Done.
-parsing GTF file: /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.TxHFacYIpR/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.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.TxHFacYIpR/fi_workdir/659_ecd-T1-TRNA-1_B23WHTKLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.TxHFacYIpR/fi_workdir/659_ecd-T1-TRNA-1_B23WHTKLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_ecd-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_ecd-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:30:19 : INFO : Done.
-parsing GTF file: /tmp/nxf.TxHFacYIpR/fi_workdir/659_ecd-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.TxHFacYIpR/fi_workdir/659_ecd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam
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[5380000] -done parsing /tmp/nxf.TxHFacYIpR/fi_workdir/659_ecd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 6,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 21,
'num_hits: 7 != num_counted_on_fusion_contigs 6 ' => 18,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 12,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 4981,
'seq-similar region overlap' => 149,
'num_hits: 9 != num_counted_on_fusion_contigs 7 ' => 7,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 5364,
'num_hits: 8 != num_counted_on_fusion_contigs 7 ' => 7,
'num_hits: 8 != num_counted_on_fusion_contigs 5 ' => 5,
'per_id < 96' => 18001,
'num_hits: 10 != num_counted_on_fusion_contigs 6 ' => 6,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 9072,
'num_hits: 9 != num_counted_on_fusion_contigs 5 ' => 10,
'num genes matched < 2' => 212,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 28,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 55,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
'excessive soft clipping' => 34514,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 3348,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 447,
' ** passed ** ' => 13833,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 37,
'num_hits: 7 != num_counted_on_fusion_contigs 3 ' => 3,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 135,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 634,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 6878,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 339,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 2,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 632,
'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 8,
'low complexity anchor region' => 124,
'num_hits: 10 != num_counted_on_fusion_contigs 9 ' => 9,
'small anchor length' => 40
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.TxHFacYIpR/fi_workdir/659_ecd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[106000] -fusion SPANNING read extraction for scaff: AC012313.1--FRY
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[188000] -fusion SPANNING read extraction for scaff: AC060780.1--ANKS1A
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[10000] -fusion SPANNING read extraction for scaff: AC090735.1--PRKCA
-fusion SPANNING read extraction for scaff: AC129926.2--NBEAP1
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[2000] -fusion SPANNING read extraction for scaff: AC242842.2--RIIAD1
[1000] -fusion SPANNING read extraction for scaff: AC242842.2--AL589765.1
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[92000] -fusion SPANNING read extraction for scaff: APOBEC3B--TNKS2
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[46000] -fusion SPANNING read extraction for scaff: CCSER1--GRID2
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[116000] -fusion SPANNING read extraction for scaff: CD46--SCCPDH
-fusion SPANNING read extraction for scaff: CYCTP--PDE11A
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[115000] -fusion SPANNING read extraction for scaff: DOT1L--CLIP3
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[6000] -fusion SPANNING read extraction for scaff: EPHA5--RYR3
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[72000] -fusion SPANNING read extraction for scaff: EPS15L1--SLC35E1
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[625000] -fusion SPANNING read extraction for scaff: FGFR3--TACC3
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[33000] -fusion SPANNING read extraction for scaff: FNTB--FOXN3
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[18000] -fusion SPANNING read extraction for scaff: GPD1L--RPL21P40
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[29000] -fusion SPANNING read extraction for scaff: GPD1L--OSBPL10
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[43000] -fusion SPANNING read extraction for scaff: GRIPAP1--PCSK1N
-fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2
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[28000] -fusion SPANNING read extraction for scaff: HYDIN2--GPR89A
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[59000] -fusion SPANNING read extraction for scaff: IKZF2--ERBB4
