Done.
-parsing GTF file: /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.3W55byG9If/ctat_genome_lib_build_dir/ref_genome.fa.star.idx  --outSAMtype BAM SortedByCoordinate  --twopassMode None  --alignSJDBoverhangMin 10  --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705  --alignInsertionFlush Right   --alignMatesGapMax 100000  --alignIntronMax 100000  --outSAMattributes All  --readFilesIn /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.3W55byG9If/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.3W55byG9If/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
11:30:25 : INFO : Done.
-parsing GTF file: /tmp/nxf.3W55byG9If/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.3W55byG9If/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam

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[4510000]   -done parsing /tmp/nxf.3W55byG9If/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 26,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 163,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 683,
          ' ** passed ** ' => 5589,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 50,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 62,
          'low complexity anchor region' => 3,
          'per_id < 96' => 26546,
          'small anchor length' => 276,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 22,
          'exons hit < 2' => 31,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 16,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 21,
          'excessive soft clipping' => 36957,
          'num genes matched < 2' => 126
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.3W55byG9If/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[90000]   -fusion SPANNING read extraction for scaff: AC233699.1--TBC1D3

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[213000]   -fusion SPANNING read extraction for scaff: ADAP1--SNX8

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[1395000]   -fusion SPANNING read extraction for scaff: COL1A1--SLC45A4

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[206000]   -fusion SPANNING read extraction for scaff: COX19--SNX8

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[96000]   -fusion SPANNING read extraction for scaff: DNAAF5--AC009412.1

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[96000]   -fusion SPANNING read extraction for scaff: DNAAF5--FAM220A

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[36000]   -fusion SPANNING read extraction for scaff: GOLGA6L10--GOLGA2P6

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[371000]   -fusion SPANNING read extraction for scaff: INTS1--GLCCI1

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[80000]   
[81000]   -fusion SPANNING read extraction for scaff: MAD1L1--CHST12

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[51000]   -fusion SPANNING read extraction for scaff: MAD1L1--OR7E39P

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[759000]   
[760000]   -fusion SPANNING read extraction for scaff: PHF14--TNRC18

[1000]   
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[138000]   
[139000]   -fusion SPANNING read extraction for scaff: SUN1--GRIFIN

[1000]   
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[183000]   -fusion SPANNING read extraction for scaff: SUN1--LFNG

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[767000]   -fusion SPANNING read extraction for scaff: TNRC18--MAD1L1

