183836.574152
EM: Round [32] log likelihood: -1183836.537843
EM: Round [33] log likelihood: -1183836.505417
EM: Round [34] log likelihood: -1183836.476391
EM: Round [35] log likelihood: -1183836.450350
EM: Round [36] log likelihood: -1183836.426937
EM: Round [37] log likelihood: -1183836.405844
EM: Round [38] log likelihood: -1183836.386805
EM: Round [39] log likelihood: -1183836.369586
EM: Round [40] log likelihood: -1183836.353986
EM: Round [41] log likelihood: -1183836.339827
EM: Round [42] log likelihood: -1183836.326954
EM: Round [43] log likelihood: -1183836.315231
EM: Round [44] log likelihood: -1183836.304539
EM: Round [45] log likelihood: -1183836.294770
EM: Round [46] log likelihood: -1183836.285833
EM: Round [47] log likelihood: -1183836.277643
EM: Round [48] log likelihood: -1183836.270127
EM: Round [49] log likelihood: -1183836.263220
EM: Round [50] log likelihood: -1183836.256863
EM: Round [51] log likelihood: -1183836.251005
EM: Round [52] log likelihood: -1183836.245599
EM: Round [53] log likelihood: -1183836.240604
EM: Round [54] log likelihood: -1183836.235983
EM: Round [55] log likelihood: -1183836.231702
EM: Round [56] log likelihood: -1183836.227731
EM: Round [57] log likelihood: -1183836.224044
EM: Round [58] log likelihood: -1183836.220617
EM: Round [59] log likelihood: -1183836.217426
EM: Round [60] log likelihood: -1183836.214453
EM: Round [61] log likelihood: -1183836.211680
EM: Round [62] log likelihood: -1183836.209091
EM: Round [63] log likelihood: -1183836.206671
EM: Round [64] log likelihood: -1183836.204407
EM: Round [65] log likelihood: -1183836.202286
EM: Round [66] log likelihood: -1183836.200298
EM: Round [67] log likelihood: -1183836.198433
EM: Round [68] log likelihood: -1183836.196682
EM: Round [69] log likelihood: -1183836.195036
EM: Round [70] log likelihood: -1183836.193488
EM: Round [71] log likelihood: -1183836.192030
EM: Round [72] log likelihood: -1183836.190658
EM: Round [73] log likelihood: -1183836.189364
EM: Round [74] log likelihood: -1183836.188143
EM: Round [75] log likelihood: -1183836.186991
EM: Round [76] log likelihood: -1183836.185902
EM: Round [77] log likelihood: -1183836.184874
EM: Round [78] log likelihood: -1183836.183901
EM: Round [79] log likelihood: -1183836.182980
EM: Round [80] log likelihood: -1183836.182109
EM: Round [81] log likelihood: -1183836.181284
EM: Round [82] log likelihood: -1183836.180501
EM: Round [83] log likelihood: -1183836.179760
EM: Round [84] log likelihood: -1183836.179056
EM: Round [85] log likelihood: -1183836.178389
EM: Round [86] log likelihood: -1183836.177755
EM: Round [87] log likelihood: -1183836.177153
EM: Round [88] log likelihood: -1183836.176581
EM: Round [89] log likelihood: -1183836.176037
EM: Round [90] log likelihood: -1183836.175521
EM: Round [91] log likelihood: -1183836.175029
EM: Round [92] log likelihood: -1183836.174562
EM: Round [93] log likelihood: -1183836.174117
EM: Round [94] log likelihood: -1183836.173693
EM: Round [95] log likelihood: -1183836.173290
EM: Round [96] log likelihood: -1183836.172906
EM: Round [97] log likelihood: -1183836.172540
EM: Round [98] log likelihood: -1183836.172191
EM: Round [99] log likelihood: -1183836.171859
EM: Round [100] log likelihood: -1183836.171542
EM: Round [101] log likelihood: -1183836.171240
EM: Round [102] log likelihood: -1183836.170952
EM: Round [103] log likelihood: -1183836.170677
EM: Round [104] log likelihood: -1183836.170415
EM: Round [105] log likelihood: -1183836.170165
EM: Round [106] log likelihood: -1183836.169926
EM: Round [107] log likelihood: -1183836.169698
EM: Round [108] log likelihood: -1183836.169480
EM: Round [109] log likelihood: -1183836.169272
EM: Round [110] log likelihood: -1183836.169074
EM: Round [111] log likelihood: -1183836.168884
EM: Round [112] log likelihood: -1183836.168703
EM: Round [113] log likelihood: -1183836.168530
EM: Round [114] log likelihood: -1183836.168365
EM: Round [115] log likelihood: -1183836.168207
EM: Round [116] log likelihood: -1183836.168056
EM: Round [117] log likelihood: -1183836.167911
EM: Round [118] log likelihood: -1183836.167773
EM: Round [119] log likelihood: -1183836.167641
EM: Round [120] log likelihood: -1183836.167515
EM: Round [121] log likelihood: -1183836.167395
EM: Round [122] log likelihood: -1183836.167279
EM: Round [123] log likelihood: -1183836.167169
EM: Round [124] log likelihood: -1183836.167063
EM: Round [125] log likelihood: -1183836.166962
EM: Round [126] log likelihood: -1183836.166865
EM: Stopping iterations at round 126 due to insufficient improvement in likelihood.
