Done.
-parsing GTF file: /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.fX3YIVekf1/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.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.fX3YIVekf1/fi_workdir/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.fX3YIVekf1/fi_workdir/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.star.sortedByCoord.out.bam
10:32:07 : INFO : Done.
-parsing GTF file: /tmp/nxf.fX3YIVekf1/fi_workdir/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.gtf
-parsing /tmp/nxf.fX3YIVekf1/fi_workdir/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam

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[1280000]   -done parsing /tmp/nxf.fX3YIVekf1/fi_workdir/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 9416,
          'exons hit < 2' => 3,
          'small anchor length' => 161,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 6,
          'seq-similar region overlap' => 1,
          ' ** passed ** ' => 23280,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 29,
          'low complexity anchor region' => 24,
          'excessive soft clipping' => 10389,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 57,
          'num genes matched < 2' => 12
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.fX3YIVekf1/fi_workdir/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[21000]   -fusion SPANNING read extraction for scaff: AC097532.3--GPR39

[1000]   -fusion SPANNING read extraction for scaff: ATCAY--AC068025.1

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

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[628000]   
[629000]   
[630000]   
[631000]   
[632000]   -fusion SPANNING read extraction for scaff: EWSR1--FLI1

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[71000]   
[72000]   -fusion SPANNING read extraction for scaff: NUFIP2--AL133167.1

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[24000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[44000]   
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[48000]   
[49000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[34000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[38000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[30000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[34000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[42000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[104000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[13000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[27000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[109000]   -fusion SPANNING read extraction for scaff: ZCCHC8--RSRC2
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 1169,
          'seq similar region alignment' => 37083
        };
EM: Starting log likelihood: -5948.838667
EM: Round [1] log likelihood: -5948.829128
EM: Round [2] log likelihood: -5948.819689
EM: Round [3] log likelihood: -5948.810349
EM: Round [4] log likelihood: -5948.801105
EM: Round [5] log likelihood: -5948.791955
EM: Round [6] log likelihood: -5948.782899
EM: Round [7] log likelihood: -5948.773933
EM: Round [8] log likelihood: -5948.765056
EM: Round [9] log likelihood: -5948.756267
EM: Round [10] log likelihood: -5948.747563
EM: Round [11] log likelihood: -5948.738944
EM: Round [12] log likelihood: -5948.730408
EM: Round [13] log likelihood: -5948.721953
EM: Round [14] log likelihood: -5948.713578
EM: Round [15] log likelihood: -5948.705282
EM: Round [16] log likelihood: -5948.697062
EM: Round [17] log likelihood: -5948.688919
EM: Round [18] log likelihood: -5948.680850
EM: Round [19] log likelihood: -5948.672853
EM: Round [20] log likelihood: -5948.664929
EM: Round [21] log likelihood: -5948.657076
EM: Round [22] log likelihood: -5948.649292
EM: Round [23] log likelihood: -5948.641577
EM: Round [24] log likelihood: -5948.633928
EM: Round [25] log likelihood: -5948.626347
EM: Round [26] log likelihood: -5948.618830
EM: Round [27] log likelihood: -5948.611377
EM: Round [28] log likelihood: -5948.603987
EM: Round [29] log likelihood: -5948.596660
EM: Round [30] log likelihood: -5948.589393
EM: Round [31] log likelihood: -5948.582187
EM: Round [32] log likelihood: -5948.575040
EM: Round [33] log likelihood: -5948.567951
EM: Round [34] log likelihood: -5948.560919
EM: Round [35] log likelihood: -5948.553945
EM: Round [36] log likelihood: -5948.547026
