Done.
-parsing GTF file: /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.uMS6WptGv5/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.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00614_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00614_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:44:03 : INFO : Done.
-parsing GTF file: /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[5330000] -done parsing /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 360,
'seq-similar region overlap' => 273,
'excessive soft clipping' => 44795,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 143,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 146,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 30,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 56,
' ** passed ** ' => 17832,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 18,
'per_id < 96' => 16838,
'low complexity anchor region' => 8,
'num genes matched < 2' => 24,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
'small anchor length' => 104
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[8000] -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1
[1000] -fusion SPANNING read extraction for scaff: AC110588.1--GABRG3
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[12000] -fusion SPANNING read extraction for scaff: AC239859.5--AC013734.1
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[284000] -fusion SPANNING read extraction for scaff: AFAP1--KCNIP4
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[281000] -fusion SPANNING read extraction for scaff: AFAP1--LINC02501
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[281000] -fusion SPANNING read extraction for scaff: AFAP1--AC027369.1
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[281000] -fusion SPANNING read extraction for scaff: AFAP1--TRIM53CP
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[60000] -fusion SPANNING read extraction for scaff: AKAP10--RB1
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[118000] -fusion SPANNING read extraction for scaff: ANKRD27--ZNF507
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[11000] -fusion SPANNING read extraction for scaff: AOPEP--AL450426.1
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[78000] -fusion SPANNING read extraction for scaff: APBB2--AC093878.1
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[78000] -fusion SPANNING read extraction for scaff: APBB2--AC097535.2
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[48000] -fusion SPANNING read extraction for scaff: C11orf49--TTC17
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[27000] -fusion SPANNING read extraction for scaff: CCNE1--CDH9
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[32000] -fusion SPANNING read extraction for scaff: CHCHD6--ZBTB20
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[100000] -fusion SPANNING read extraction for scaff: CWC27--CPLANE1
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[39000] -fusion SPANNING read extraction for scaff: CWC27--RGS7BP
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[33000] -fusion SPANNING read extraction for scaff: CWC27--MRPL49P1
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[11000] -fusion SPANNING read extraction for scaff: DARS2--ESRRG
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[26000] -fusion SPANNING read extraction for scaff: DARS2--GPATCH2
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[28000] -fusion SPANNING read extraction for scaff: DNAJC3--ADPRHL1
[1000] -fusion SPANNING read extraction for scaff: FAM149B1P1--GABRG3
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[7000] -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1
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[19000] -fusion SPANNING read extraction for scaff: GPATCH2--LRRC7
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[75000] -fusion SPANNING read extraction for scaff: KCTD8--RELL1
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[12000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[24000] -fusion SPANNING read extraction for scaff: LIMCH1--TRIM64C
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[20000] -fusion SPANNING read extraction for scaff: LIMCH1--AC116611.1
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[20000] -fusion SPANNING read extraction for scaff: LIMCH1--LINC02353