CMD: /usr/local/src/STAR-Fusion/util/../FusionFilter/blast_and_promiscuity_filter.pl --out_prefix /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion --max_promiscuity 10 --min_pct_dom_promiscuity 20 --fusion_preds /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter --genome_lib_dir /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter --genome_lib_dir /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 20
CMD: cp /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.pre_blast_filter.post_blast_filter.post_promisc_filter /tmp/nxf.rYzp0iHBGp/./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.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter JunctionReads,SpanningFrags > /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter.abridged
CMD: ln -sf /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.filter.intermediates_dir/star-fusion.post_blast_and_promiscuity_filter /tmp/nxf.rYzp0iHBGp/./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.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered 201017995 > /tmp/nxf.rYzp0iHBGp/./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.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.filtered.FFPM /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir > /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo
* Running CMD: /usr/local/src/STAR-Fusion/FusionAnnotator/FusionAnnotator --genome_lib_dir /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir --annotate /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo > /tmp/nxf.rYzp0iHBGp/./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.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot --genome_lib_dir /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir
-done, see /tmp/nxf.rYzp0iHBGp/./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.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass --genome_lib_dir /tmp/nxf.rYzp0iHBGp/ctat_genome_lib_build_dir
-filter_likely_RT_artifacts: (pass: 1437, filtered: 7365)
* Running CMD: /usr/local/src/STAR-Fusion/util/filter_by_min_FFPM.pl /tmp/nxf.rYzp0iHBGp/./star-fusion.preliminary/star-fusion.fusion_candidates.preliminary.wSpliceInfo.wAnnot.annot_filter.pass.RTartifact.pass 0.00001
* Running CMD: cp /tmp/nxf.rYzp0iHBGp/./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.rYzp0iHBGp/ctat_genome_lib_build_dir > star-fusion.fusion_predictions.abridged.coding_effect.tsv
WARNING, no entry stored in dbm for [IGH-.g@-ext]
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WARNING, no entry stored in dbm for [ENSG00000172965.17]
WARNING, no entry stored in dbm for [ENSG00000204745.4]
WARNING, no entry stored in dbm for [ENSG00000267519.6]
WARNING, no entry stored in dbm for [ENSG00000229641.1]
WARNING, no entry stored in dbm for [ENSG00000240024.5]
WARNING, no entry stored in dbm for [ENSG00000245694.10]
WARNING, no entry stored in dbm for [ENSG00000281903.2]
WARNING, no entry stored in dbm for [ENSG00000288042.1]
WARNING, no entry stored in dbm for [ENSG00000239335.4]
WARNING, no entry stored in dbm for [ENSG00000234222.6]
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 [ENSG00000255666.7]
WARNING, no entry stored in dbm for [ENSG00000241288.8]
WARNING, no entry stored in dbm for [ENSG00000226453.2]
WARNING, no entry stored in dbm for [ENSG00000259719.6]
WARNING, no entry stored in dbm for [ENSG00000250891.2]
WARNING, no entry stored in dbm for [ENSG00000234634.2]
WARNING, no entry stored in dbm for [ENSG00000223382.5]
WARNING, no entry stored in dbm for [ENSG00000205611.5]
WARNING, no entry stored in dbm for [ENSG00000234766.2]
WARNING, no entry stored in dbm for [ENSG00000229981.8]