[1000]   
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[22000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 12191,
          'lacks exon overlap' => 23762
        };
EM: Starting log likelihood: -5227.471400
EM: Round [1] log likelihood: -5227.441052
EM: Round [2] log likelihood: -5227.411318
EM: Round [3] log likelihood: -5227.382181
EM: Round [4] log likelihood: -5227.353621
EM: Round [5] log likelihood: -5227.325624
EM: Round [6] log likelihood: -5227.298171
EM: Round [7] log likelihood: -5227.271249
EM: Round [8] log likelihood: -5227.244842
EM: Round [9] log likelihood: -5227.218936
EM: Round [10] log likelihood: -5227.193518
EM: Round [11] log likelihood: -5227.168573
EM: Round [12] log likelihood: -5227.144090
EM: Round [13] log likelihood: -5227.120056
EM: Round [14] log likelihood: -5227.096460
EM: Round [15] log likelihood: -5227.073290
EM: Round [16] log likelihood: -5227.050536
EM: Round [17] log likelihood: -5227.028186
EM: Round [18] log likelihood: -5227.006231
EM: Round [19] log likelihood: -5226.984660
EM: Round [20] log likelihood: -5226.963466
EM: Round [21] log likelihood: -5226.942638
EM: Round [22] log likelihood: -5226.922167
EM: Round [23] log likelihood: -5226.902045
EM: Round [24] log likelihood: -5226.882265
EM: Round [25] log likelihood: -5226.862817
EM: Round [26] log likelihood: -5226.843694
EM: Round [27] log likelihood: -5226.824890
EM: Round [28] log likelihood: -5226.806395
EM: Round [29] log likelihood: -5226.788205
EM: Round [30] log likelihood: -5226.770311
EM: Round [31] log likelihood: -5226.752707
EM: Round [32] log likelihood: -5226.735387
EM: Round [33] log likelihood: -5226.718345
EM: Round [34] log likelihood: -5226.701574
EM: Round [35] log likelihood: -5226.685069
EM: Round [36] log likelihood: -5226.668825
EM: Round [37] log likelihood: -5226.652835
EM: Round [38] log likelihood: -5226.637095
EM: Round [39] log likelihood: -5226.621599
EM: Round [40] log likelihood: -5226.606342
EM: Round [41] log likelihood: -5226.591320
EM: Round [42] log likelihood: -5226.576527
EM: Round [43] log likelihood: -5226.561960
EM: Round [44] log likelihood: -5226.547612
EM: Round [45] log likelihood: -5226.533481
EM: Round [46] log likelihood: -5226.519562
EM: Round [47] log likelihood: -5226.505851
EM: Round [48] log likelihood: -5226.492343
EM: Round [49] log likelihood: -5226.479036
EM: Round [50] log likelihood: -5226.465924
EM: Round [51] log likelihood: -5226.453004
EM: Round [52] log likelihood: -5226.440274
EM: Round [53] log likelihood: -5226.427728
EM: Round [54] log likelihood: -5226.415364
EM: Round [55] log likelihood: -5226.403178
EM: Round [56] log likelihood: -5226.391168
EM: Round [57] log likelihood: -5226.379329
EM: Round [58] log likelihood: -5226.367659
EM: Round [59] log likelihood: -5226.356154
EM: Round [60] log likelihood: -5226.344812
EM: Round [61] log likelihood: -5226.333630
EM: Round [62] log likelihood: -5226.322605
EM: Round [63] log likelihood: -5226.311734
EM: Round [64] log likelihood: -5226.301015
EM: Round [65] log likelihood: -5226.290445
EM: Round [66] log likelihood: -5226.280020
EM: Round [67] log likelihood: -5226.269740
EM: Round [68] log likelihood: -5226.259601
EM: Round [69] log likelihood: -5226.249600
EM: Round [70] log likelihood: -5226.239736
EM: Round [71] log likelihood: -5226.230007
EM: Round [72] log likelihood: -5226.220409
EM: Round [73] log likelihood: -5226.210941
EM: Round [74] log likelihood: -5226.201601
EM: Round [75] log likelihood: -5226.192386
EM: Round [76] log likelihood: -5226.183295
EM: Round [77] log likelihood: -5226.174325
EM: Round [78] log likelihood: -5226.165475
EM: Round [79] log likelihood: -5226.156742
EM: Round [80] log likelihood: -5226.148124
EM: Round [81] log likelihood: -5226.139621