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[99000] -fusion SPANNING read extraction for scaff: IQSEC1--AC006504.5
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[99000] -fusion SPANNING read extraction for scaff: IQSEC1--AC006504.2
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[68000] -fusion SPANNING read extraction for scaff: ITGB5--SNX4
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[82000] -fusion SPANNING read extraction for scaff: KIF1C--AC004771.4
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[83000] -fusion SPANNING read extraction for scaff: KIF1C--AC004771.2
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[237000] -fusion SPANNING read extraction for scaff: KMT2C--TPTE
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[86000] -fusion SPANNING read extraction for scaff: KYAT3--GBP2
-fusion SPANNING read extraction for scaff: LINC00381--NKAIN2
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-fusion SPANNING read extraction for scaff: LINC01674--POTED
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[6000] -fusion SPANNING read extraction for scaff: LINC02835--RYR3
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[22000] -fusion SPANNING read extraction for scaff: MECP2--AC244097.1
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[22000] -fusion SPANNING read extraction for scaff: MECP2--TEX28
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[21000] -fusion SPANNING read extraction for scaff: MED12L--PRKCA
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[36000] -fusion SPANNING read extraction for scaff: MINDY1--THEM4
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[18000] -fusion SPANNING read extraction for scaff: MORN1--PEX10
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[39000] -fusion SPANNING read extraction for scaff: NBPF20--FMO5
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[139000] -fusion SPANNING read extraction for scaff: NOTCH2NLC--HRNR
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[10000] -fusion SPANNING read extraction for scaff: NR2C2AP--BORCS8
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[53000] -fusion SPANNING read extraction for scaff: OTUD7B--PLEKHO1
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[34000] -fusion SPANNING read extraction for scaff: OTUD7B--AC242988.2
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[16000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[21000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[19000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[14000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[18000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[16000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[26000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[27000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[23000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[70000] -fusion SPANNING read extraction for scaff: PHIP--IL20RA
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[169000] -fusion SPANNING read extraction for scaff: PI4KB--CTSS
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[29000] -fusion SPANNING read extraction for scaff: RAB25--OLFML2B
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[88000] -fusion SPANNING read extraction for scaff: RBMXL1--GBP2
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[53000] -fusion SPANNING read extraction for scaff: RNF115--KALRN
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[45000] -fusion SPANNING read extraction for scaff: RPRD2--CTXND2
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[132000] -fusion SPANNING read extraction for scaff: RPRD2--SETDB1
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[13000] -fusion SPANNING read extraction for scaff: SETD7--AC112236.1
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[30000] -fusion SPANNING read extraction for scaff: SETD7--MGST2
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[24000] -fusion SPANNING read extraction for scaff: SNX27--IGKV1OR1-1
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[24000] -fusion SPANNING read extraction for scaff: SNX27--AC244015.1
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[30000] -fusion SPANNING read extraction for scaff: SRGAP2B--LSP1P5
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[72000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[43000] -fusion SPANNING read extraction for scaff: SYF2--RSRP1
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[29000] -fusion SPANNING read extraction for scaff: TDP1--TTC7B
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[30000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[94000] -fusion SPANNING read extraction for scaff: TPTE--BAGE2
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[49000] -fusion SPANNING read extraction for scaff: TUFT1--LCE4A
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[20000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[28000] -fusion SPANNING read extraction for scaff: UMPS--AC242852.2