WARNING, no entry stored in dbm for [ENSG00000229981.8]
WARNING, no entry stored in dbm for [ENSG00000249550.7]
WARNING, no entry stored in dbm for [ENSG00000281404.2]
WARNING, no entry stored in dbm for [ENSG00000230142.2]
WARNING, no entry stored in dbm for [ENSG00000229723.1]
WARNING, no entry stored in dbm for [ENSG00000228393.4]
WARNING, no entry stored in dbm for [ENSG00000225269.3]
WARNING, no entry stored in dbm for [ENSG00000244342.5]
WARNING, no entry stored in dbm for [ENSG00000215190.9]
WARNING, no entry stored in dbm for [ENSG00000237854.3]
WARNING, no entry stored in dbm for [ENSG00000259129.6]
WARNING, no entry stored in dbm for [ENSG00000215483.11]
WARNING, no entry stored in dbm for [ENSG00000231028.9]
WARNING, no entry stored in dbm for [ENSG00000204177.10]
WARNING, no entry stored in dbm for [ENSG00000233652.1]
WARNING, no entry stored in dbm for [ENSG00000250686.2]
WARNING, no entry stored in dbm for [ENSG00000250686.2]
WARNING, no entry stored in dbm for [ENSG00000237978.6]
WARNING, no entry stored in dbm for [ENSG00000251138.7]
WARNING, no entry stored in dbm for [ENSG00000257386.1]
WARNING, no entry stored in dbm for [ENSG00000229127.2]
WARNING, no entry stored in dbm for [ENSG00000198590.12]
WARNING, no entry stored in dbm for [ENSG00000259673.6]
WARNING, no entry stored in dbm for [ENSG00000254034.2]
WARNING, no entry stored in dbm for [ENSG00000250326.2]
WARNING, no entry stored in dbm for [ENSG00000227018.1]
WARNING, no entry stored in dbm for [ENSG00000279329.1]
WARNING, no entry stored in dbm for [ENSG00000231721.7]
WARNING, no entry stored in dbm for [ENSG00000227619.3]
WARNING, no entry stored in dbm for [ENSG00000226810.3]
WARNING, no entry stored in dbm for [ENSG00000234996.4]
WARNING, no entry stored in dbm for [ENSG00000236373.2]
WARNING, no entry stored in dbm for [ENSG00000254369.6]
WARNING, no entry stored in dbm for [ENSG00000230330.1]
WARNING, no entry stored in dbm for [ENSG00000232916.1]
WARNING, no entry stored in dbm for [ENSG00000231471.1]
WARNING, no entry stored in dbm for [ENSG00000253954.3]
WARNING, no entry stored in dbm for [ENSG00000215283.3]
WARNING, no entry stored in dbm for [ENSG00000255391.1]
WARNING, no entry stored in dbm for [ENSG00000237005.1]
WARNING, no entry stored in dbm for [ENSG00000236012.2]
WARNING, no entry stored in dbm for [ENSG00000233299.1]
WARNING, no entry stored in dbm for [ENSG00000224007.1]
WARNING, no entry stored in dbm for [ENSG00000258741.4]
WARNING, no entry stored in dbm for [ENSG00000286591.1]
WARNING, no entry stored in dbm for [ENSG00000227252.2]
WARNING, no entry stored in dbm for [ENSG00000226002.1]
WARNING, no entry stored in dbm for [ENSG00000226002.1]
WARNING, no entry stored in dbm for [ENSG00000235421.1]
WARNING, no entry stored in dbm for [ENSG00000277053.4]
WARNING, no entry stored in dbm for [ENSG00000226930.1]
WARNING, no entry stored in dbm for [ENSG00000233910.1]
WARNING, no entry stored in dbm for [ENSG00000260254.1]
WARNING, no entry stored in dbm for [ENSG00000257277.2]
WARNING, no entry stored in dbm for [ENSG00000263716.1]
WARNING, no entry stored in dbm for [ENSG00000244055.2]
WARNING, no entry stored in dbm for [ENSG00000247498.10]
WARNING, no entry stored in dbm for [ENSG00000247498.10]
WARNING, no entry stored in dbm for [ENSG00000205333.5]
WARNING, no entry stored in dbm for [ENSG00000250959.2]
WARNING, no entry stored in dbm for [ENSG00000250959.2]
WARNING, no entry stored in dbm for [ENSG00000163081.4]
WARNING, no entry stored in dbm for [ENSG00000215302.8]
WARNING, no entry stored in dbm for [ENSG00000258891.1]
WARNING, no entry stored in dbm for [ENSG00000225137.1]
WARNING, no entry stored in dbm for [ENSG00000282870.1]