EM: Round [82] log likelihood: -5226.131229
EM: Round [83] log likelihood: -5226.122947
EM: Round [84] log likelihood: -5226.114774
EM: Round [85] log likelihood: -5226.106708
EM: Round [86] log likelihood: -5226.098746
EM: Round [87] log likelihood: -5226.090888
EM: Round [88] log likelihood: -5226.083132
EM: Round [89] log likelihood: -5226.075476
EM: Round [90] log likelihood: -5226.067919
EM: Round [91] log likelihood: -5226.060459
EM: Round [92] log likelihood: -5226.053094
EM: Round [93] log likelihood: -5226.045824
EM: Round [94] log likelihood: -5226.038646
EM: Round [95] log likelihood: -5226.031560
EM: Round [96] log likelihood: -5226.024564
EM: Round [97] log likelihood: -5226.017656
EM: Round [98] log likelihood: -5226.010836
EM: Round [99] log likelihood: -5226.004102
EM: Round [100] log likelihood: -5225.997453
EM: Round [101] log likelihood: -5225.990887
EM: Round [102] log likelihood: -5225.984403
EM: Round [103] log likelihood: -5225.978000
EM: Round [104] log likelihood: -5225.971678
EM: Round [105] log likelihood: -5225.965434
EM: Round [106] log likelihood: -5225.959267
EM: Round [107] log likelihood: -5225.953177
EM: Round [108] log likelihood: -5225.947163
EM: Round [109] log likelihood: -5225.941223
EM: Round [110] log likelihood: -5225.935356
EM: Round [111] log likelihood: -5225.929561
EM: Round [112] log likelihood: -5225.923837
EM: Round [113] log likelihood: -5225.918183
EM: Round [114] log likelihood: -5225.912599
EM: Round [115] log likelihood: -5225.907083
EM: Round [116] log likelihood: -5225.901634
EM: Round [117] log likelihood: -5225.896251
EM: Round [118] log likelihood: -5225.890934
EM: Round [119] log likelihood: -5225.885681
EM: Round [120] log likelihood: -5225.880491
EM: Round [121] log likelihood: -5225.875365
EM: Round [122] log likelihood: -5225.870300
EM: Round [123] log likelihood: -5225.865296
EM: Round [124] log likelihood: -5225.860353
EM: Round [125] log likelihood: -5225.855468
EM: Round [126] log likelihood: -5225.850642
EM: Round [127] log likelihood: -5225.845874
EM: Round [128] log likelihood: -5225.841163
EM: Round [129] log likelihood: -5225.836508
EM: Round [130] log likelihood: -5225.831909
EM: Round [131] log likelihood: -5225.827364
EM: Round [132] log likelihood: -5225.822873
EM: Round [133] log likelihood: -5225.818435
EM: Round [134] log likelihood: -5225.814050
EM: Round [135] log likelihood: -5225.809716
EM: Round [136] log likelihood: -5225.805434
EM: Round [137] log likelihood: -5225.801202
EM: Round [138] log likelihood: -5225.797020
EM: Round [139] log likelihood: -5225.792888
EM: Round [140] log likelihood: -5225.788803
EM: Round [141] log likelihood: -5225.784767
EM: Round [142] log likelihood: -5225.780778
EM: Round [143] log likelihood: -5225.776835
EM: Round [144] log likelihood: -5225.772938
EM: Round [145] log likelihood: -5225.769087
EM: Round [146] log likelihood: -5225.765281
EM: Round [147] log likelihood: -5225.761519
EM: Round [148] log likelihood: -5225.757801
EM: Round [149] log likelihood: -5225.754125
EM: Round [150] log likelihood: -5225.750493
EM: Round [151] log likelihood: -5225.746902
EM: Round [152] log likelihood: -5225.743353
EM: Round [153] log likelihood: -5225.739845
EM: Round [154] log likelihood: -5225.736377
EM: Round [155] log likelihood: -5225.732949
EM: Round [156] log likelihood: -5225.729561
EM: Round [157] log likelihood: -5225.726212
EM: Round [158] log likelihood: -5225.722901
EM: Round [159] log likelihood: -5225.719628
EM: Round [160] log likelihood: -5225.716392
EM: Round [161] log likelihood: -5225.713194
EM: Round [162] log likelihood: -5225.710032
EM: Round [163] log likelihood: -5225.706906
EM: Round [164] log likelihood: -5225.703816
EM: Round [165] log likelihood: -5225.700761