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[133000] -fusion SPANNING read extraction for scaff: LSM14A--ZNF460
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[53000] -fusion SPANNING read extraction for scaff: LSM14A--ZNF460-AS1
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[128000] -fusion SPANNING read extraction for scaff: MED13--RIPK1
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[14000] -fusion SPANNING read extraction for scaff: NDUFS4--AC010327.4
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[109000] -fusion SPANNING read extraction for scaff: NRDC--AGBL4
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[56000] -fusion SPANNING read extraction for scaff: NUP155--SHISAL2B
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10
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[5000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5
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[4000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4
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[10000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
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[37000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9
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[6000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7
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[19000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA10
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[5000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC5
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[10000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA8
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[38000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGC3
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[7000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA9
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[6000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB6
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA11
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[9000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGB7
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA3--PCDHGA12
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[47000] -fusion SPANNING read extraction for scaff: PPP1R8--STX12
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[11000] -fusion SPANNING read extraction for scaff: PSG8--CD177
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[131000] -fusion SPANNING read extraction for scaff: RRAS2--COPB1
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[123000] -fusion SPANNING read extraction for scaff: SCP2--COPB1
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[186000] -fusion SPANNING read extraction for scaff: SLIT2--AC024230.1
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[62000] -fusion SPANNING read extraction for scaff: SMIM14--PI4K2B
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[6000] -fusion SPANNING read extraction for scaff: SMIM14--AC007106.1
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[6000] -fusion SPANNING read extraction for scaff: SMIM14--AC093791.2
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[66000] -fusion SPANNING read extraction for scaff: SNX29--MARF1
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[49000] -fusion SPANNING read extraction for scaff: SUSD1--PTBP3
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[31000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[32000] -fusion SPANNING read extraction for scaff: TLK2--CCDC144NL-AS1
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[15000] -fusion SPANNING read extraction for scaff: TP53--DLEU1
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[21000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[94000] -fusion SPANNING read extraction for scaff: XPO6--ZP2
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[94000] -fusion SPANNING read extraction for scaff: XPO6--ANKS4B
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[71000] -fusion SPANNING read extraction for scaff: ZNF507--AC010485.1
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[71000] -fusion SPANNING read extraction for scaff: ZNF507--RPL21P131