EM: Round [37] log likelihood: -5948.540162
EM: Round [38] log likelihood: -5948.533352
EM: Round [39] log likelihood: -5948.526595
EM: Round [40] log likelihood: -5948.519891
EM: Round [41] log likelihood: -5948.513238
EM: Round [42] log likelihood: -5948.506637
EM: Round [43] log likelihood: -5948.500086
EM: Round [44] log likelihood: -5948.493585
EM: Round [45] log likelihood: -5948.487132
EM: Round [46] log likelihood: -5948.480728
EM: Round [47] log likelihood: -5948.474372
EM: Round [48] log likelihood: -5948.468062
EM: Round [49] log likelihood: -5948.461799
EM: Round [50] log likelihood: -5948.455581
EM: Round [51] log likelihood: -5948.449408
EM: Round [52] log likelihood: -5948.443280
EM: Round [53] log likelihood: -5948.437196
EM: Round [54] log likelihood: -5948.431155
EM: Round [55] log likelihood: -5948.425156
EM: Round [56] log likelihood: -5948.419200
EM: Round [57] log likelihood: -5948.413286
EM: Round [58] log likelihood: -5948.407412
EM: Round [59] log likelihood: -5948.401579
EM: Round [60] log likelihood: -5948.395786
EM: Round [61] log likelihood: -5948.390033
EM: Round [62] log likelihood: -5948.384319
EM: Round [63] log likelihood: -5948.378643
EM: Round [64] log likelihood: -5948.373006
EM: Round [65] log likelihood: -5948.367406
EM: Round [66] log likelihood: -5948.361843
EM: Round [67] log likelihood: -5948.356317
EM: Round [68] log likelihood: -5948.350827
EM: Round [69] log likelihood: -5948.345373
EM: Round [70] log likelihood: -5948.339954
EM: Round [71] log likelihood: -5948.334571
EM: Round [72] log likelihood: -5948.329222
EM: Round [73] log likelihood: -5948.323907
EM: Round [74] log likelihood: -5948.318626
EM: Round [75] log likelihood: -5948.313378
EM: Round [76] log likelihood: -5948.308163
EM: Round [77] log likelihood: -5948.302981
EM: Round [78] log likelihood: -5948.297832
EM: Round [79] log likelihood: -5948.292714
EM: Round [80] log likelihood: -5948.287627
EM: Round [81] log likelihood: -5948.282572
EM: Round [82] log likelihood: -5948.277548
EM: Round [83] log likelihood: -5948.272554
EM: Round [84] log likelihood: -5948.267590
EM: Round [85] log likelihood: -5948.262656
EM: Round [86] log likelihood: -5948.257751
EM: Round [87] log likelihood: -5948.252876
EM: Round [88] log likelihood: -5948.248030
EM: Round [89] log likelihood: -5948.243212
EM: Round [90] log likelihood: -5948.238422
EM: Round [91] log likelihood: -5948.233661
EM: Round [92] log likelihood: -5948.228927
EM: Round [93] log likelihood: -5948.224220
EM: Round [94] log likelihood: -5948.219540
EM: Round [95] log likelihood: -5948.214888
EM: Round [96] log likelihood: -5948.210261
EM: Round [97] log likelihood: -5948.205661
EM: Round [98] log likelihood: -5948.201087
EM: Round [99] log likelihood: -5948.196539
EM: Round [100] log likelihood: -5948.192016
EM: Round [101] log likelihood: -5948.187519
EM: Round [102] log likelihood: -5948.183046
EM: Round [103] log likelihood: -5948.178598
EM: Round [104] log likelihood: -5948.174174
EM: Round [105] log likelihood: -5948.169775
EM: Round [106] log likelihood: -5948.165400
EM: Round [107] log likelihood: -5948.161048
EM: Round [108] log likelihood: -5948.156720
EM: Round [109] log likelihood: -5948.152415
EM: Round [110] log likelihood: -5948.148133
EM: Round [111] log likelihood: -5948.143875
EM: Round [112] log likelihood: -5948.139638
EM: Round [113] log likelihood: -5948.135424
EM: Round [114] log likelihood: -5948.131233
EM: Round [115] log likelihood: -5948.127063
EM: Round [116] log likelihood: -5948.122915
EM: Round [117] log likelihood: -5948.118789
EM: Round [118] log likelihood: -5948.114683
EM: Round [119] log likelihood: -5948.110600
EM: Round [120] log likelihood: -5948.106537
EM: Round [121] log likelihood: -5948.102495
EM: Round [122] log likelihood: -5948.098473
EM: Round [123] log likelihood: -5948.094472
EM: Round [124] log likelihood: -5948.090491
EM: Round [125] log likelihood: -5948.086530
EM: Round [126] log likelihood: -5948.082590
EM: Round [127] log likelihood: -5948.078668
EM: Round [128] log likelihood: -5948.074767
EM: Round [129] log likelihood: -5948.070884
EM: Round [130] log likelihood: -5948.067021
EM: Round [131] log likelihood: -5948.063177
EM: Round [132] log likelihood: -5948.059351
EM: Round [133] log likelihood: -5948.055545
EM: Round [134] log likelihood: -5948.051756
EM: Round [135] log likelihood: -5948.047986
EM: Round [136] log likelihood: -5948.044235