EM: Round [166] log likelihood: -5225.697741
EM: Round [167] log likelihood: -5225.694755
EM: Round [168] log likelihood: -5225.691803
EM: Round [169] log likelihood: -5225.688884
EM: Round [170] log likelihood: -5225.685999
EM: Round [171] log likelihood: -5225.683146
EM: Round [172] log likelihood: -5225.680326
EM: Round [173] log likelihood: -5225.677538
EM: Round [174] log likelihood: -5225.674781
EM: Round [175] log likelihood: -5225.672055
EM: Round [176] log likelihood: -5225.669359
EM: Round [177] log likelihood: -5225.666695
EM: Round [178] log likelihood: -5225.664060
EM: Round [179] log likelihood: -5225.661455
EM: Round [180] log likelihood: -5225.658879
EM: Round [181] log likelihood: -5225.656332
EM: Round [182] log likelihood: -5225.653813
EM: Round [183] log likelihood: -5225.651323
EM: Round [184] log likelihood: -5225.648861
EM: Round [185] log likelihood: -5225.646426
EM: Round [186] log likelihood: -5225.644018
EM: Round [187] log likelihood: -5225.641638
EM: Round [188] log likelihood: -5225.639284
EM: Round [189] log likelihood: -5225.636956
EM: Round [190] log likelihood: -5225.634654
EM: Round [191] log likelihood: -5225.632378
EM: Round [192] log likelihood: -5225.630127
EM: Round [193] log likelihood: -5225.627901
EM: Round [194] log likelihood: -5225.625700
EM: Round [195] log likelihood: -5225.623523
EM: Round [196] log likelihood: -5225.621370
EM: Round [197] log likelihood: -5225.619242
EM: Round [198] log likelihood: -5225.617136
EM: Round [199] log likelihood: -5225.615055
EM: Round [200] log likelihood: -5225.612996
EM: Round [201] log likelihood: -5225.610960
EM: Round [202] log likelihood: -5225.608946
EM: Round [203] log likelihood: -5225.606955
EM: Round [204] log likelihood: -5225.604986
EM: Round [205] log likelihood: -5225.603038
EM: Round [206] log likelihood: -5225.601112
EM: Round [207] log likelihood: -5225.599207
EM: Round [208] log likelihood: -5225.597323
EM: Round [209] log likelihood: -5225.595460
EM: Round [210] log likelihood: -5225.593617
EM: Round [211] log likelihood: -5225.591794
EM: Round [212] log likelihood: -5225.589992
EM: Round [213] log likelihood: -5225.588209
EM: Round [214] log likelihood: -5225.586446
EM: Round [215] log likelihood: -5225.584702
EM: Round [216] log likelihood: -5225.582977
EM: Round [217] log likelihood: -5225.581271
EM: Round [218] log likelihood: -5225.579584
EM: Round [219] log likelihood: -5225.577915
EM: Round [220] log likelihood: -5225.576265
EM: Round [221] log likelihood: -5225.574632
EM: Round [222] log likelihood: -5225.573017
EM: Round [223] log likelihood: -5225.571420
EM: Round [224] log likelihood: -5225.569840
EM: Round [225] log likelihood: -5225.568278
EM: Round [226] log likelihood: -5225.566733
EM: Round [227] log likelihood: -5225.565204
EM: Round [228] log likelihood: -5225.563692
EM: Round [229] log likelihood: -5225.562196
EM: Round [230] log likelihood: -5225.560717
EM: Round [231] log likelihood: -5225.559254
EM: Round [232] log likelihood: -5225.557807
EM: Round [233] log likelihood: -5225.556375
EM: Round [234] log likelihood: -5225.554959
EM: Round [235] log likelihood: -5225.553558
EM: Round [236] log likelihood: -5225.552173
EM: Round [237] log likelihood: -5225.550802
EM: Round [238] log likelihood: -5225.549447
EM: Round [239] log likelihood: -5225.548106
EM: Round [240] log likelihood: -5225.546779
EM: Round [241] log likelihood: -5225.545467
EM: Round [242] log likelihood: -5225.544169
EM: Round [243] log likelihood: -5225.542885
EM: Round [244] log likelihood: -5225.541615
EM: Round [245] log likelihood: -5225.540359
EM: Round [246] log likelihood: -5225.539116
EM: Round [247] log likelihood: -5225.537886
EM: Round [248] log likelihood: -5225.536670
EM: Round [249] log likelihood: -5225.535467