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[78000] -fusion SPANNING read extraction for scaff: ZNF785--ADD1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 25415,
'seq similar region alignment' => 15902
};
EM: Starting log likelihood: -13984.250979
EM: Round [1] log likelihood: -13981.328137
EM: Round [2] log likelihood: -13979.551462
EM: Round [3] log likelihood: -13978.108621
EM: Round [4] log likelihood: -13976.929530
EM: Round [5] log likelihood: -13975.960836
EM: Round [6] log likelihood: -13975.161185
EM: Round [7] log likelihood: -13974.498142
EM: Round [8] log likelihood: -13973.946034
EM: Round [9] log likelihood: -13973.484393
EM: Round [10] log likelihood: -13973.096811
EM: Round [11] log likelihood: -13972.770068
EM: Round [12] log likelihood: -13972.493471
EM: Round [13] log likelihood: -13972.258340
EM: Round [14] log likelihood: -13972.057602
EM: Round [15] log likelihood: -13971.885483
EM: Round [16] log likelihood: -13971.737250
EM: Round [17] log likelihood: -13971.609015
EM: Round [18] log likelihood: -13971.497574
EM: Round [19] log likelihood: -13971.400282
EM: Round [20] log likelihood: -13971.314949
EM: Round [21] log likelihood: -13971.239753
EM: Round [22] log likelihood: -13971.173180
EM: Round [23] log likelihood: -13971.113964
EM: Round [24] log likelihood: -13971.061046
EM: Round [25] log likelihood: -13971.013537
EM: Round [26] log likelihood: -13970.970686
EM: Round [27] log likelihood: -13970.931862
EM: Round [28] log likelihood: -13970.896528
EM: Round [29] log likelihood: -13970.864230
EM: Round [30] log likelihood: -13970.834581
EM: Round [31] log likelihood: -13970.807248
EM: Round [32] log likelihood: -13970.781949
EM: Round [33] log likelihood: -13970.758440
EM: Round [34] log likelihood: -13970.736510
EM: Round [35] log likelihood: -13970.715980
EM: Round [36] log likelihood: -13970.696692
EM: Round [37] log likelihood: -13970.678509
EM: Round [38] log likelihood: -13970.661313
EM: Round [39] log likelihood: -13970.645000
EM: Round [40] log likelihood: -13970.629480
EM: Round [41] log likelihood: -13970.614673
EM: Round [42] log likelihood: -13970.600510
EM: Round [43] log likelihood: -13970.586928
EM: Round [44] log likelihood: -13970.573875
EM: Round [45] log likelihood: -13970.561301
EM: Round [46] log likelihood: -13970.549165
EM: Round [47] log likelihood: -13970.537428
EM: Round [48] log likelihood: -13970.526057
EM: Round [49] log likelihood: -13970.515023
EM: Round [50] log likelihood: -13970.504297
EM: Round [51] log likelihood: -13970.493858
EM: Round [52] log likelihood: -13970.483683
EM: Round [53] log likelihood: -13970.473752
EM: Round [54] log likelihood: -13970.464050
EM: Round [55] log likelihood: -13970.454560
EM: Round [56] log likelihood: -13970.445269
EM: Round [57] log likelihood: -13970.436164
EM: Round [58] log likelihood: -13970.427233
EM: Round [59] log likelihood: -13970.418467
EM: Round [60] log likelihood: -13970.409855
EM: Round [61] log likelihood: -13970.401391
EM: Round [62] log likelihood: -13970.393065
EM: Round [63] log likelihood: -13970.384870
EM: Round [64] log likelihood: -13970.376802
EM: Round [65] log likelihood: -13970.368853
EM: Round [66] log likelihood: -13970.361018
EM: Round [67] log likelihood: -13970.353292
EM: Round [68] log likelihood: -13970.345671
EM: Round [69] log likelihood: -13970.338151
EM: Round [70] log likelihood: -13970.330728
EM: Round [71] log likelihood: -13970.323399
EM: Round [72] log likelihood: -13970.316159
EM: Round [73] log likelihood: -13970.309006
EM: Round [74] log likelihood: -13970.301938
EM: Round [75] log likelihood: -13970.294951
EM: Round [76] log likelihood: -13970.288044
EM: Round [77] log likelihood: -13970.281213
EM: Round [78] log likelihood: -13970.274458
EM: Round [79] log likelihood: -13970.267775
EM: Round [80] log likelihood: -13970.261163
EM: Round [81] log likelihood: -13970.254620
EM: Round [82] log likelihood: -13970.248145
EM: Round [83] log likelihood: -13970.241736
EM: Round [84] log likelihood: -13970.235391
EM: Round [85] log likelihood: -13970.229110
EM: Round [86] log likelihood: -13970.222890
EM: Round [87] log likelihood: -13970.216730
EM: Round [88] log likelihood: -13970.210630
EM: Round [89] log likelihood: -13970.204588
EM: Round [90] log likelihood: -13970.198602
EM: Round [91] log likelihood: -13970.192673
EM: Round [92] log likelihood: -13970.186798
EM: Round [93] log likelihood: -13970.180978
EM: Round [94] log likelihood: -13970.175210