EM: Round [137] log likelihood: -5948.040501
EM: Round [138] log likelihood: -5948.036785
EM: Round [139] log likelihood: -5948.033087
EM: Round [140] log likelihood: -5948.029407
EM: Round [141] log likelihood: -5948.025744
EM: Round [142] log likelihood: -5948.022098
EM: Round [143] log likelihood: -5948.018470
EM: Round [144] log likelihood: -5948.014858
EM: Round [145] log likelihood: -5948.011264
EM: Round [146] log likelihood: -5948.007686
EM: Round [147] log likelihood: -5948.004124
EM: Round [148] log likelihood: -5948.000579
EM: Round [149] log likelihood: -5947.997051
EM: Round [150] log likelihood: -5947.993538
EM: Round [151] log likelihood: -5947.990042
EM: Round [152] log likelihood: -5947.986561
EM: Round [153] log likelihood: -5947.983097
EM: Round [154] log likelihood: -5947.979648
EM: Round [155] log likelihood: -5947.976214
EM: Round [156] log likelihood: -5947.972796
EM: Round [157] log likelihood: -5947.969394
EM: Round [158] log likelihood: -5947.966006
EM: Round [159] log likelihood: -5947.962634
EM: Round [160] log likelihood: -5947.959276
EM: Round [161] log likelihood: -5947.955934
EM: Round [162] log likelihood: -5947.952606
EM: Round [163] log likelihood: -5947.949292
EM: Round [164] log likelihood: -5947.945993
EM: Round [165] log likelihood: -5947.942709
EM: Round [166] log likelihood: -5947.939439
EM: Round [167] log likelihood: -5947.936183
EM: Round [168] log likelihood: -5947.932941
EM: Round [169] log likelihood: -5947.929713
EM: Round [170] log likelihood: -5947.926498
EM: Round [171] log likelihood: -5947.923298
EM: Round [172] log likelihood: -5947.920111
EM: Round [173] log likelihood: -5947.916938
EM: Round [174] log likelihood: -5947.913778
EM: Round [175] log likelihood: -5947.910632
EM: Round [176] log likelihood: -5947.907498
EM: Round [177] log likelihood: -5947.904378
EM: Round [178] log likelihood: -5947.901271
EM: Round [179] log likelihood: -5947.898177
EM: Round [180] log likelihood: -5947.895096
EM: Round [181] log likelihood: -5947.892027
EM: Round [182] log likelihood: -5947.888971
EM: Round [183] log likelihood: -5947.885928
EM: Round [184] log likelihood: -5947.882897
EM: Round [185] log likelihood: -5947.879879
EM: Round [186] log likelihood: -5947.876873
EM: Round [187] log likelihood: -5947.873879
EM: Round [188] log likelihood: -5947.870898
EM: Round [189] log likelihood: -5947.867928
EM: Round [190] log likelihood: -5947.864971
EM: Round [191] log likelihood: -5947.862025
EM: Round [192] log likelihood: -5947.859091
EM: Round [193] log likelihood: -5947.856169
EM: Round [194] log likelihood: -5947.853258
EM: Round [195] log likelihood: -5947.850359
EM: Round [196] log likelihood: -5947.847472
EM: Round [197] log likelihood: -5947.844596
EM: Round [198] log likelihood: -5947.841731
EM: Round [199] log likelihood: -5947.838877
EM: Round [200] log likelihood: -5947.836035
EM: Round [201] log likelihood: -5947.833204
EM: Round [202] log likelihood: -5947.830384
EM: Round [203] log likelihood: -5947.827574
EM: Round [204] log likelihood: -5947.824776
EM: Round [205] log likelihood: -5947.821989
EM: Round [206] log likelihood: -5947.819212
EM: Round [207] log likelihood: -5947.816446
EM: Round [208] log likelihood: -5947.813690
EM: Round [209] log likelihood: -5947.810945
EM: Round [210] log likelihood: -5947.808211
EM: Round [211] log likelihood: -5947.805486
EM: Round [212] log likelihood: -5947.802773
EM: Round [213] log likelihood: -5947.800069
EM: Round [214] log likelihood: -5947.797376
EM: Round [215] log likelihood: -5947.794692
EM: Round [216] log likelihood: -5947.792019
EM: Round [217] log likelihood: -5947.789356
EM: Round [218] log likelihood: -5947.786703
EM: Round [219] log likelihood: -5947.784059
EM: Round [220] log likelihood: -5947.781425
EM: Round [221] log likelihood: -5947.778802
EM: Round [222] log likelihood: -5947.776187
EM: Round [223] log likelihood: -5947.773583
EM: Round [224] log likelihood: -5947.770988
EM: Round [225] log likelihood: -5947.768402
EM: Round [226] log likelihood: -5947.765826
EM: Round [227] log likelihood: -5947.763259
EM: Round [228] log likelihood: -5947.760702
EM: Round [229] log likelihood: -5947.758154
EM: Round [230] log likelihood: -5947.755615
EM: Round [231] log likelihood: -5947.753085
EM: Round [232] log likelihood: -5947.750565
EM: Round [233] log likelihood: -5947.748053