EM: Round [250] log likelihood: -5225.534277
EM: Round [251] log likelihood: -5225.533100
EM: Round [252] log likelihood: -5225.531935
EM: Round [253] log likelihood: -5225.530783
EM: Round [254] log likelihood: -5225.529644
EM: Round [255] log likelihood: -5225.528516
EM: Round [256] log likelihood: -5225.527401
EM: Round [257] log likelihood: -5225.526298
EM: Round [258] log likelihood: -5225.525206
EM: Round [259] log likelihood: -5225.524127
EM: Round [260] log likelihood: -5225.523059
EM: Round [261] log likelihood: -5225.522002
EM: Round [262] log likelihood: -5225.520957
EM: Round [263] log likelihood: -5225.519923
EM: Round [264] log likelihood: -5225.518900
EM: Round [265] log likelihood: -5225.517887
EM: Round [266] log likelihood: -5225.516886
EM: Round [267] log likelihood: -5225.515896
EM: Round [268] log likelihood: -5225.514916
EM: Round [269] log likelihood: -5225.513947
EM: Round [270] log likelihood: -5225.512987
EM: Round [271] log likelihood: -5225.512039
EM: Round [272] log likelihood: -5225.511100
EM: Round [273] log likelihood: -5225.510171
EM: Round [274] log likelihood: -5225.509253
EM: Round [275] log likelihood: -5225.508344
EM: Round [276] log likelihood: -5225.507445
EM: Round [277] log likelihood: -5225.506555
EM: Round [278] log likelihood: -5225.505675
EM: Round [279] log likelihood: -5225.504805
EM: Round [280] log likelihood: -5225.503943
EM: Round [281] log likelihood: -5225.503091
EM: Round [282] log likelihood: -5225.502248
EM: Round [283] log likelihood: -5225.501414
EM: Round [284] log likelihood: -5225.500588
EM: Round [285] log likelihood: -5225.499772
EM: Round [286] log likelihood: -5225.498964
EM: Round [287] log likelihood: -5225.498165
EM: Round [288] log likelihood: -5225.497374
EM: Round [289] log likelihood: -5225.496592
EM: Round [290] log likelihood: -5225.495818
EM: Round [291] log likelihood: -5225.495053
EM: Round [292] log likelihood: -5225.494295
EM: Round [293] log likelihood: -5225.493546
EM: Round [294] log likelihood: -5225.492804
EM: Round [295] log likelihood: -5225.492070
EM: Round [296] log likelihood: -5225.491344
EM: Round [297] log likelihood: -5225.490626
EM: Round [298] log likelihood: -5225.489916
EM: Round [299] log likelihood: -5225.489213
EM: Round [300] log likelihood: -5225.488517
EM: Round [301] log likelihood: -5225.487829
EM: Round [302] log likelihood: -5225.487148
EM: Round [303] log likelihood: -5225.486475
EM: Round [304] log likelihood: -5225.485808
EM: Round [305] log likelihood: -5225.485149
EM: Round [306] log likelihood: -5225.484496
EM: Round [307] log likelihood: -5225.483851
EM: Round [308] log likelihood: -5225.483212
EM: Round [309] log likelihood: -5225.482580
EM: Round [310] log likelihood: -5225.481955
EM: Round [311] log likelihood: -5225.481336
EM: Round [312] log likelihood: -5225.480724
EM: Round [313] log likelihood: -5225.480119
EM: Round [314] log likelihood: -5225.479519
EM: Round [315] log likelihood: -5225.478927
EM: Round [316] log likelihood: -5225.478340
EM: Round [317] log likelihood: -5225.477760
EM: Round [318] log likelihood: -5225.477185
EM: Round [319] log likelihood: -5225.476617
EM: Round [320] log likelihood: -5225.476055
EM: Round [321] log likelihood: -5225.475499
EM: Round [322] log likelihood: -5225.474949
EM: Round [323] log likelihood: -5225.474404
EM: Round [324] log likelihood: -5225.473865
EM: Round [325] log likelihood: -5225.473332
EM: Round [326] log likelihood: -5225.472805
EM: Round [327] log likelihood: -5225.472283
EM: Round [328] log likelihood: -5225.471766
EM: Round [329] log likelihood: -5225.471255
EM: Round [330] log likelihood: -5225.470750
EM: Round [331] log likelihood: -5225.470250
EM: Round [332] log likelihood: -5225.469755
EM: Round [333] log likelihood: -5225.469265