EM: Round [95] log likelihood: -13970.169494
EM: Round [96] log likelihood: -13970.163830
EM: Round [97] log likelihood: -13970.158216
EM: Round [98] log likelihood: -13970.152651
EM: Round [99] log likelihood: -13970.147135
EM: Round [100] log likelihood: -13970.141667
EM: Round [101] log likelihood: -13970.136246
EM: Round [102] log likelihood: -13970.130872
EM: Round [103] log likelihood: -13970.125544
EM: Round [104] log likelihood: -13970.120260
EM: Round [105] log likelihood: -13970.115021
EM: Round [106] log likelihood: -13970.109826
EM: Round [107] log likelihood: -13970.104674
EM: Round [108] log likelihood: -13970.099565
EM: Round [109] log likelihood: -13970.094498
EM: Round [110] log likelihood: -13970.089472
EM: Round [111] log likelihood: -13970.084487
EM: Round [112] log likelihood: -13970.079542
EM: Round [113] log likelihood: -13970.074637
EM: Round [114] log likelihood: -13970.069771
EM: Round [115] log likelihood: -13970.064944
EM: Round [116] log likelihood: -13970.060155
EM: Round [117] log likelihood: -13970.055403
EM: Round [118] log likelihood: -13970.050689
EM: Round [119] log likelihood: -13970.046012
EM: Round [120] log likelihood: -13970.041371
EM: Round [121] log likelihood: -13970.036766
EM: Round [122] log likelihood: -13970.032196
EM: Round [123] log likelihood: -13970.027661
EM: Round [124] log likelihood: -13970.023161
EM: Round [125] log likelihood: -13970.018695
EM: Round [126] log likelihood: -13970.014262
EM: Round [127] log likelihood: -13970.009863
EM: Round [128] log likelihood: -13970.005496
EM: Round [129] log likelihood: -13970.001162
EM: Round [130] log likelihood: -13969.996860
EM: Round [131] log likelihood: -13969.992590
EM: Round [132] log likelihood: -13969.988351
EM: Round [133] log likelihood: -13969.984144
EM: Round [134] log likelihood: -13969.979966
EM: Round [135] log likelihood: -13969.975820
EM: Round [136] log likelihood: -13969.971703
EM: Round [137] log likelihood: -13969.967615
EM: Round [138] log likelihood: -13969.963557
EM: Round [139] log likelihood: -13969.959528
EM: Round [140] log likelihood: -13969.955527
EM: Round [141] log likelihood: -13969.951555
EM: Round [142] log likelihood: -13969.947611
EM: Round [143] log likelihood: -13969.943694
EM: Round [144] log likelihood: -13969.939805
EM: Round [145] log likelihood: -13969.935943
EM: Round [146] log likelihood: -13969.932108
EM: Round [147] log likelihood: -13969.928299
EM: Round [148] log likelihood: -13969.924516
EM: Round [149] log likelihood: -13969.920759
EM: Round [150] log likelihood: -13969.917028
EM: Round [151] log likelihood: -13969.913323
EM: Round [152] log likelihood: -13969.909642
EM: Round [153] log likelihood: -13969.905986
EM: Round [154] log likelihood: -13969.902355
EM: Round [155] log likelihood: -13969.898749
EM: Round [156] log likelihood: -13969.895166
EM: Round [157] log likelihood: -13969.891607
EM: Round [158] log likelihood: -13969.888072
EM: Round [159] log likelihood: -13969.884560
EM: Round [160] log likelihood: -13969.881072
EM: Round [161] log likelihood: -13969.877606
EM: Round [162] log likelihood: -13969.874163
EM: Round [163] log likelihood: -13969.870742
EM: Round [164] log likelihood: -13969.867344
EM: Round [165] log likelihood: -13969.863968
EM: Round [166] log likelihood: -13969.860613
EM: Round [167] log likelihood: -13969.857280
EM: Round [168] log likelihood: -13969.853969
EM: Round [169] log likelihood: -13969.850678
EM: Round [170] log likelihood: -13969.847409
EM: Round [171] log likelihood: -13969.844160
EM: Round [172] log likelihood: -13969.840932
EM: Round [173] log likelihood: -13969.837724
EM: Round [174] log likelihood: -13969.834536
EM: Round [175] log likelihood: -13969.831368
EM: Round [176] log likelihood: -13969.828221
EM: Round [177] log likelihood: -13969.825092
EM: Round [178] log likelihood: -13969.821983
EM: Round [179] log likelihood: -13969.818894
EM: Round [180] log likelihood: -13969.815823
EM: Round [181] log likelihood: -13969.812772
EM: Round [182] log likelihood: -13969.809739
EM: Round [183] log likelihood: -13969.806724
EM: Round [184] log likelihood: -13969.803728
EM: Round [185] log likelihood: -13969.800750
EM: Round [186] log likelihood: -13969.797791
EM: Round [187] log likelihood: -13969.794849
EM: Round [188] log likelihood: -13969.791925
EM: Round [189] log likelihood: -13969.789018