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[28000] -fusion SPANNING read extraction for scaff: UMPS--FP700111.2
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[38000] -fusion SPANNING read extraction for scaff: UMPS--HYDIN
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[73000] -fusion SPANNING read extraction for scaff: USP31--COG7
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[113000] -fusion SPANNING read extraction for scaff: VGLL4--PCNX1
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[55000] -fusion SPANNING read extraction for scaff: XRN1--LINC02038
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[55000] -fusion SPANNING read extraction for scaff: XRN1--LINC02026
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[69000] -fusion SPANNING read extraction for scaff: ZMPSTE24--RLF
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[180000] -fusion SPANNING read extraction for scaff: ZNF687--CDC42SE1
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[8000] -fusion SPANNING read extraction for scaff: ZNF816--AC008507.5
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[8000] -fusion SPANNING read extraction for scaff: ZNF816--AC005597.1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 80193,
'seq similar region alignment' => 46582
};
EM: Starting log likelihood: -23690.213651
EM: Round [1] log likelihood: -23653.614416
EM: Round [2] log likelihood: -23650.841044
EM: Round [3] log likelihood: -23649.781939
EM: Round [4] log likelihood: -23649.127417
EM: Round [5] log likelihood: -23648.622992
EM: Round [6] log likelihood: -23648.204445
EM: Round [7] log likelihood: -23647.847474
EM: Round [8] log likelihood: -23647.539010
EM: Round [9] log likelihood: -23647.270344
EM: Round [10] log likelihood: -23647.034977
EM: Round [11] log likelihood: -23646.827783
EM: Round [12] log likelihood: -23646.644603
EM: Round [13] log likelihood: -23646.482013
EM: Round [14] log likelihood: -23646.337162
EM: Round [15] log likelihood: -23646.207666
EM: Round [16] log likelihood: -23646.091513
EM: Round [17] log likelihood: -23645.987000
EM: Round [18] log likelihood: -23645.892679
EM: Round [19] log likelihood: -23645.807314
EM: Round [20] log likelihood: -23645.729844
EM: Round [21] log likelihood: -23645.659357
EM: Round [22] log likelihood: -23645.595066
EM: Round [23] log likelihood: -23645.536289
EM: Round [24] log likelihood: -23645.482433
EM: Round [25] log likelihood: -23645.432982
EM: Round [26] log likelihood: -23645.387484
EM: Round [27] log likelihood: -23645.345544
EM: Round [28] log likelihood: -23645.306813
EM: Round [29] log likelihood: -23645.270985
EM: Round [30] log likelihood: -23645.237788
EM: Round [31] log likelihood: -23645.206981
EM: Round [32] log likelihood: -23645.178352
EM: Round [33] log likelihood: -23645.151707
EM: Round [34] log likelihood: -23645.126878
EM: Round [35] log likelihood: -23645.103712
EM: Round [36] log likelihood: -23645.082070
EM: Round [37] log likelihood: -23645.061830
EM: Round [38] log likelihood: -23645.042879
EM: Round [39] log likelihood: -23645.025117
EM: Round [40] log likelihood: -23645.008453
EM: Round [41] log likelihood: -23644.992802
EM: Round [42] log likelihood: -23644.978089
EM: Round [43] log likelihood: -23644.964245
EM: Round [44] log likelihood: -23644.951208
EM: Round [45] log likelihood: -23644.938918
EM: Round [46] log likelihood: -23644.927324
EM: Round [47] log likelihood: -23644.916376
EM: Round [48] log likelihood: -23644.906030
EM: Round [49] log likelihood: -23644.896244
EM: Round [50] log likelihood: -23644.886981
EM: Round [51] log likelihood: -23644.878206
EM: Round [52] log likelihood: -23644.869885
EM: Round [53] log likelihood: -23644.861990
EM: Round [54] log likelihood: -23644.854492
EM: Round [55] log likelihood: -23644.847365
EM: Round [56] log likelihood: -23644.840587
EM: Round [57] log likelihood: -23644.834133
EM: Round [58] log likelihood: -23644.827984
EM: Round [59] log likelihood: -23644.822121
EM: Round [60] log likelihood: -23644.816526
EM: Round [61] log likelihood: -23644.811182
EM: Round [62] log likelihood: -23644.806074
EM: Round [63] log likelihood: -23644.801187
EM: Round [64] log likelihood: -23644.796507
EM: Round [65] log likelihood: -23644.792023
EM: Round [66] log likelihood: -23644.787722
EM: Round [67] log likelihood: -23644.783594
EM: Round [68] log likelihood: -23644.779628
EM: Round [69] log likelihood: -23644.775815
EM: Round [70] log likelihood: -23644.772146
EM: Round [71] log likelihood: -23644.768612
EM: Round [72] log likelihood: -23644.765206
EM: Round [73] log likelihood: -23644.761919
EM: Round [74] log likelihood: -23644.758747
EM: Round [75] log likelihood: -23644.755681
EM: Round [76] log likelihood: -23644.752716
EM: Round [77] log likelihood: -23644.749846
EM: Round [78] log likelihood: -23644.747067
EM: Round [79] log likelihood: -23644.744372
EM: Round [80] log likelihood: -23644.741758
EM: Round [81] log likelihood: -23644.739220
EM: Round [82] log likelihood: -23644.736754