WARNING, no entry stored in dbm for [ENSG00000213468.7]
WARNING, no entry stored in dbm for [ENSG00000233064.2]
WARNING, no entry stored in dbm for [ENSG00000231806.3]
WARNING, no entry stored in dbm for [ENSG00000173295.8]
WARNING, no entry stored in dbm for [ENSG00000244699.1]
WARNING, no entry stored in dbm for [ENSG00000231528.3]
WARNING, no entry stored in dbm for [ENSG00000232615.4]
WARNING, no entry stored in dbm for [ENSG00000225271.1]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000267858.6]
WARNING, no entry stored in dbm for [ENSG00000230424.1]
WARNING, no entry stored in dbm for [ENSG00000230424.1]
WARNING, no entry stored in dbm for [ENSG00000236814.1]
WARNING, no entry stored in dbm for [ENSG00000255035.2]
WARNING, no entry stored in dbm for [ENSG00000235838.1]
WARNING, no entry stored in dbm for [ENSG00000258792.4]
WARNING, no entry stored in dbm for [ENSG00000279356.1]
WARNING, no entry stored in dbm for [ENSG00000224609.8]
WARNING, no entry stored in dbm for [ENSG00000205534.6]
WARNING, no entry stored in dbm for [ENSG00000231346.5]
WARNING, no entry stored in dbm for [ENSG00000231952.3]
WARNING, no entry stored in dbm for [ENSG00000235736.1]
WARNING, no entry stored in dbm for [ENSG00000266279.1]
WARNING, no entry stored in dbm for [ENSG00000234840.2]
WARNING, no entry stored in dbm for [ENSG00000224699.9]
WARNING, no entry stored in dbm for [ENSG00000236819.2]
WARNING, no entry stored in dbm for [ENSG00000200087.1]
WARNING, no entry stored in dbm for [ENSG00000200463.1]
WARNING, no entry stored in dbm for [ENSG00000235244.4]
WARNING, no entry stored in dbm for [ENSG00000241494.1]
WARNING, no entry stored in dbm for [ENSG00000278903.3]
WARNING, no entry stored in dbm for [ENSG00000100058.12]
WARNING, no entry stored in dbm for [ENSG00000236088.10]
WARNING, no entry stored in dbm for [ENSG00000215154.6]
WARNING, no entry stored in dbm for [ENSG00000201641.1]
WARNING, no entry stored in dbm for [ENSG00000216352.1]
WARNING, no entry stored in dbm for [ENSG00000260896.6]
WARNING, no entry stored in dbm for [ENSG00000225393.1]
WARNING, no entry stored in dbm for [ENSG00000224216.1]
WARNING, no entry stored in dbm for [ENSG00000164616.16]
WARNING, no entry stored in dbm for [ENSG00000214973.3]
WARNING, no entry stored in dbm for [ENSG00000272888.7]
WARNING, no entry stored in dbm for [ENSG00000234841.4]
WARNING, no entry stored in dbm for [ENSG00000251264.1]
WARNING, no entry stored in dbm for [ENSG00000286277.1]
WARNING, no entry stored in dbm for [ENSG00000230910.4]
WARNING, no entry stored in dbm for [ENSG00000246982.7]
WARNING, no entry stored in dbm for [ENSG00000279593.1]
WARNING, no entry stored in dbm for [ENSG00000254560.6]
WARNING, no entry stored in dbm for [ENSG00000223745.8]
WARNING, no entry stored in dbm for [ENSG00000223745.8]
WARNING, no entry stored in dbm for [ENSG00000240606.3]
WARNING, no entry stored in dbm for [ENSG00000285413.1]
WARNING, no entry stored in dbm for [ENSG00000228146.8]
WARNING, no entry stored in dbm for [ENSG00000203321.2]
WARNING, no entry stored in dbm for [ENSG00000287649.1]
WARNING, no entry stored in dbm for [ENSG00000227591.5]
WARNING, no entry stored in dbm for [ENSG00000251629.7]
WARNING, no entry stored in dbm for [ENSG00000280424.1]
WARNING, no entry stored in dbm for [ENSG00000216657.1]
WARNING, no entry stored in dbm for [ENSG00000215030.5]
WARNING, no entry stored in dbm for [ENSG00000248935.1]
WARNING, no entry stored in dbm for [ENSG00000268120.1]
WARNING, no entry stored in dbm for [ENSG00000255074.1]
WARNING, no entry stored in dbm for [ENSG00000233967.7]
WARNING, no entry stored in dbm for [ENSG00000244302.2]