EM: Round [190] log likelihood: -13969.786129
EM: Round [191] log likelihood: -13969.783257
EM: Round [192] log likelihood: -13969.780402
EM: Round [193] log likelihood: -13969.777564
EM: Round [194] log likelihood: -13969.774743
EM: Round [195] log likelihood: -13969.771939
EM: Round [196] log likelihood: -13969.769151
EM: Round [197] log likelihood: -13969.766379
EM: Round [198] log likelihood: -13969.763624
EM: Round [199] log likelihood: -13969.760885
EM: Round [200] log likelihood: -13969.758162
EM: Round [201] log likelihood: -13969.755454
EM: Round [202] log likelihood: -13969.752762
EM: Round [203] log likelihood: -13969.750086
EM: Round [204] log likelihood: -13969.747425
EM: Round [205] log likelihood: -13969.744780
EM: Round [206] log likelihood: -13969.742149
EM: Round [207] log likelihood: -13969.739534
EM: Round [208] log likelihood: -13969.736934
EM: Round [209] log likelihood: -13969.734348
EM: Round [210] log likelihood: -13969.731777
EM: Round [211] log likelihood: -13969.729221
EM: Round [212] log likelihood: -13969.726679
EM: Round [213] log likelihood: -13969.724151
EM: Round [214] log likelihood: -13969.721638
EM: Round [215] log likelihood: -13969.719138
EM: Round [216] log likelihood: -13969.716653
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EM: Round [677] log likelihood: -13969.242321
EM: Round [678] log likelihood: -13969.241954
EM: Round [679] log likelihood: -13969.241588
EM: Round [680] log likelihood: -13969.241224
EM: Round [681] log likelihood: -13969.240860
EM: Round [682] log likelihood: -13969.240498
EM: Round [683] log likelihood: -13969.240138
EM: Round [684] log likelihood: -13969.239778
EM: Round [685] log likelihood: -13969.239420
EM: Round [686] log likelihood: -13969.239063
EM: Round [687] log likelihood: -13969.238707
EM: Round [688] log likelihood: -13969.238352
EM: Round [689] log likelihood: -13969.237999
EM: Round [690] log likelihood: -13969.237647
EM: Round [691] log likelihood: -13969.237296
EM: Round [692] log likelihood: -13969.236946
EM: Round [693] log likelihood: -13969.236598
EM: Round [694] log likelihood: -13969.236251
EM: Round [695] log likelihood: -13969.235905
EM: Round [696] log likelihood: -13969.235560
EM: Round [697] log likelihood: -13969.235216
EM: Round [698] log likelihood: -13969.234873
EM: Round [699] log likelihood: -13969.234532
EM: Round [700] log likelihood: -13969.234192
EM: Round [701] log likelihood: -13969.233853
EM: Round [702] log likelihood: -13969.233515
EM: Round [703] log likelihood: -13969.233179
EM: Round [704] log likelihood: -13969.232843
EM: Round [705] log likelihood: -13969.232509
EM: Round [706] log likelihood: -13969.232176
EM: Round [707] log likelihood: -13969.231843
EM: Round [708] log likelihood: -13969.231513
EM: Round [709] log likelihood: -13969.231183
EM: Round [710] log likelihood: -13969.230854
EM: Round [711] log likelihood: -13969.230527
EM: Round [712] log likelihood: -13969.230200
EM: Round [713] log likelihood: -13969.229875
EM: Round [714] log likelihood: -13969.229551
EM: Round [715] log likelihood: -13969.229228
EM: Round [716] log likelihood: -13969.228906
EM: Round [717] log likelihood: -13969.228585
EM: Round [718] log likelihood: -13969.228265
EM: Round [719] log likelihood: -13969.227947
EM: Round [720] log likelihood: -13969.227629
EM: Round [721] log likelihood: -13969.227313
EM: Round [722] log likelihood: -13969.226997
EM: Round [723] log likelihood: -13969.226683
EM: Round [724] log likelihood: -13969.226370
EM: Round [725] log likelihood: -13969.226058
EM: Round [726] log likelihood: -13969.225747
EM: Round [727] log likelihood: -13969.225437
EM: Round [728] log likelihood: -13969.225128
EM: Round [729] log likelihood: -13969.224820
EM: Round [730] log likelihood: -13969.224513
EM: Round [731] log likelihood: -13969.224207
EM: Round [732] log likelihood: -13969.223902
EM: Round [733] log likelihood: -13969.223598
EM: Round [734] log likelihood: -13969.223296
EM: Round [735] log likelihood: -13969.222994
EM: Round [736] log likelihood: -13969.222693
EM: Round [737] log likelihood: -13969.222394
EM: Round [738] log likelihood: -13969.222095
EM: Round [739] log likelihood: -13969.221798
EM: Round [740] log likelihood: -13969.221501
EM: Round [741] log likelihood: -13969.221206
EM: Round [742] log likelihood: -13969.220911
EM: Round [743] log likelihood: -13969.220617
EM: Round [744] log likelihood: -13969.220325