EM: Round [83] log likelihood: -23644.734356
EM: Round [84] log likelihood: -23644.732023
EM: Round [85] log likelihood: -23644.729751
EM: Round [86] log likelihood: -23644.727537
EM: Round [87] log likelihood: -23644.725378
EM: Round [88] log likelihood: -23644.723271
EM: Round [89] log likelihood: -23644.721214
EM: Round [90] log likelihood: -23644.719204
EM: Round [91] log likelihood: -23644.717239
EM: Round [92] log likelihood: -23644.715316
EM: Round [93] log likelihood: -23644.713434
EM: Round [94] log likelihood: -23644.711591
EM: Round [95] log likelihood: -23644.709785
EM: Round [96] log likelihood: -23644.708014
EM: Round [97] log likelihood: -23644.706277
EM: Round [98] log likelihood: -23644.704571
EM: Round [99] log likelihood: -23644.702897
EM: Round [100] log likelihood: -23644.701252
EM: Round [101] log likelihood: -23644.699635
EM: Round [102] log likelihood: -23644.698044
EM: Round [103] log likelihood: -23644.696480
EM: Round [104] log likelihood: -23644.694940
EM: Round [105] log likelihood: -23644.693424
EM: Round [106] log likelihood: -23644.691931
EM: Round [107] log likelihood: -23644.690460
EM: Round [108] log likelihood: -23644.689010
EM: Round [109] log likelihood: -23644.687581
EM: Round [110] log likelihood: -23644.686171
EM: Round [111] log likelihood: -23644.684780
EM: Round [112] log likelihood: -23644.683407
EM: Round [113] log likelihood: -23644.682052
EM: Round [114] log likelihood: -23644.680714
EM: Round [115] log likelihood: -23644.679392
EM: Round [116] log likelihood: -23644.678086
EM: Round [117] log likelihood: -23644.676796
EM: Round [118] log likelihood: -23644.675521
EM: Round [119] log likelihood: -23644.674260
EM: Round [120] log likelihood: -23644.673014
EM: Round [121] log likelihood: -23644.671781
EM: Round [122] log likelihood: -23644.670562
EM: Round [123] log likelihood: -23644.669355
EM: Round [124] log likelihood: -23644.668161
EM: Round [125] log likelihood: -23644.666980
EM: Round [126] log likelihood: -23644.665810
EM: Round [127] log likelihood: -23644.664653
EM: Round [128] log likelihood: -23644.663507
EM: Round [129] log likelihood: -23644.662371
EM: Round [130] log likelihood: -23644.661247
EM: Round [131] log likelihood: -23644.660134
EM: Round [132] log likelihood: -23644.659031
EM: Round [133] log likelihood: -23644.657938
EM: Round [134] log likelihood: -23644.656855
EM: Round [135] log likelihood: -23644.655782
EM: Round [136] log likelihood: -23644.654719
EM: Round [137] log likelihood: -23644.653665
EM: Round [138] log likelihood: -23644.652621
EM: Round [139] log likelihood: -23644.651586
EM: Round [140] log likelihood: -23644.650559
EM: Round [141] log likelihood: -23644.649542
EM: Round [142] log likelihood: -23644.648533
EM: Round [143] log likelihood: -23644.647532
EM: Round [144] log likelihood: -23644.646540
EM: Round [145] log likelihood: -23644.645556
EM: Round [146] log likelihood: -23644.644581
EM: Round [147] log likelihood: -23644.643613
EM: Round [148] log likelihood: -23644.642653
EM: Round [149] log likelihood: -23644.641702
EM: Round [150] log likelihood: -23644.640757
EM: Round [151] log likelihood: -23644.639821
EM: Round [152] log likelihood: -23644.638891
EM: Round [153] log likelihood: -23644.637969
EM: Round [154] log likelihood: -23644.637055
EM: Round [155] log likelihood: -23644.636147
EM: Round [156] log likelihood: -23644.635247
EM: Round [157] log likelihood: -23644.634354
EM: Round [158] log likelihood: -23644.633467
EM: Round [159] log likelihood: -23644.632588
EM: Round [160] log likelihood: -23644.631715
EM: Round [161] log likelihood: -23644.630849
EM: Round [162] log likelihood: -23644.629989
EM: Round [163] log likelihood: -23644.629136
EM: Round [164] log likelihood: -23644.628290
EM: Round [165] log likelihood: -23644.627449
EM: Round [166] log likelihood: -23644.626616
EM: Round [167] log likelihood: -23644.625788
EM: Round [168] log likelihood: -23644.624967
EM: Round [169] log likelihood: -23644.624152
EM: Round [170] log likelihood: -23644.623342
EM: Round [171] log likelihood: -23644.622539
EM: Round [172] log likelihood: -23644.621742
EM: Round [173] log likelihood: -23644.620951
EM: Round [174] log likelihood: -23644.620165
EM: Round [175] log likelihood: -23644.619386
EM: Round [176] log likelihood: -23644.618612
EM: Round [177] log likelihood: -23644.617844
EM: Round [178] log likelihood: -23644.617081
EM: Round [179] log likelihood: -23644.616324
EM: Round [180] log likelihood: -23644.615572
EM: Round [181] log likelihood: -23644.614826
EM: Round [182] log likelihood: -23644.614086
EM: Round [183] log likelihood: -23644.613350
EM: Round [184] log likelihood: -23644.612621
EM: Round [185] log likelihood: -23644.611896
EM: Round [186] log likelihood: -23644.611176
EM: Round [187] log likelihood: -23644.610462
EM: Round [188] log likelihood: -23644.609753
EM: Round [189] log likelihood: -23644.609049
EM: Round [190] log likelihood: -23644.608350
EM: Round [191] log likelihood: -23644.607656
EM: Round [192] log likelihood: -23644.606967