EM: Round [334] log likelihood: -5225.468780
EM: Round [335] log likelihood: -5225.468301
EM: Round [336] log likelihood: -5225.467826
EM: Round [337] log likelihood: -5225.467357
EM: Round [338] log likelihood: -5225.466893
EM: Round [339] log likelihood: -5225.466433
EM: Round [340] log likelihood: -5225.465978
EM: Round [341] log likelihood: -5225.465528
EM: Round [342] log likelihood: -5225.465083
EM: Round [343] log likelihood: -5225.464642
EM: Round [344] log likelihood: -5225.464207
EM: Round [345] log likelihood: -5225.463775
EM: Round [346] log likelihood: -5225.463349
EM: Round [347] log likelihood: -5225.462926
EM: Round [348] log likelihood: -5225.462508
EM: Round [349] log likelihood: -5225.462095
EM: Round [350] log likelihood: -5225.461686
EM: Round [351] log likelihood: -5225.461281
EM: Round [352] log likelihood: -5225.460881
EM: Round [353] log likelihood: -5225.460484
EM: Round [354] log likelihood: -5225.460092
EM: Round [355] log likelihood: -5225.459704
EM: Round [356] log likelihood: -5225.459320
EM: Round [357] log likelihood: -5225.458940
EM: Round [358] log likelihood: -5225.458564
EM: Round [359] log likelihood: -5225.458192
EM: Round [360] log likelihood: -5225.457824
EM: Round [361] log likelihood: -5225.457460
EM: Round [362] log likelihood: -5225.457100
EM: Round [363] log likelihood: -5225.456743
EM: Round [364] log likelihood: -5225.456390
EM: Round [365] log likelihood: -5225.456041
EM: Round [366] log likelihood: -5225.455695
EM: Round [367] log likelihood: -5225.455354
EM: Round [368] log likelihood: -5225.455015
EM: Round [369] log likelihood: -5225.454681
EM: Round [370] log likelihood: -5225.454349
EM: Round [371] log likelihood: -5225.454022
EM: Round [372] log likelihood: -5225.453697
EM: Round [373] log likelihood: -5225.453376
EM: Round [374] log likelihood: -5225.453059
EM: Round [375] log likelihood: -5225.452745
EM: Round [376] log likelihood: -5225.452434
EM: Round [377] log likelihood: -5225.452126
EM: Round [378] log likelihood: -5225.451822
EM: Round [379] log likelihood: -5225.451520
EM: Round [380] log likelihood: -5225.451222
EM: Round [381] log likelihood: -5225.450927
EM: Round [382] log likelihood: -5225.450635
EM: Round [383] log likelihood: -5225.450347
EM: Round [384] log likelihood: -5225.450061
EM: Round [385] log likelihood: -5225.449778
EM: Round [386] log likelihood: -5225.449498
EM: Round [387] log likelihood: -5225.449221
EM: Round [388] log likelihood: -5225.448947
EM: Round [389] log likelihood: -5225.448676
EM: Round [390] log likelihood: -5225.448408
EM: Round [391] log likelihood: -5225.448142
EM: Round [392] log likelihood: -5225.447880
EM: Round [393] log likelihood: -5225.447620
EM: Round [394] log likelihood: -5225.447362
EM: Round [395] log likelihood: -5225.447108
EM: Round [396] log likelihood: -5225.446856
EM: Round [397] log likelihood: -5225.446607
EM: Round [398] log likelihood: -5225.446360
EM: Round [399] log likelihood: -5225.446116
EM: Round [400] log likelihood: -5225.445875
EM: Round [401] log likelihood: -5225.445636
EM: Round [402] log likelihood: -5225.445399
EM: Round [403] log likelihood: -5225.445165
EM: Round [404] log likelihood: -5225.444934
EM: Round [405] log likelihood: -5225.444704
EM: Round [406] log likelihood: -5225.444478
EM: Round [407] log likelihood: -5225.444253
EM: Round [408] log likelihood: -5225.444031
EM: Round [409] log likelihood: -5225.443812
EM: Round [410] log likelihood: -5225.443594
EM: Round [411] log likelihood: -5225.443379
EM: Round [412] log likelihood: -5225.443166
EM: Round [413] log likelihood: -5225.442955
EM: Round [414] log likelihood: -5225.442747
EM: Round [415] log likelihood: -5225.442541
EM: Round [416] log likelihood: -5225.442337
EM: Round [417] log likelihood: -5225.442135