EM: Round [745] log likelihood: -13969.220033
EM: Round [746] log likelihood: -13969.219743
EM: Round [747] log likelihood: -13969.219453
EM: Round [748] log likelihood: -13969.219165
EM: Round [749] log likelihood: -13969.218877
EM: Round [750] log likelihood: -13969.218590
EM: Round [751] log likelihood: -13969.218305
EM: Round [752] log likelihood: -13969.218020
EM: Round [753] log likelihood: -13969.217736
EM: Round [754] log likelihood: -13969.217453
EM: Round [755] log likelihood: -13969.217172
EM: Round [756] log likelihood: -13969.216891
EM: Round [757] log likelihood: -13969.216611
EM: Round [758] log likelihood: -13969.216332
EM: Round [759] log likelihood: -13969.216054
EM: Round [760] log likelihood: -13969.215777
EM: Round [761] log likelihood: -13969.215501
EM: Round [762] log likelihood: -13969.215225
EM: Round [763] log likelihood: -13969.214951
EM: Round [764] log likelihood: -13969.214678
EM: Round [765] log likelihood: -13969.214405
EM: Round [766] log likelihood: -13969.214134
EM: Round [767] log likelihood: -13969.213863
EM: Round [768] log likelihood: -13969.213593
EM: Round [769] log likelihood: -13969.213325
EM: Round [770] log likelihood: -13969.213057
EM: Round [771] log likelihood: -13969.212790
EM: Round [772] log likelihood: -13969.212524
EM: Round [773] log likelihood: -13969.212259
EM: Round [774] log likelihood: -13969.211994
EM: Round [775] log likelihood: -13969.211731
EM: Round [776] log likelihood: -13969.211468
EM: Round [777] log likelihood: -13969.211207
EM: Round [778] log likelihood: -13969.210946
EM: Round [779] log likelihood: -13969.210686
EM: Round [780] log likelihood: -13969.210427
EM: Round [781] log likelihood: -13969.210169
EM: Round [782] log likelihood: -13969.209912
EM: Round [783] log likelihood: -13969.209655
EM: Round [784] log likelihood: -13969.209400
EM: Round [785] log likelihood: -13969.209145
EM: Round [786] log likelihood: -13969.208891
EM: Round [787] log likelihood: -13969.208639
EM: Round [788] log likelihood: -13969.208386
EM: Round [789] log likelihood: -13969.208135
EM: Round [790] log likelihood: -13969.207885
EM: Round [791] log likelihood: -13969.207635
EM: Round [792] log likelihood: -13969.207386
EM: Round [793] log likelihood: -13969.207139
EM: Round [794] log likelihood: -13969.206891
EM: Round [795] log likelihood: -13969.206645
EM: Round [796] log likelihood: -13969.206400
EM: Round [797] log likelihood: -13969.206155
EM: Round [798] log likelihood: -13969.205911
EM: Round [799] log likelihood: -13969.205668
EM: Round [800] log likelihood: -13969.205426
EM: Round [801] log likelihood: -13969.205185
EM: Round [802] log likelihood: -13969.204944
EM: Round [803] log likelihood: -13969.204705
EM: Round [804] log likelihood: -13969.204466
EM: Round [805] log likelihood: -13969.204228
EM: Round [806] log likelihood: -13969.203990
EM: Round [807] log likelihood: -13969.203754
EM: Round [808] log likelihood: -13969.203518
EM: Round [809] log likelihood: -13969.203283
EM: Round [810] log likelihood: -13969.203049
EM: Round [811] log likelihood: -13969.202815
EM: Round [812] log likelihood: -13969.202583
EM: Round [813] log likelihood: -13969.202351
EM: Round [814] log likelihood: -13969.202120
EM: Round [815] log likelihood: -13969.201890
EM: Round [816] log likelihood: -13969.201660
EM: Round [817] log likelihood: -13969.201431
EM: Round [818] log likelihood: -13969.201203
EM: Round [819] log likelihood: -13969.200976
EM: Round [820] log likelihood: -13969.200750
EM: Round [821] log likelihood: -13969.200524
EM: Round [822] log likelihood: -13969.200299
EM: Round [823] log likelihood: -13969.200075
EM: Round [824] log likelihood: -13969.199851
EM: Round [825] log likelihood: -13969.199629
EM: Round [826] log likelihood: -13969.199407
EM: Round [827] log likelihood: -13969.199185
EM: Round [828] log likelihood: -13969.198965
EM: Round [829] log likelihood: -13969.198745
EM: Round [830] log likelihood: -13969.198526
EM: Round [831] log likelihood: -13969.198308
EM: Round [832] log likelihood: -13969.198090
EM: Round [833] log likelihood: -13969.197873
EM: Round [834] log likelihood: -13969.197657
EM: Round [835] log likelihood: -13969.197441
EM: Round [836] log likelihood: -13969.197227
EM: Round [837] log likelihood: -13969.197013
EM: Round [838] log likelihood: -13969.196799
EM: Round [839] log likelihood: -13969.196587