EM: Round [193] log likelihood: -23644.606283
EM: Round [194] log likelihood: -23644.605604
EM: Round [195] log likelihood: -23644.604930
EM: Round [196] log likelihood: -23644.604260
EM: Round [197] log likelihood: -23644.603596
EM: Round [198] log likelihood: -23644.602936
EM: Round [199] log likelihood: -23644.602281
EM: Round [200] log likelihood: -23644.601630
EM: Round [201] log likelihood: -23644.600984
EM: Round [202] log likelihood: -23644.600342
EM: Round [203] log likelihood: -23644.599706
EM: Round [204] log likelihood: -23644.599073
EM: Round [205] log likelihood: -23644.598445
EM: Round [206] log likelihood: -23644.597822
EM: Round [207] log likelihood: -23644.597203
EM: Round [208] log likelihood: -23644.596588
EM: Round [209] log likelihood: -23644.595978
EM: Round [210] log likelihood: -23644.595372
EM: Round [211] log likelihood: -23644.594770
EM: Round [212] log likelihood: -23644.594172
EM: Round [213] log likelihood: -23644.593579
EM: Round [214] log likelihood: -23644.592990
EM: Round [215] log likelihood: -23644.592404
EM: Round [216] log likelihood: -23644.591823
EM: Round [217] log likelihood: -23644.591247
EM: Round [218] log likelihood: -23644.590674
EM: Round [219] log likelihood: -23644.590105
EM: Round [220] log likelihood: -23644.589540
EM: Round [221] log likelihood: -23644.588979
EM: Round [222] log likelihood: -23644.588422
EM: Round [223] log likelihood: -23644.587869
EM: Round [224] log likelihood: -23644.587319
EM: Round [225] log likelihood: -23644.586774
EM: Round [226] log likelihood: -23644.586232
EM: Round [227] log likelihood: -23644.585694
EM: Round [228] log likelihood: -23644.585160
EM: Round [229] log likelihood: -23644.584630
EM: Round [230] log likelihood: -23644.584103
EM: Round [231] log likelihood: -23644.583580
EM: Round [232] log likelihood: -23644.583060
EM: Round [233] log likelihood: -23644.582544
EM: Round [234] log likelihood: -23644.582032
EM: Round [235] log likelihood: -23644.581523
EM: Round [236] log likelihood: -23644.581018
EM: Round [237] log likelihood: -23644.580516
EM: Round [238] log likelihood: -23644.580018
EM: Round [239] log likelihood: -23644.579523
EM: Round [240] log likelihood: -23644.579031
EM: Round [241] log likelihood: -23644.578543
EM: Round [242] log likelihood: -23644.578059
EM: Round [243] log likelihood: -23644.577577
EM: Round [244] log likelihood: -23644.577099
EM: Round [245] log likelihood: -23644.576625
EM: Round [246] log likelihood: -23644.576153
EM: Round [247] log likelihood: -23644.575685
EM: Round [248] log likelihood: -23644.575220
EM: Round [249] log likelihood: -23644.574758
EM: Round [250] log likelihood: -23644.574300
EM: Round [251] log likelihood: -23644.573844
EM: Round [252] log likelihood: -23644.573392
EM: Round [253] log likelihood: -23644.572942
EM: Round [254] log likelihood: -23644.572496
EM: Round [255] log likelihood: -23644.572053
EM: Round [256] log likelihood: -23644.571613
EM: Round [257] log likelihood: -23644.571176
EM: Round [258] log likelihood: -23644.570742
EM: Round [259] log likelihood: -23644.570311
EM: Round [260] log likelihood: -23644.569883
EM: Round [261] log likelihood: -23644.569457
EM: Round [262] log likelihood: -23644.569035
EM: Round [263] log likelihood: -23644.568616
EM: Round [264] log likelihood: -23644.568199
EM: Round [265] log likelihood: -23644.567785
EM: Round [266] log likelihood: -23644.567374
EM: Round [267] log likelihood: -23644.566966
EM: Round [268] log likelihood: -23644.566561
EM: Round [269] log likelihood: -23644.566158
EM: Round [270] log likelihood: -23644.565759
EM: Round [271] log likelihood: -23644.565361
EM: Round [272] log likelihood: -23644.564967
EM: Round [273] log likelihood: -23644.564575
EM: Round [274] log likelihood: -23644.564186
EM: Round [275] log likelihood: -23644.563800
EM: Round [276] log likelihood: -23644.563416
EM: Round [277] log likelihood: -23644.563035
EM: Round [278] log likelihood: -23644.562656
EM: Round [279] log likelihood: -23644.562280
EM: Round [280] log likelihood: -23644.561907
EM: Round [281] log likelihood: -23644.561536
EM: Round [282] log likelihood: -23644.561167
EM: Round [283] log likelihood: -23644.560802
EM: Round [284] log likelihood: -23644.560438
EM: Round [285] log likelihood: -23644.560077
EM: Round [286] log likelihood: -23644.559719
EM: Round [287] log likelihood: -23644.559362
EM: Round [288] log likelihood: -23644.559009
EM: Round [289] log likelihood: -23644.558657
EM: Round [290] log likelihood: -23644.558308
EM: Round [291] log likelihood: -23644.557962
EM: Round [292] log likelihood: -23644.557618
EM: Round [293] log likelihood: -23644.557276
EM: Round [294] log likelihood: -23644.556936
EM: Round [295] log likelihood: -23644.556599
EM: Round [296] log likelihood: -23644.556264
EM: Round [297] log likelihood: -23644.555931
EM: Round [298] log likelihood: -23644.555600
EM: Round [299] log likelihood: -23644.555272
EM: Round [300] log likelihood: -23644.554946
EM: Round [301] log likelihood: -23644.554622
EM: Round [302] log likelihood: -23644.554300