EM: Round [418] log likelihood: -5225.441935
EM: Round [419] log likelihood: -5225.441737
EM: Round [420] log likelihood: -5225.441541
EM: Round [421] log likelihood: -5225.441348
EM: Round [422] log likelihood: -5225.441156
EM: Round [423] log likelihood: -5225.440966
EM: Round [424] log likelihood: -5225.440779
EM: Round [425] log likelihood: -5225.440593
EM: Round [426] log likelihood: -5225.440409
EM: Round [427] log likelihood: -5225.440227
EM: Round [428] log likelihood: -5225.440047
EM: Round [429] log likelihood: -5225.439869
EM: Round [430] log likelihood: -5225.439693
EM: Round [431] log likelihood: -5225.439518
EM: Round [432] log likelihood: -5225.439346
EM: Round [433] log likelihood: -5225.439175
EM: Round [434] log likelihood: -5225.439006
EM: Round [435] log likelihood: -5225.438839
EM: Round [436] log likelihood: -5225.438673
EM: Round [437] log likelihood: -5225.438510
EM: Round [438] log likelihood: -5225.438348
EM: Round [439] log likelihood: -5225.438187
EM: Round [440] log likelihood: -5225.438029
EM: Round [441] log likelihood: -5225.437872
EM: Round [442] log likelihood: -5225.437716
EM: Round [443] log likelihood: -5225.437562
EM: Round [444] log likelihood: -5225.437410
EM: Round [445] log likelihood: -5225.437260
EM: Round [446] log likelihood: -5225.437111
EM: Round [447] log likelihood: -5225.436963
EM: Round [448] log likelihood: -5225.436817
EM: Round [449] log likelihood: -5225.436673
EM: Round [450] log likelihood: -5225.436530
EM: Round [451] log likelihood: -5225.436389
EM: Round [452] log likelihood: -5225.436249
EM: Round [453] log likelihood: -5225.436110
EM: Round [454] log likelihood: -5225.435973
EM: Round [455] log likelihood: -5225.435838
EM: Round [456] log likelihood: -5225.435704
EM: Round [457] log likelihood: -5225.435571
EM: Round [458] log likelihood: -5225.435439
EM: Round [459] log likelihood: -5225.435309
EM: Round [460] log likelihood: -5225.435181
EM: Round [461] log likelihood: -5225.435053
EM: Round [462] log likelihood: -5225.434927
EM: Round [463] log likelihood: -5225.434803
EM: Round [464] log likelihood: -5225.434679
EM: Round [465] log likelihood: -5225.434557
EM: Round [466] log likelihood: -5225.434436
EM: Round [467] log likelihood: -5225.434317
EM: Round [468] log likelihood: -5225.434198
EM: Round [469] log likelihood: -5225.434081
EM: Round [470] log likelihood: -5225.433966
EM: Round [471] log likelihood: -5225.433851
EM: Round [472] log likelihood: -5225.433737
EM: Round [473] log likelihood: -5225.433625
EM: Round [474] log likelihood: -5225.433514
EM: Round [475] log likelihood: -5225.433404
EM: Round [476] log likelihood: -5225.433295
EM: Round [477] log likelihood: -5225.433188
EM: Round [478] log likelihood: -5225.433081
EM: Round [479] log likelihood: -5225.432976
EM: Round [480] log likelihood: -5225.432871
EM: Round [481] log likelihood: -5225.432768
EM: Round [482] log likelihood: -5225.432666
EM: Round [483] log likelihood: -5225.432565
EM: Round [484] log likelihood: -5225.432465
EM: Round [485] log likelihood: -5225.432366
EM: Stopping iterations at round 485 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.3W55byG9If/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.3W55byG9If/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.3W55byG9If/fi_workdir/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3724.202051
EM: Round [1] log likelihood: -3724.202051
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 293843791
Warning - not locating file: /tmp/nxf.3W55byG9If/1173_G2E_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000261499.2]
WARNING, no entry stored in dbm for [ENSG00000273252.1]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
ls: cannot access 'IGV_inputs': No such file or directory