EM: Round [234] log likelihood: -5947.745550
EM: Round [235] log likelihood: -5947.743057
EM: Round [236] log likelihood: -5947.740572
EM: Round [237] log likelihood: -5947.738096
EM: Round [238] log likelihood: -5947.735629
EM: Round [239] log likelihood: -5947.733170
EM: Round [240] log likelihood: -5947.730720
EM: Round [241] log likelihood: -5947.728279
EM: Round [242] log likelihood: -5947.725846
EM: Round [243] log likelihood: -5947.723422
EM: Round [244] log likelihood: -5947.721006
EM: Round [245] log likelihood: -5947.718599
EM: Round [246] log likelihood: -5947.716200
EM: Round [247] log likelihood: -5947.713810
EM: Round [248] log likelihood: -5947.711427
EM: Round [249] log likelihood: -5947.709053
EM: Round [250] log likelihood: -5947.706687
EM: Round [251] log likelihood: -5947.704329
EM: Round [252] log likelihood: -5947.701980
EM: Round [253] log likelihood: -5947.699638
EM: Round [254] log likelihood: -5947.697304
EM: Round [255] log likelihood: -5947.694978
EM: Round [256] log likelihood: -5947.692660
EM: Round [257] log likelihood: -5947.690350
EM: Round [258] log likelihood: -5947.688048
EM: Round [259] log likelihood: -5947.685754
EM: Round [260] log likelihood: -5947.683467
EM: Round [261] log likelihood: -5947.681188
EM: Round [262] log likelihood: -5947.678916
EM: Round [263] log likelihood: -5947.676652
EM: Round [264] log likelihood: -5947.674396
EM: Round [265] log likelihood: -5947.672147
EM: Round [266] log likelihood: -5947.669906
EM: Round [267] log likelihood: -5947.667672
EM: Round [268] log likelihood: -5947.665445
EM: Round [269] log likelihood: -5947.663226
EM: Round [270] log likelihood: -5947.661014
EM: Round [271] log likelihood: -5947.658809
EM: Round [272] log likelihood: -5947.656611
EM: Round [273] log likelihood: -5947.654421
EM: Round [274] log likelihood: -5947.652238
EM: Round [275] log likelihood: -5947.650062
EM: Round [276] log likelihood: -5947.647893
EM: Round [277] log likelihood: -5947.645731
EM: Round [278] log likelihood: -5947.643576
EM: Round [279] log likelihood: -5947.641428
EM: Round [280] log likelihood: -5947.639286
EM: Round [281] log likelihood: -5947.637152
EM: Round [282] log likelihood: -5947.635025
EM: Round [283] log likelihood: -5947.632904
EM: Round [284] log likelihood: -5947.630790
EM: Round [285] log likelihood: -5947.628683
EM: Round [286] log likelihood: -5947.626582
EM: Round [287] log likelihood: -5947.624489
EM: Round [288] log likelihood: -5947.622401
EM: Round [289] log likelihood: -5947.620321
EM: Round [290] log likelihood: -5947.618247
EM: Round [291] log likelihood: -5947.616179
EM: Round [292] log likelihood: -5947.614118
EM: Round [293] log likelihood: -5947.612063
EM: Round [294] log likelihood: -5947.610015
EM: Round [295] log likelihood: -5947.607973
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EM: Round [756] log likelihood: -5947.053650
EM: Round [757] log likelihood: -5947.052938
EM: Round [758] log likelihood: -5947.052227
EM: Round [759] log likelihood: -5947.051518
EM: Round [760] log likelihood: -5947.050809
EM: Round [761] log likelihood: -5947.050102
EM: Round [762] log likelihood: -5947.049396
EM: Round [763] log likelihood: -5947.048692
EM: Round [764] log likelihood: -5947.047988
EM: Round [765] log likelihood: -5947.047286
EM: Round [766] log likelihood: -5947.046586
EM: Round [767] log likelihood: -5947.045886
EM: Round [768] log likelihood: -5947.045188
EM: Round [769] log likelihood: -5947.044491
EM: Round [770] log likelihood: -5947.043795
EM: Round [771] log likelihood: -5947.043100
EM: Round [772] log likelihood: -5947.042407
EM: Round [773] log likelihood: -5947.041714
EM: Round [774] log likelihood: -5947.041023
EM: Round [775] log likelihood: -5947.040334
EM: Round [776] log likelihood: -5947.039645
EM: Round [777] log likelihood: -5947.038958
EM: Round [778] log likelihood: -5947.038272
EM: Round [779] log likelihood: -5947.037587
EM: Round [780] log likelihood: -5947.036903
EM: Round [781] log likelihood: -5947.036221
EM: Round [782] log likelihood: -5947.035539
EM: Round [783] log likelihood: -5947.034859
EM: Round [784] log likelihood: -5947.034180
EM: Round [785] log likelihood: -5947.033503
EM: Round [786] log likelihood: -5947.032826
EM: Round [787] log likelihood: -5947.032151
EM: Round [788] log likelihood: -5947.031477
EM: Round [789] log likelihood: -5947.030804
EM: Round [790] log likelihood: -5947.030132