EM: Round [303] log likelihood: -23644.553981
EM: Round [304] log likelihood: -23644.553663
EM: Round [305] log likelihood: -23644.553348
EM: Round [306] log likelihood: -23644.553035
EM: Round [307] log likelihood: -23644.552724
EM: Round [308] log likelihood: -23644.552415
EM: Round [309] log likelihood: -23644.552108
EM: Round [310] log likelihood: -23644.551803
EM: Round [311] log likelihood: -23644.551500
EM: Round [312] log likelihood: -23644.551199
EM: Round [313] log likelihood: -23644.550901
EM: Round [314] log likelihood: -23644.550604
EM: Round [315] log likelihood: -23644.550309
EM: Round [316] log likelihood: -23644.550016
EM: Round [317] log likelihood: -23644.549726
EM: Round [318] log likelihood: -23644.549437
EM: Round [319] log likelihood: -23644.549150
EM: Round [320] log likelihood: -23644.548865
EM: Round [321] log likelihood: -23644.548582
EM: Round [322] log likelihood: -23644.548300
EM: Round [323] log likelihood: -23644.548021
EM: Round [324] log likelihood: -23644.547744
EM: Round [325] log likelihood: -23644.547468
EM: Round [326] log likelihood: -23644.547194
EM: Round [327] log likelihood: -23644.546922
EM: Round [328] log likelihood: -23644.546652
EM: Round [329] log likelihood: -23644.546384
EM: Round [330] log likelihood: -23644.546117
EM: Round [331] log likelihood: -23644.545853
EM: Round [332] log likelihood: -23644.545590
EM: Round [333] log likelihood: -23644.545328
EM: Round [334] log likelihood: -23644.545069
EM: Round [335] log likelihood: -23644.544811
EM: Round [336] log likelihood: -23644.544555
EM: Round [337] log likelihood: -23644.544301
EM: Round [338] log likelihood: -23644.544048
EM: Round [339] log likelihood: -23644.543797
EM: Round [340] log likelihood: -23644.543548
EM: Round [341] log likelihood: -23644.543300
EM: Round [342] log likelihood: -23644.543054
EM: Round [343] log likelihood: -23644.542810
EM: Round [344] log likelihood: -23644.542567
EM: Round [345] log likelihood: -23644.542326
EM: Round [346] log likelihood: -23644.542087
EM: Round [347] log likelihood: -23644.541849
EM: Round [348] log likelihood: -23644.541613
EM: Round [349] log likelihood: -23644.541378
EM: Round [350] log likelihood: -23644.541145
EM: Round [351] log likelihood: -23644.540913
EM: Round [352] log likelihood: -23644.540683
EM: Round [353] log likelihood: -23644.540454
EM: Round [354] log likelihood: -23644.540227
EM: Round [355] log likelihood: -23644.540002
EM: Round [356] log likelihood: -23644.539778
EM: Round [357] log likelihood: -23644.539555
EM: Round [358] log likelihood: -23644.539334
EM: Round [359] log likelihood: -23644.539114
EM: Round [360] log likelihood: -23644.538896
EM: Round [361] log likelihood: -23644.538679
EM: Round [362] log likelihood: -23644.538464
EM: Round [363] log likelihood: -23644.538250
EM: Round [364] log likelihood: -23644.538038
EM: Round [365] log likelihood: -23644.537827
EM: Round [366] log likelihood: -23644.537617
EM: Round [367] log likelihood: -23644.537409
EM: Round [368] log likelihood: -23644.537202
EM: Round [369] log likelihood: -23644.536997
EM: Round [370] log likelihood: -23644.536792
EM: Round [371] log likelihood: -23644.536590
EM: Round [372] log likelihood: -23644.536388
EM: Round [373] log likelihood: -23644.536188
EM: Round [374] log likelihood: -23644.535989
EM: Round [375] log likelihood: -23644.535792
EM: Round [376] log likelihood: -23644.535596
EM: Round [377] log likelihood: -23644.535401
EM: Round [378] log likelihood: -23644.535207
EM: Round [379] log likelihood: -23644.535015
EM: Round [380] log likelihood: -23644.534824
EM: Round [381] log likelihood: -23644.534634
EM: Round [382] log likelihood: -23644.534445
EM: Round [383] log likelihood: -23644.534258
EM: Round [384] log likelihood: -23644.534072
EM: Round [385] log likelihood: -23644.533887
EM: Round [386] log likelihood: -23644.533703
EM: Round [387] log likelihood: -23644.533521
EM: Round [388] log likelihood: -23644.533340
EM: Round [389] log likelihood: -23644.533160
EM: Round [390] log likelihood: -23644.532981
EM: Round [391] log likelihood: -23644.532803
EM: Round [392] log likelihood: -23644.532627
EM: Round [393] log likelihood: -23644.532452
EM: Round [394] log likelihood: -23644.532277
EM: Round [395] log likelihood: -23644.532104
EM: Round [396] log likelihood: -23644.531933
EM: Round [397] log likelihood: -23644.531762
EM: Round [398] log likelihood: -23644.531592
EM: Round [399] log likelihood: -23644.531424
EM: Round [400] log likelihood: -23644.531256
EM: Round [401] log likelihood: -23644.531090
EM: Round [402] log likelihood: -23644.530925
EM: Round [403] log likelihood: -23644.530761
EM: Round [404] log likelihood: -23644.530598
EM: Round [405] log likelihood: -23644.530436
EM: Round [406] log likelihood: -23644.530275
EM: Round [407] log likelihood: -23644.530115
EM: Round [408] log likelihood: -23644.529956
EM: Round [409] log likelihood: -23644.529798
EM: Round [410] log likelihood: -23644.529642
EM: Round [411] log likelihood: -23644.529486