EM: Round [840] log likelihood: -13969.196375
EM: Round [841] log likelihood: -13969.196164
EM: Round [842] log likelihood: -13969.195953
EM: Round [843] log likelihood: -13969.195743
EM: Round [844] log likelihood: -13969.195534
EM: Round [845] log likelihood: -13969.195326
EM: Round [846] log likelihood: -13969.195118
EM: Round [847] log likelihood: -13969.194911
EM: Round [848] log likelihood: -13969.194705
EM: Round [849] log likelihood: -13969.194499
EM: Round [850] log likelihood: -13969.194294
EM: Round [851] log likelihood: -13969.194090
EM: Round [852] log likelihood: -13969.193886
EM: Round [853] log likelihood: -13969.193683
EM: Round [854] log likelihood: -13969.193481
EM: Round [855] log likelihood: -13969.193280
EM: Round [856] log likelihood: -13969.193079
EM: Round [857] log likelihood: -13969.192878
EM: Round [858] log likelihood: -13969.192679
EM: Round [859] log likelihood: -13969.192480
EM: Round [860] log likelihood: -13969.192281
EM: Round [861] log likelihood: -13969.192084
EM: Round [862] log likelihood: -13969.191887
EM: Round [863] log likelihood: -13969.191690
EM: Round [864] log likelihood: -13969.191495
EM: Round [865] log likelihood: -13969.191300
EM: Round [866] log likelihood: -13969.191105
EM: Round [867] log likelihood: -13969.190912
EM: Round [868] log likelihood: -13969.190718
EM: Round [869] log likelihood: -13969.190526
EM: Round [870] log likelihood: -13969.190334
EM: Round [871] log likelihood: -13969.190143
EM: Round [872] log likelihood: -13969.189952
EM: Round [873] log likelihood: -13969.189762
EM: Round [874] log likelihood: -13969.189573
EM: Round [875] log likelihood: -13969.189384
EM: Round [876] log likelihood: -13969.189196
EM: Round [877] log likelihood: -13969.189009
EM: Round [878] log likelihood: -13969.188822
EM: Round [879] log likelihood: -13969.188636
EM: Round [880] log likelihood: -13969.188450
EM: Round [881] log likelihood: -13969.188265
EM: Round [882] log likelihood: -13969.188081
EM: Round [883] log likelihood: -13969.187897
EM: Round [884] log likelihood: -13969.187714
EM: Round [885] log likelihood: -13969.187531
EM: Round [886] log likelihood: -13969.187349
EM: Round [887] log likelihood: -13969.187168
EM: Round [888] log likelihood: -13969.186987
EM: Round [889] log likelihood: -13969.186807
EM: Round [890] log likelihood: -13969.186627
EM: Round [891] log likelihood: -13969.186448
EM: Round [892] log likelihood: -13969.186270
EM: Round [893] log likelihood: -13969.186092
EM: Round [894] log likelihood: -13969.185915
EM: Round [895] log likelihood: -13969.185738
EM: Round [896] log likelihood: -13969.185562
EM: Round [897] log likelihood: -13969.185386
EM: Round [898] log likelihood: -13969.185211
EM: Round [899] log likelihood: -13969.185037
EM: Round [900] log likelihood: -13969.184863
EM: Round [901] log likelihood: -13969.184690
EM: Round [902] log likelihood: -13969.184517
EM: Round [903] log likelihood: -13969.184345
EM: Round [904] log likelihood: -13969.184174
EM: Round [905] log likelihood: -13969.184003
EM: Round [906] log likelihood: -13969.183832
EM: Round [907] log likelihood: -13969.183662
EM: Round [908] log likelihood: -13969.183493
EM: Round [909] log likelihood: -13969.183324
EM: Round [910] log likelihood: -13969.183156
EM: Round [911] log likelihood: -13969.182988
EM: Round [912] log likelihood: -13969.182821
EM: Round [913] log likelihood: -13969.182655
EM: Round [914] log likelihood: -13969.182489
EM: Round [915] log likelihood: -13969.182323
EM: Round [916] log likelihood: -13969.182158
EM: Round [917] log likelihood: -13969.181994
EM: Round [918] log likelihood: -13969.181830
EM: Round [919] log likelihood: -13969.181667
EM: Round [920] log likelihood: -13969.181504
EM: Round [921] log likelihood: -13969.181342
EM: Round [922] log likelihood: -13969.181180
EM: Round [923] log likelihood: -13969.181019
EM: Round [924] log likelihood: -13969.180858
EM: Round [925] log likelihood: -13969.180698
EM: Round [926] log likelihood: -13969.180539
EM: Round [927] log likelihood: -13969.180379
EM: Round [928] log likelihood: -13969.180221
EM: Round [929] log likelihood: -13969.180063
EM: Round [930] log likelihood: -13969.179905
EM: Round [931] log likelihood: -13969.179748
EM: Round [932] log likelihood: -13969.179592
EM: Round [933] log likelihood: -13969.179436
EM: Round [934] log likelihood: -13969.179280
EM: Round [935] log likelihood: -13969.179125