EM: Round [791] log likelihood: -5947.029461
EM: Round [792] log likelihood: -5947.028792
EM: Round [793] log likelihood: -5947.028124
EM: Round [794] log likelihood: -5947.027457
EM: Round [795] log likelihood: -5947.026791
EM: Round [796] log likelihood: -5947.026126
EM: Round [797] log likelihood: -5947.025462
EM: Round [798] log likelihood: -5947.024800
EM: Round [799] log likelihood: -5947.024138
EM: Round [800] log likelihood: -5947.023478
EM: Round [801] log likelihood: -5947.022819
EM: Round [802] log likelihood: -5947.022161
EM: Round [803] log likelihood: -5947.021504
EM: Round [804] log likelihood: -5947.020849
EM: Round [805] log likelihood: -5947.020194
EM: Round [806] log likelihood: -5947.019541
EM: Round [807] log likelihood: -5947.018889
EM: Round [808] log likelihood: -5947.018238
EM: Round [809] log likelihood: -5947.017588
EM: Round [810] log likelihood: -5947.016939
EM: Round [811] log likelihood: -5947.016291
EM: Round [812] log likelihood: -5947.015644
EM: Round [813] log likelihood: -5947.014999
EM: Round [814] log likelihood: -5947.014355
EM: Round [815] log likelihood: -5947.013711
EM: Round [816] log likelihood: -5947.013069
EM: Round [817] log likelihood: -5947.012428
EM: Round [818] log likelihood: -5947.011788
EM: Round [819] log likelihood: -5947.011149
EM: Round [820] log likelihood: -5947.010511
EM: Round [821] log likelihood: -5947.009875
EM: Round [822] log likelihood: -5947.009239
EM: Round [823] log likelihood: -5947.008605
EM: Round [824] log likelihood: -5947.007971
EM: Round [825] log likelihood: -5947.007339
EM: Round [826] log likelihood: -5947.006708
EM: Round [827] log likelihood: -5947.006077
EM: Round [828] log likelihood: -5947.005448
EM: Round [829] log likelihood: -5947.004820
EM: Round [830] log likelihood: -5947.004193
EM: Round [831] log likelihood: -5947.003567
EM: Round [832] log likelihood: -5947.002942
EM: Round [833] log likelihood: -5947.002319
EM: Round [834] log likelihood: -5947.001696
EM: Round [835] log likelihood: -5947.001074
EM: Round [836] log likelihood: -5947.000454
EM: Round [837] log likelihood: -5946.999834
EM: Round [838] log likelihood: -5946.999216
EM: Round [839] log likelihood: -5946.998598
EM: Round [840] log likelihood: -5946.997982
EM: Round [841] log likelihood: -5946.997366
EM: Round [842] log likelihood: -5946.996752
EM: Round [843] log likelihood: -5946.996139
EM: Round [844] log likelihood: -5946.995526
EM: Round [845] log likelihood: -5946.994915
EM: Round [846] log likelihood: -5946.994305
EM: Round [847] log likelihood: -5946.993696
EM: Round [848] log likelihood: -5946.993088
EM: Round [849] log likelihood: -5946.992481
EM: Round [850] log likelihood: -5946.991874
EM: Round [851] log likelihood: -5946.991269
EM: Round [852] log likelihood: -5946.990665
EM: Round [853] log likelihood: -5946.990062
EM: Round [854] log likelihood: -5946.989460
EM: Round [855] log likelihood: -5946.988859
EM: Round [856] log likelihood: -5946.988259
EM: Round [857] log likelihood: -5946.987660
EM: Round [858] log likelihood: -5946.987062
EM: Round [859] log likelihood: -5946.986465
EM: Round [860] log likelihood: -5946.985869
EM: Round [861] log likelihood: -5946.985274
EM: Round [862] log likelihood: -5946.984680
EM: Round [863] log likelihood: -5946.984087
EM: Round [864] log likelihood: -5946.983495
EM: Round [865] log likelihood: -5946.982904
EM: Round [866] log likelihood: -5946.982314
EM: Round [867] log likelihood: -5946.981725
EM: Round [868] log likelihood: -5946.981137
EM: Round [869] log likelihood: -5946.980550
EM: Round [870] log likelihood: -5946.979963
EM: Round [871] log likelihood: -5946.979378
EM: Round [872] log likelihood: -5946.978794
EM: Round [873] log likelihood: -5946.978211
EM: Round [874] log likelihood: -5946.977629
EM: Round [875] log likelihood: -5946.977047
EM: Round [876] log likelihood: -5946.976467
EM: Round [877] log likelihood: -5946.975888
EM: Round [878] log likelihood: -5946.975309
EM: Round [879] log likelihood: -5946.974732
EM: Round [880] log likelihood: -5946.974155
EM: Round [881] log likelihood: -5946.973580
EM: Round [882] log likelihood: -5946.973005
EM: Round [883] log likelihood: -5946.972431
EM: Round [884] log likelihood: -5946.971859
EM: Round [885] log likelihood: -5946.971287
EM: Round [886] log likelihood: -5946.970716
EM: Round [887] log likelihood: -5946.970146
EM: Round [888] log likelihood: -5946.969577