EM: Round [412] log likelihood: -23644.529331
EM: Round [413] log likelihood: -23644.529178
EM: Round [414] log likelihood: -23644.529025
EM: Round [415] log likelihood: -23644.528873
EM: Round [416] log likelihood: -23644.528723
EM: Round [417] log likelihood: -23644.528573
EM: Round [418] log likelihood: -23644.528424
EM: Round [419] log likelihood: -23644.528277
EM: Round [420] log likelihood: -23644.528130
EM: Round [421] log likelihood: -23644.527984
EM: Round [422] log likelihood: -23644.527839
EM: Round [423] log likelihood: -23644.527695
EM: Round [424] log likelihood: -23644.527552
EM: Round [425] log likelihood: -23644.527410
EM: Round [426] log likelihood: -23644.527269
EM: Round [427] log likelihood: -23644.527129
EM: Round [428] log likelihood: -23644.526990
EM: Round [429] log likelihood: -23644.526852
EM: Round [430] log likelihood: -23644.526714
EM: Round [431] log likelihood: -23644.526578
EM: Round [432] log likelihood: -23644.526442
EM: Round [433] log likelihood: -23644.526308
EM: Round [434] log likelihood: -23644.526174
EM: Round [435] log likelihood: -23644.526041
EM: Round [436] log likelihood: -23644.525909
EM: Round [437] log likelihood: -23644.525777
EM: Round [438] log likelihood: -23644.525647
EM: Round [439] log likelihood: -23644.525518
EM: Round [440] log likelihood: -23644.525389
EM: Round [441] log likelihood: -23644.525261
EM: Round [442] log likelihood: -23644.525134
EM: Round [443] log likelihood: -23644.525008
EM: Round [444] log likelihood: -23644.524883
EM: Round [445] log likelihood: -23644.524758
EM: Round [446] log likelihood: -23644.524634
EM: Round [447] log likelihood: -23644.524511
EM: Round [448] log likelihood: -23644.524389
EM: Round [449] log likelihood: -23644.524268
EM: Round [450] log likelihood: -23644.524147
EM: Round [451] log likelihood: -23644.524028
EM: Round [452] log likelihood: -23644.523909
EM: Round [453] log likelihood: -23644.523791
EM: Round [454] log likelihood: -23644.523673
EM: Round [455] log likelihood: -23644.523557
EM: Round [456] log likelihood: -23644.523441
EM: Round [457] log likelihood: -23644.523326
EM: Round [458] log likelihood: -23644.523211
EM: Round [459] log likelihood: -23644.523098
EM: Round [460] log likelihood: -23644.522985
EM: Round [461] log likelihood: -23644.522873
EM: Round [462] log likelihood: -23644.522761
EM: Round [463] log likelihood: -23644.522651
EM: Round [464] log likelihood: -23644.522541
EM: Round [465] log likelihood: -23644.522431
EM: Round [466] log likelihood: -23644.522323
EM: Round [467] log likelihood: -23644.522215
EM: Round [468] log likelihood: -23644.522108
EM: Round [469] log likelihood: -23644.522002
EM: Round [470] log likelihood: -23644.521896
EM: Round [471] log likelihood: -23644.521791
EM: Round [472] log likelihood: -23644.521686
EM: Round [473] log likelihood: -23644.521583
EM: Round [474] log likelihood: -23644.521480
EM: Round [475] log likelihood: -23644.521377
EM: Round [476] log likelihood: -23644.521276
EM: Round [477] log likelihood: -23644.521175
EM: Round [478] log likelihood: -23644.521074
EM: Round [479] log likelihood: -23644.520975
EM: Stopping iterations at round 479 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.TxHFacYIpR/fi_workdir/659_ecd-T1-TRNA-1_B23WHTKLT4_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.TxHFacYIpR/fi_workdir/659_ecd-T1-TRNA-1_B23WHTKLT4_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.TxHFacYIpR/fi_workdir/659_ecd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -20971.305613
EM: Round [1] log likelihood: -20950.949588
EM: Round [2] log likelihood: -20950.099654
EM: Round [3] log likelihood: -20949.970407
EM: Round [4] log likelihood: -20949.950171
EM: Round [5] log likelihood: -20949.942760
EM: Round [6] log likelihood: -20949.936702
EM: Round [7] log likelihood: -20949.930837
EM: Round [8] log likelihood: -20949.925055
EM: Round [9] log likelihood: -20949.919343
EM: Round [10] log likelihood: -20949.913701
EM: Round [11] log likelihood: -20949.908126
EM: Round [12] log likelihood: -20949.902617
EM: Round [13] log likelihood: -20949.897173
EM: Round [14] log likelihood: -20949.891794
EM: Round [15] log likelihood: -20949.886477
EM: Round [16] log likelihood: -20949.881223
EM: Round [17] log likelihood: -20949.876029
EM: Round [18] log likelihood: -20949.870896
EM: Round [19] log likelihood: -20949.865821
EM: Round [20] log likelihood: -20949.860804
EM: Round [21] log likelihood: -20949.855844
EM: Round [22] log likelihood: -20949.850940
EM: Round [23] log likelihood: -20949.846091
EM: Round [24] log likelihood: -20949.841296
EM: Round [25] log likelihood: -20949.836555
EM: Round [26] log likelihood: -20949.831866
EM: Round [27] log likelihood: -20949.827230
EM: Round [28] log likelihood: -20949.822644
EM: Round [29] log likelihood: -20949.818108
EM: Round [30] log likelihood: -20949.813621
EM: Round [31] log likelihood: -20949.809183
EM: Round [32] log likelihood: -20949.804793
EM: Round [33] log likelihood: -20949.800450
EM: Round [34] log likelihood: -20949.796154