EM: Round [936] log likelihood: -13969.178971
EM: Round [937] log likelihood: -13969.178817
EM: Round [938] log likelihood: -13969.178663
EM: Round [939] log likelihood: -13969.178510
EM: Round [940] log likelihood: -13969.178358
EM: Round [941] log likelihood: -13969.178206
EM: Round [942] log likelihood: -13969.178055
EM: Round [943] log likelihood: -13969.177904
EM: Round [944] log likelihood: -13969.177753
EM: Round [945] log likelihood: -13969.177603
EM: Round [946] log likelihood: -13969.177454
EM: Round [947] log likelihood: -13969.177304
EM: Round [948] log likelihood: -13969.177156
EM: Round [949] log likelihood: -13969.177008
EM: Round [950] log likelihood: -13969.176860
EM: Round [951] log likelihood: -13969.176713
EM: Round [952] log likelihood: -13969.176567
EM: Round [953] log likelihood: -13969.176420
EM: Round [954] log likelihood: -13969.176275
EM: Round [955] log likelihood: -13969.176130
EM: Round [956] log likelihood: -13969.175985
EM: Round [957] log likelihood: -13969.175841
EM: Round [958] log likelihood: -13969.175697
EM: Round [959] log likelihood: -13969.175553
EM: Round [960] log likelihood: -13969.175411
EM: Round [961] log likelihood: -13969.175268
EM: Round [962] log likelihood: -13969.175126
EM: Round [963] log likelihood: -13969.174985
EM: Round [964] log likelihood: -13969.174844
EM: Round [965] log likelihood: -13969.174703
EM: Round [966] log likelihood: -13969.174563
EM: Round [967] log likelihood: -13969.174424
EM: Round [968] log likelihood: -13969.174284
EM: Round [969] log likelihood: -13969.174146
EM: Round [970] log likelihood: -13969.174007
EM: Round [971] log likelihood: -13969.173869
EM: Round [972] log likelihood: -13969.173732
EM: Round [973] log likelihood: -13969.173595
EM: Round [974] log likelihood: -13969.173459
EM: Round [975] log likelihood: -13969.173323
EM: Round [976] log likelihood: -13969.173187
EM: Round [977] log likelihood: -13969.173052
EM: Round [978] log likelihood: -13969.172917
EM: Round [979] log likelihood: -13969.172783
EM: Round [980] log likelihood: -13969.172649
EM: Round [981] log likelihood: -13969.172515
EM: Round [982] log likelihood: -13969.172382
EM: Round [983] log likelihood: -13969.172250
EM: Round [984] log likelihood: -13969.172118
EM: Round [985] log likelihood: -13969.171986
EM: Round [986] log likelihood: -13969.171855
EM: Round [987] log likelihood: -13969.171724
EM: Round [988] log likelihood: -13969.171593
EM: Round [989] log likelihood: -13969.171463
EM: Round [990] log likelihood: -13969.171334
EM: Round [991] log likelihood: -13969.171205
EM: Round [992] log likelihood: -13969.171076
EM: Round [993] log likelihood: -13969.170948
EM: Round [994] log likelihood: -13969.170820
EM: Round [995] log likelihood: -13969.170692
EM: Round [996] log likelihood: -13969.170565
EM: Round [997] log likelihood: -13969.170438
EM: Round [998] log likelihood: -13969.170312
EM: Round [999] log likelihood: -13969.170186
EM: Round [1000] log likelihood: -13969.170061
EM: Round [1001] log likelihood: -13969.169936
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_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.uMS6WptGv5/fi_workdir/tih_rna_sample_00614_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -12221.393982
EM: Round [1] log likelihood: -12221.380464
EM: Round [2] log likelihood: -12221.380402
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1_1.fastp.fastq.gz: 253418477
Warning - not locating file: /tmp/nxf.uMS6WptGv5/tih_rna_sample_00614_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000267489.5]
WARNING, no entry stored in dbm for [ENSG00000267489.5]
WARNING, no entry stored in dbm for [ENSG00000267489.5]
WARNING, no entry stored in dbm for [ENSG00000267489.5]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000283001.2]
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 [ENSG00000236548.2]
WARNING, no entry stored in dbm for [ENSG00000236548.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000277702.1]
WARNING, no entry stored in dbm for [ENSG00000277146.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000286784.1]
WARNING, no entry stored in dbm for [ENSG00000267577.1]
WARNING, no entry stored in dbm for [ENSG00000267577.1]
WARNING, no entry stored in dbm for [ENSG00000176124.15]
WARNING, no entry stored in dbm for [ENSG00000176124.15]
ls: cannot access 'IGV_inputs': No such file or directory