EM: Round [889] log likelihood: -5946.969009
EM: Round [890] log likelihood: -5946.968442
EM: Round [891] log likelihood: -5946.967876
EM: Round [892] log likelihood: -5946.967311
EM: Round [893] log likelihood: -5946.966746
EM: Round [894] log likelihood: -5946.966183
EM: Round [895] log likelihood: -5946.965621
EM: Round [896] log likelihood: -5946.965059
EM: Round [897] log likelihood: -5946.964498
EM: Round [898] log likelihood: -5946.963939
EM: Round [899] log likelihood: -5946.963380
EM: Round [900] log likelihood: -5946.962822
EM: Round [901] log likelihood: -5946.962265
EM: Round [902] log likelihood: -5946.961709
EM: Round [903] log likelihood: -5946.961154
EM: Round [904] log likelihood: -5946.960600
EM: Round [905] log likelihood: -5946.960046
EM: Round [906] log likelihood: -5946.959494
EM: Round [907] log likelihood: -5946.958942
EM: Round [908] log likelihood: -5946.958392
EM: Round [909] log likelihood: -5946.957842
EM: Round [910] log likelihood: -5946.957293
EM: Round [911] log likelihood: -5946.956745
EM: Round [912] log likelihood: -5946.956198
EM: Round [913] log likelihood: -5946.955652
EM: Round [914] log likelihood: -5946.955107
EM: Round [915] log likelihood: -5946.954562
EM: Round [916] log likelihood: -5946.954019
EM: Round [917] log likelihood: -5946.953476
EM: Round [918] log likelihood: -5946.952934
EM: Round [919] log likelihood: -5946.952394
EM: Round [920] log likelihood: -5946.951854
EM: Round [921] log likelihood: -5946.951314
EM: Round [922] log likelihood: -5946.950776
EM: Round [923] log likelihood: -5946.950239
EM: Round [924] log likelihood: -5946.949702
EM: Round [925] log likelihood: -5946.949167
EM: Round [926] log likelihood: -5946.948632
EM: Round [927] log likelihood: -5946.948098
EM: Round [928] log likelihood: -5946.947565
EM: Round [929] log likelihood: -5946.947032
EM: Round [930] log likelihood: -5946.946501
EM: Round [931] log likelihood: -5946.945971
EM: Round [932] log likelihood: -5946.945441
EM: Round [933] log likelihood: -5946.944912
EM: Round [934] log likelihood: -5946.944384
EM: Round [935] log likelihood: -5946.943857
EM: Round [936] log likelihood: -5946.943331
EM: Round [937] log likelihood: -5946.942805
EM: Round [938] log likelihood: -5946.942281
EM: Round [939] log likelihood: -5946.941757
EM: Round [940] log likelihood: -5946.941234
EM: Round [941] log likelihood: -5946.940712
EM: Round [942] log likelihood: -5946.940191
EM: Round [943] log likelihood: -5946.939670
EM: Round [944] log likelihood: -5946.939151
EM: Round [945] log likelihood: -5946.938632
EM: Round [946] log likelihood: -5946.938114
EM: Round [947] log likelihood: -5946.937597
EM: Round [948] log likelihood: -5946.937081
EM: Round [949] log likelihood: -5946.936565
EM: Round [950] log likelihood: -5946.936050
EM: Round [951] log likelihood: -5946.935537
EM: Round [952] log likelihood: -5946.935024
EM: Round [953] log likelihood: -5946.934511
EM: Round [954] log likelihood: -5946.934000
EM: Round [955] log likelihood: -5946.933489
EM: Round [956] log likelihood: -5946.932980
EM: Round [957] log likelihood: -5946.932471
EM: Round [958] log likelihood: -5946.931963
EM: Round [959] log likelihood: -5946.931455
EM: Round [960] log likelihood: -5946.930949
EM: Round [961] log likelihood: -5946.930443
EM: Round [962] log likelihood: -5946.929938
EM: Round [963] log likelihood: -5946.929434
EM: Round [964] log likelihood: -5946.928931
EM: Round [965] log likelihood: -5946.928428
EM: Round [966] log likelihood: -5946.927926
EM: Round [967] log likelihood: -5946.927425
EM: Round [968] log likelihood: -5946.926925
EM: Round [969] log likelihood: -5946.926426
EM: Round [970] log likelihood: -5946.925927
EM: Round [971] log likelihood: -5946.925429
EM: Round [972] log likelihood: -5946.924932
EM: Round [973] log likelihood: -5946.924436
EM: Round [974] log likelihood: -5946.923941
EM: Round [975] log likelihood: -5946.923446
EM: Round [976] log likelihood: -5946.922952
EM: Round [977] log likelihood: -5946.922459
EM: Round [978] log likelihood: -5946.921967
EM: Round [979] log likelihood: -5946.921475
EM: Round [980] log likelihood: -5946.920984
EM: Round [981] log likelihood: -5946.920494
EM: Round [982] log likelihood: -5946.920005
EM: Round [983] log likelihood: -5946.919516
EM: Round [984] log likelihood: -5946.919028
EM: Round [985] log likelihood: -5946.918541
EM: Round [986] log likelihood: -5946.918055