WARNING, no entry stored in dbm for [ENSG00000234652.1]
WARNING, no entry stored in dbm for [ENSG00000249781.7]
WARNING, no entry stored in dbm for [ENSG00000197595.4]
WARNING, no entry stored in dbm for [ENSG00000224280.1]
WARNING, no entry stored in dbm for [ENSG00000288079.1]
WARNING, no entry stored in dbm for [ENSG00000200434.1]
WARNING, no entry stored in dbm for [ENSG00000286708.1]
WARNING, no entry stored in dbm for [ENSG00000255479.1]
WARNING, no entry stored in dbm for [ENSG00000267143.1]
WARNING, no entry stored in dbm for [ENSG00000188599.17]
WARNING, no entry stored in dbm for [ENSG00000267108.1]
WARNING, no entry stored in dbm for [ENSG00000246889.2]
WARNING, no entry stored in dbm for [ENSG00000261302.6]
WARNING, no entry stored in dbm for [ENSG00000237094.12]
WARNING, no entry stored in dbm for [ENSG00000227706.4]
WARNING, no entry stored in dbm for [ENSG00000285473.1]
WARNING, no entry stored in dbm for [ENSG00000270094.1]
WARNING, no entry stored in dbm for [ENSG00000287700.1]
WARNING, no entry stored in dbm for [ENSG00000232295.7]
WARNING, no entry stored in dbm for [ENSG00000170161.7]
WARNING, no entry stored in dbm for [ENSG00000231212.1]
WARNING, no entry stored in dbm for [ENSG00000170161.7]
WARNING, no entry stored in dbm for [ENSG00000231212.1]
WARNING, no entry stored in dbm for [ENSG00000287811.1]
WARNING, no entry stored in dbm for [ENSG00000231533.2]
WARNING, no entry stored in dbm for [ENSG00000235749.3]
WARNING, no entry stored in dbm for [ENSG00000232347.1]
WARNING, no entry stored in dbm for [ENSG00000233967.7]
WARNING, no entry stored in dbm for [ENSG00000237461.2]
WARNING, no entry stored in dbm for [ENSG00000279571.3]
WARNING, no entry stored in dbm for [ENSG00000228436.3]
WARNING, no entry stored in dbm for [ENSG00000234683.1]
WARNING, no entry stored in dbm for [ENSG00000219274.1]
WARNING, no entry stored in dbm for [ENSG00000287559.1]
WARNING, no entry stored in dbm for [ENSG00000278784.1]
WARNING, no entry stored in dbm for [ENSG00000217648.1]
WARNING, no entry stored in dbm for [ENSG00000258028.3]
WARNING, no entry stored in dbm for [ENSG00000271335.6]
WARNING, no entry stored in dbm for [ENSG00000259116.2]
WARNING, no entry stored in dbm for [ENSG00000231416.1]
WARNING, no entry stored in dbm for [ENSG00000288543.1]
WARNING, no entry stored in dbm for [ENSG00000278012.1]
WARNING, no entry stored in dbm for [ENSG00000232599.1]
WARNING, no entry stored in dbm for [ENSG00000274376.4]
WARNING, no entry stored in dbm for [ENSG00000229186.4]
WARNING, no entry stored in dbm for [ENSG00000270641.1]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000224016.2]
WARNING, no entry stored in dbm for [ENSG00000279558.1]
WARNING, no entry stored in dbm for [ENSG00000283453.2]
WARNING, no entry stored in dbm for [ENSG00000287394.1]
WARNING, no entry stored in dbm for [ENSG00000275839.1]
WARNING, no entry stored in dbm for [ENSG00000235065.1]
WARNING, no entry stored in dbm for [ENSG00000237188.5]
WARNING, no entry stored in dbm for [ENSG00000223612.3]
WARNING, no entry stored in dbm for [ENSG00000224216.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000277125.1]
WARNING, no entry stored in dbm for [ENSG00000214243.3]
WARNING, no entry stored in dbm for [ENSG00000249413.2]
WARNING, no entry stored in dbm for [ENSG00000235421.1]
WARNING, no entry stored in dbm for [ENSG00000265478.2]
WARNING, no entry stored in dbm for [ENSG00000228933.8]
WARNING, no entry stored in dbm for [ENSG00000277146.1]
WARNING, no entry stored in dbm for [ENSG00000170089.15]
WARNING, no entry stored in dbm for [ENSG00000261007.2]
WARNING, no entry stored in dbm for [ENSG00000250159.7]