EM: Round [35] log likelihood: -20949.791903
EM: Round [36] log likelihood: -20949.787698
EM: Round [37] log likelihood: -20949.783536
EM: Round [38] log likelihood: -20949.779419
EM: Round [39] log likelihood: -20949.775345
EM: Round [40] log likelihood: -20949.771313
EM: Round [41] log likelihood: -20949.767323
EM: Round [42] log likelihood: -20949.763374
EM: Round [43] log likelihood: -20949.759466
EM: Round [44] log likelihood: -20949.755598
EM: Round [45] log likelihood: -20949.751770
EM: Round [46] log likelihood: -20949.747981
EM: Round [47] log likelihood: -20949.744230
EM: Round [48] log likelihood: -20949.740517
EM: Round [49] log likelihood: -20949.736841
EM: Round [50] log likelihood: -20949.733203
EM: Round [51] log likelihood: -20949.729600
EM: Round [52] log likelihood: -20949.726034
EM: Round [53] log likelihood: -20949.722503
EM: Round [54] log likelihood: -20949.719007
EM: Round [55] log likelihood: -20949.715546
EM: Round [56] log likelihood: -20949.712118
EM: Round [57] log likelihood: -20949.708724
EM: Round [58] log likelihood: -20949.705363
EM: Round [59] log likelihood: -20949.702035
EM: Round [60] log likelihood: -20949.698739
EM: Round [61] log likelihood: -20949.695475
EM: Round [62] log likelihood: -20949.692243
EM: Round [63] log likelihood: -20949.689041
EM: Round [64] log likelihood: -20949.685870
EM: Round [65] log likelihood: -20949.682730
EM: Round [66] log likelihood: -20949.679619
EM: Round [67] log likelihood: -20949.676538
EM: Round [68] log likelihood: -20949.673485
EM: Round [69] log likelihood: -20949.670462
EM: Round [70] log likelihood: -20949.667467
EM: Round [71] log likelihood: -20949.664500
EM: Round [72] log likelihood: -20949.661561
EM: Round [73] log likelihood: -20949.658649
EM: Round [74] log likelihood: -20949.655764
EM: Round [75] log likelihood: -20949.652906
EM: Round [76] log likelihood: -20949.650075
EM: Round [77] log likelihood: -20949.647269
EM: Round [78] log likelihood: -20949.644489
EM: Round [79] log likelihood: -20949.641735
EM: Round [80] log likelihood: -20949.639005
EM: Round [81] log likelihood: -20949.636301
EM: Round [82] log likelihood: -20949.633621
EM: Round [83] log likelihood: -20949.630966
EM: Round [84] log likelihood: -20949.628334
EM: Round [85] log likelihood: -20949.625726
EM: Round [86] log likelihood: -20949.623142
EM: Round [87] log likelihood: -20949.620580
EM: Round [88] log likelihood: -20949.618042
EM: Round [89] log likelihood: -20949.615526
EM: Round [90] log likelihood: -20949.613033
EM: Round [91] log likelihood: -20949.610562
EM: Round [92] log likelihood: -20949.608112
EM: Round [93] log likelihood: -20949.605684
EM: Round [94] log likelihood: -20949.603278
EM: Round [95] log likelihood: -20949.600893
EM: Round [96] log likelihood: -20949.598529
EM: Round [97] log likelihood: -20949.596185
EM: Round [98] log likelihood: -20949.593862
EM: Round [99] log likelihood: -20949.591559
EM: Round [100] log likelihood: -20949.589276
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EM: Round [530] log likelihood: -20949.303196
EM: Round [531] log likelihood: -20949.303089
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EM: Round [539] log likelihood: -20949.302257
EM: Round [540] log likelihood: -20949.302156
EM: Round [541] log likelihood: -20949.302055
EM: Round [542] log likelihood: -20949.301955
EM: Stopping iterations at round 542 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 296106793
Warning - not locating file: /tmp/nxf.TxHFacYIpR/659_ecd-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000267002.4]
WARNING, no entry stored in dbm for [ENSG00000267002.4]
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WARNING, no entry stored in dbm for [ENSG00000226240.2]
WARNING, no entry stored in dbm for [ENSG00000277009.1]
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WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000232098.3]
WARNING, no entry stored in dbm for [ENSG00000285822.1]
WARNING, no entry stored in dbm for [ENSG00000258590.5]
WARNING, no entry stored in dbm for [ENSG00000285822.1]
WARNING, no entry stored in dbm for [ENSG00000258590.5]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000228159.2]
WARNING, no entry stored in dbm for [ENSG00000276975.3]
WARNING, no entry stored in dbm for [ENSG00000276975.3]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000187172.15]
WARNING, no entry stored in dbm for [ENSG00000249909.1]
WARNING, no entry stored in dbm for [ENSG00000262678.1]
WARNING, no entry stored in dbm for [ENSG00000284964.1]
WARNING, no entry stored in dbm for [ENSG00000227045.1]
WARNING, no entry stored in dbm for [ENSG00000235670.1]
WARNING, no entry stored in dbm for [ENSG00000253784.1]
WARNING, no entry stored in dbm for [ENSG00000262227.1]
WARNING, no entry stored in dbm for [ENSG00000262227.1]
WARNING, no entry stored in dbm for [ENSG00000273825.1]
WARNING, no entry stored in dbm for [ENSG00000267575.7]
WARNING, no entry stored in dbm for [ENSG00000267575.7]
ls: cannot access 'IGV_inputs': No such file or directory