EM: Round [987] log likelihood: -5946.917570
EM: Round [988] log likelihood: -5946.917085
EM: Round [989] log likelihood: -5946.916601
EM: Round [990] log likelihood: -5946.916118
EM: Round [991] log likelihood: -5946.915635
EM: Round [992] log likelihood: -5946.915154
EM: Round [993] log likelihood: -5946.914673
EM: Round [994] log likelihood: -5946.914193
EM: Round [995] log likelihood: -5946.913713
EM: Round [996] log likelihood: -5946.913234
EM: Round [997] log likelihood: -5946.912756
EM: Round [998] log likelihood: -5946.912279
EM: Round [999] log likelihood: -5946.911803
EM: Round [1000] log likelihood: -5946.911327
EM: Round [1001] log likelihood: -5946.910852
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam into /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords

CMD: touch /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords > /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords > /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.fX3YIVekf1/fi_workdir/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.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.fX3YIVekf1/fi_workdir/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.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.fX3YIVekf1/fi_workdir/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5628.927677
EM: Round [1] log likelihood: -5628.920234
EM: Round [2] log likelihood: -5628.912854
EM: Round [3] log likelihood: -5628.905536
EM: Round [4] log likelihood: -5628.898279
EM: Round [5] log likelihood: -5628.891082
EM: Round [6] log likelihood: -5628.883944
EM: Round [7] log likelihood: -5628.876865
EM: Round [8] log likelihood: -5628.869842
EM: Round [9] log likelihood: -5628.862876
EM: Round [10] log likelihood: -5628.855966
EM: Round [11] log likelihood: -5628.849110
EM: Round [12] log likelihood: -5628.842309
EM: Round [13] log likelihood: -5628.835560
EM: Round [14] log likelihood: -5628.828864
EM: Round [15] log likelihood: -5628.822220
EM: Round [16] log likelihood: -5628.815627
EM: Round [17] log likelihood: -5628.809084
EM: Round [18] log likelihood: -5628.802590
EM: Round [19] log likelihood: -5628.796145
EM: Round [20] log likelihood: -5628.789749
EM: Round [21] log likelihood: -5628.783399
EM: Round [22] log likelihood: -5628.777097
EM: Round [23] log likelihood: -5628.770841
EM: Round [24] log likelihood: -5628.764630
EM: Round [25] log likelihood: -5628.758465
EM: Round [26] log likelihood: -5628.752343
EM: Round [27] log likelihood: -5628.746266
EM: Round [28] log likelihood: -5628.740231
EM: Round [29] log likelihood: -5628.734240
EM: Round [30] log likelihood: -5628.728290
EM: Round [31] log likelihood: -5628.722382
EM: Round [32] log likelihood: -5628.716515
EM: Round [33] log likelihood: -5628.710688
EM: Round [34] log likelihood: -5628.704902
EM: Round [35] log likelihood: -5628.699155
EM: Round [36] log likelihood: -5628.693446
EM: Round [37] log likelihood: -5628.687777
EM: Round [38] log likelihood: -5628.682145
EM: Round [39] log likelihood: -5628.676551
EM: Round [40] log likelihood: -5628.670994
EM: Round [41] log likelihood: -5628.665474
EM: Round [42] log likelihood: -5628.659989
EM: Round [43] log likelihood: -5628.654541
EM: Round [44] log likelihood: -5628.649128
EM: Round [45] log likelihood: -5628.643750
EM: Round [46] log likelihood: -5628.638406
EM: Round [47] log likelihood: -5628.633097
EM: Round [48] log likelihood: -5628.627821
EM: Round [49] log likelihood: -5628.622578
EM: Round [50] log likelihood: -5628.617369
EM: Round [51] log likelihood: -5628.612192
EM: Round [52] log likelihood: -5628.607047
EM: Round [53] log likelihood: -5628.601934
EM: Round [54] log likelihood: -5628.596852
EM: Round [55] log likelihood: -5628.591802
EM: Round [56] log likelihood: -5628.586782
EM: Round [57] log likelihood: -5628.581793
EM: Round [58] log likelihood: -5628.576834
EM: Round [59] log likelihood: -5628.571905
EM: Round [60] log likelihood: -5628.567005
EM: Round [61] log likelihood: -5628.562134
EM: Round [62] log likelihood: -5628.557292
EM: Round [63] log likelihood: -5628.552479
EM: Round [64] log likelihood: -5628.547694
EM: Round [65] log likelihood: -5628.542936
EM: Round [66] log likelihood: -5628.538207
EM: Round [67] log likelihood: -5628.533504
EM: Round [68] log likelihood: -5628.528829
EM: Round [69] log likelihood: -5628.524180
EM: Round [70] log likelihood: -5628.519558