WARNING, no entry stored in dbm for [ENSG00000270265.1]
WARNING, no entry stored in dbm for [ENSG00000274835.1]
WARNING, no entry stored in dbm for [ENSG00000258590.5]
WARNING, no entry stored in dbm for [ENSG00000286436.1]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000287129.1]
WARNING, no entry stored in dbm for [ENSG00000231646.6]
WARNING, no entry stored in dbm for [ENSG00000228303.1]
WARNING, no entry stored in dbm for [ENSG00000287985.1]
WARNING, no entry stored in dbm for [ENSG00000251652.1]
WARNING, no entry stored in dbm for [ENSG00000251391.5]
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 [ENSG00000253766.1]
WARNING, no entry stored in dbm for [ENSG00000239969.5]
WARNING, no entry stored in dbm for [ENSG00000267160.1]
WARNING, no entry stored in dbm for [ENSG00000262533.1]
WARNING, no entry stored in dbm for [ENSG00000254337.2]
WARNING, no entry stored in dbm for [ENSG00000287232.1]
WARNING, no entry stored in dbm for [ENSG00000287022.1]
WARNING, no entry stored in dbm for [ENSG00000287041.1]
WARNING, no entry stored in dbm for [ENSG00000227210.2]
WARNING, no entry stored in dbm for [ENSG00000227769.7]
WARNING, no entry stored in dbm for [ENSG00000229886.1]
WARNING, no entry stored in dbm for [ENSG00000247765.2]
WARNING, no entry stored in dbm for [ENSG00000258590.5]
WARNING, no entry stored in dbm for [ENSG00000249664.1]
WARNING, no entry stored in dbm for [ENSG00000259354.5]
WARNING, no entry stored in dbm for [ENSG00000250764.1]
WARNING, no entry stored in dbm for [ENSG00000251131.2]
WARNING, no entry stored in dbm for [ENSG00000259429.5]
WARNING, no entry stored in dbm for [ENSG00000272140.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000237807.4]
WARNING, no entry stored in dbm for [ENSG00000272800.3]
WARNING, no entry stored in dbm for [ENSG00000269032.1]
WARNING, no entry stored in dbm for [ENSG00000223508.5]
WARNING, no entry stored in dbm for [ENSG00000277146.1]
WARNING, no entry stored in dbm for [ENSG00000267437.1]
WARNING, no entry stored in dbm for [ENSG00000261670.1]
WARNING, no entry stored in dbm for [ENSG00000243829.1]
WARNING, no entry stored in dbm for [ENSG00000254363.6]
WARNING, no entry stored in dbm for [ENSG00000277977.1]
WARNING, no entry stored in dbm for [ENSG00000235253.1]
WARNING, no entry stored in dbm for [ENSG00000234352.9]
WARNING, no entry stored in dbm for [ENSG00000279764.1]
WARNING, no entry stored in dbm for [ENSG00000284649.1]
WARNING, no entry stored in dbm for [ENSG00000257403.2]
WARNING, no entry stored in dbm for [ENSG00000189149.12]
WARNING, no entry stored in dbm for [ENSG00000250258.1]
WARNING, no entry stored in dbm for [ENSG00000273569.1]
WARNING, no entry stored in dbm for [ENSG00000267166.5]
WARNING, no entry stored in dbm for [ENSG00000264497.1]
WARNING, no entry stored in dbm for [ENSG00000260086.3]
WARNING, no entry stored in dbm for [ENSG00000238165.1]
WARNING, no entry stored in dbm for [ENSG00000238041.3]
WARNING, no entry stored in dbm for [ENSG00000266897.1]
WARNING, no entry stored in dbm for [ENSG00000274712.2]
WARNING, no entry stored in dbm for [ENSG00000273314.1]
WARNING, no entry stored in dbm for [ENSG00000283662.1]
WARNING, no entry stored in dbm for [ENSG00000285704.1]
WARNING, no entry stored in dbm for [ENSG00000261996.1]
WARNING, no entry stored in dbm for [ENSG00000286067.1]
WARNING, no entry stored in dbm for [ENSG00000237298.10]
WARNING, no entry stored in dbm for [ENSG00000277423.1]
WARNING, no entry stored in dbm for [ENSG00000240216.7]
WARNING, no entry stored in dbm for [ENSG00000262943.7]
* STAR-Fusion complete. See output: /tmp/nxf.rYzp0iHBGp/./star-fusion.fusion_predictions.tsv (or .abridged.tsv version)