EM: Round [71] log likelihood: -5628.514962
EM: Round [72] log likelihood: -5628.510392
EM: Round [73] log likelihood: -5628.505848
EM: Round [74] log likelihood: -5628.501329
EM: Round [75] log likelihood: -5628.496836
EM: Round [76] log likelihood: -5628.492367
EM: Round [77] log likelihood: -5628.487923
EM: Round [78] log likelihood: -5628.483503
EM: Round [79] log likelihood: -5628.479107
EM: Round [80] log likelihood: -5628.474736
EM: Round [81] log likelihood: -5628.470388
EM: Round [82] log likelihood: -5628.466063
EM: Round [83] log likelihood: -5628.461762
EM: Round [84] log likelihood: -5628.457484
EM: Round [85] log likelihood: -5628.453229
EM: Round [86] log likelihood: -5628.448996
EM: Round [87] log likelihood: -5628.444785
EM: Round [88] log likelihood: -5628.440597
EM: Round [89] log likelihood: -5628.436431
EM: Round [90] log likelihood: -5628.432286
EM: Round [91] log likelihood: -5628.428163
EM: Round [92] log likelihood: -5628.424062
EM: Round [93] log likelihood: -5628.419981
EM: Round [94] log likelihood: -5628.415921
EM: Round [95] log likelihood: -5628.411883
EM: Round [96] log likelihood: -5628.407864
EM: Round [97] log likelihood: -5628.403866
EM: Round [98] log likelihood: -5628.399889
EM: Round [99] log likelihood: -5628.395931
EM: Round [100] log likelihood: -5628.391993
EM: Round [101] log likelihood: -5628.388075
EM: Round [102] log likelihood: -5628.384176
EM: Round [103] log likelihood: -5628.380297
EM: Round [104] log likelihood: -5628.376437
EM: Round [105] log likelihood: -5628.372595
EM: Round [106] log likelihood: -5628.368773
EM: Round [107] log likelihood: -5628.364969
EM: Round [108] log likelihood: -5628.361184
EM: Round [109] log likelihood: -5628.357417
EM: Round [110] log likelihood: -5628.353668
EM: Round [111] log likelihood: -5628.349937
EM: Round [112] log likelihood: -5628.346224
EM: Round [113] log likelihood: -5628.342529
EM: Round [114] log likelihood: -5628.338851
EM: Round [115] log likelihood: -5628.335191
EM: Round [116] log likelihood: -5628.331548
EM: Round [117] log likelihood: -5628.327922
EM: Round [118] log likelihood: -5628.324313
EM: Round [119] log likelihood: -5628.320721
EM: Round [120] log likelihood: -5628.317146
EM: Round [121] log likelihood: -5628.313587
EM: Round [122] log likelihood: -5628.310045
EM: Round [123] log likelihood: -5628.306519
EM: Round [124] log likelihood: -5628.303009
EM: Round [125] log likelihood: -5628.299515
EM: Round [126] log likelihood: -5628.296037
EM: Round [127] log likelihood: -5628.292575
EM: Round [128] log likelihood: -5628.289128
EM: Round [129] log likelihood: -5628.285697
EM: Round [130] log likelihood: -5628.282282
EM: Round [131] log likelihood: -5628.278881
EM: Round [132] log likelihood: -5628.275496
EM: Round [133] log likelihood: -5628.272126
EM: Round [134] log likelihood: -5628.268771
EM: Round [135] log likelihood: -5628.265430
EM: Round [136] log likelihood: -5628.262105
EM: Round [137] log likelihood: -5628.258794
EM: Round [138] log likelihood: -5628.255497
EM: Round [139] log likelihood: -5628.252215
EM: Round [140] log likelihood: -5628.248947
EM: Round [141] log likelihood: -5628.245693
EM: Round [142] log likelihood: -5628.242453
EM: Round [143] log likelihood: -5628.239227
EM: Round [144] log likelihood: -5628.236015
EM: Round [145] log likelihood: -5628.232817
EM: Round [146] log likelihood: -5628.229632
EM: Round [147] log likelihood: -5628.226461
EM: Round [148] log likelihood: -5628.223303
EM: Round [149] log likelihood: -5628.220159
EM: Round [150] log likelihood: -5628.217028
EM: Round [151] log likelihood: -5628.213910
EM: Round [152] log likelihood: -5628.210805
EM: Round [153] log likelihood: -5628.207713
EM: Round [154] log likelihood: -5628.204633
EM: Round [155] log likelihood: -5628.201567
EM: Round [156] log likelihood: -5628.198513
EM: Round [157] log likelihood: -5628.195472
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-total frags in /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2_1.fastp.fastq.gz: 215125293
Warning - not locating file: /tmp/nxf.fX3YIVekf1/1173_K7E_T1_RNA_SLD_01_A23T55JLT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000258516.2]
WARNING, no entry stored in dbm for [ENSG00000258516.2]
WARNING, no entry stored in dbm for [ENSG00000264808.1]
WARNING, no entry stored in dbm for [ENSG00000286833.1]
ls: cannot access 'IGV_inputs': No such file or directory