Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29297095 29297246 . - . gene_id "5_8S_rRNA^ENSG00000283568.1"; transcript_id "ENST00000637374.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.9-201"; exon_number 1; exon_id "ENSE00003799614.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283568.1"; orig_coord_info "chr20,29297095,29297246,-";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 29741510 29741661 . - . gene_id "5_8S_rRNA^ENSG00000283291.1"; transcript_id "ENST00000638132.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.8-201"; exon_number 1; exon_id "ENSE00003794628.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000283291.1"; orig_coord_info "chr20,29741510,29741661,-";
Error, chr discrepancy in gtf info for chr20 ENSEMBL exon 30484925 30485076 . - . gene_id "5_8S_rRNA^ENSG00000275877.1"; transcript_id "ENST00000614365.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.3-201"; exon_number 1; exon_id "ENSE00003742842.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000275877.1"; orig_coord_info "chr20,30484925,30485076,-";
Error, chr discrepancy in gtf info for chr21 ENSEMBL exon 8256781 8256933 . + . gene_id "5_8S_rRNA^ENSG00000277739.1"; transcript_id "ENST00000610460.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.5-201"; exon_number 1; exon_id "ENSE00003746458.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000277739.1"; orig_coord_info "chr21,8256781,8256933,+";
Error, chr discrepancy in gtf info for chr22 ENSEMBL exon 11249809 11249959 . - . gene_id "5_8S_rRNA^ENSG00000276871.1"; transcript_id "ENST00000612732.1"; gene_type "rRNA"; gene_name "5_8S_rRNA"; transcript_type "rRNA"; transcript_name "5_8S_rRNA.4-201"; exon_number 1; exon_id "ENSE00003735240.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "5_8S_rRNA^ENSG00000276871.1"; orig_coord_info "chr22,11249809,11249959,-";
Done.
-parsing GTF file: /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.oDa2yAvfMx/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.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam
* Running CMD: samtools index A673_FFPE_RNA_0001_B23LG7FLT4_3.star.sortedByCoord.out.bam
11:25:16 : INFO : Done.
-parsing GTF file: /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.gtf
-parsing /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam
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[4820000] -done parsing /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 134,
'excessive soft clipping' => 32806,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 31,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 43,
' ** passed ** ' => 35312,
'num genes matched < 2' => 21,
'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 11,
'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 60,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 55,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 1422,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 12,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 15,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 39,
'seq-similar region overlap' => 1104,
'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 8,
'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 685,
'exons hit < 2' => 11,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 32,
'per_id < 96' => 26728,
'num_hits: 9 != num_counted_on_fusion_contigs 3 ' => 18,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 72,
'small anchor length' => 119,
'low complexity anchor region' => 26,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 24,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 308,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 212,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1111
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[116000] -fusion SPANNING read extraction for scaff: AC096555.1--PCSK2
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[116000] -fusion SPANNING read extraction for scaff: ACKR2--PCSK2
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[877000] -fusion SPANNING read extraction for scaff: EWSR1--FLI1
-fusion SPANNING read extraction for scaff: FRG1DP--MLLT10P1
-fusion SPANNING read extraction for scaff: FRG1DP--5_8S_rRNA
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[93000] -fusion SPANNING read extraction for scaff: IGH-@-ext--SPG7
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[93000] -fusion SPANNING read extraction for scaff: IGH@-ext--SPG7
[1000] -fusion SPANNING read extraction for scaff: ITGA9--AC108752.1
[1000] -fusion SPANNING read extraction for scaff: ITGA9--MRPS17P3
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[1155000] -fusion SPANNING read extraction for scaff: NPM1--MT-RNR2
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[4000] -fusion SPANNING read extraction for scaff: OR4A11P--OR4A16
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[83000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[96000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[98000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[120000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[107000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[123000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[113000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[111000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[98000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[78000] -fusion SPANNING read extraction for scaff: PCDHA8--PCDHA10
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[34000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
[1000]
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
[1000]
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[9000]
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[11000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
[1000]
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[25000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
[1000]
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
[1000]
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[72000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
[1000]
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[28000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
[1000]
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[95000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[33000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[24000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[26000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[71000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[28000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[94000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[34000] -fusion SPANNING read extraction for scaff: SMURF2P1--SP2
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[120000] -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408
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[58000] -fusion SPANNING read extraction for scaff: SPG7--PLSCR5
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[58000] -fusion SPANNING read extraction for scaff: SPG7--AC092957.1
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[16000] -fusion SPANNING read extraction for scaff: SUCLA2--AL158828.1
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[16000] -fusion SPANNING read extraction for scaff: SUCLA2--AL353613.1
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[77000] -fusion SPANNING read extraction for scaff: SUPT20H--CHRDL2
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[35000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[44000] -fusion SPANNING read extraction for scaff: TMEM132B--TDG
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[140000] -fusion SPANNING read extraction for scaff: ZNF875--PCSK2
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 213784,
'lacks exon overlap' => 72048
};
EM: Starting log likelihood: -16152.747457
EM: Round [1] log likelihood: -16139.164232
EM: Round [2] log likelihood: -16135.933948
EM: Round [3] log likelihood: -16133.557758
EM: Round [4] log likelihood: -16131.561569
EM: Round [5] log likelihood: -16129.836822
EM: Round [6] log likelihood: -16128.330842
EM: Round [7] log likelihood: -16127.007231
EM: Round [8] log likelihood: -16125.837873
EM: Round [9] log likelihood: -16124.800110
EM: Round [10] log likelihood: -16123.875299
EM: Round [11] log likelihood: -16123.047911
EM: Round [12] log likelihood: -16122.304895
EM: Round [13] log likelihood: -16121.635213
EM: Round [14] log likelihood: -16121.029480
EM: Round [15] log likelihood: -16120.479677
EM: Round [16] log likelihood: -16119.978928
EM: Round [17] log likelihood: -16119.521313
EM: Round [18] log likelihood: -16119.101724
EM: Round [19] log likelihood: -16118.715738
EM: Round [20] log likelihood: -16118.359516
EM: Round [21] log likelihood: -16118.029721
EM: Round [22] log likelihood: -16117.723444
EM: Round [23] log likelihood: -16117.438146
EM: Round [24] log likelihood: -16117.171605
EM: Round [25] log likelihood: -16116.921876
EM: Round [26] log likelihood: -16116.687254
EM: Round [27] log likelihood: -16116.466237
EM: Round [28] log likelihood: -16116.257509
EM: Round [29] log likelihood: -16116.059906
EM: Round [30] log likelihood: -16115.872404
EM: Round [31] log likelihood: -16115.694097
EM: Round [32] log likelihood: -16115.524183
EM: Round [33] log likelihood: -16115.361952
EM: Round [34] log likelihood: -16115.206775
EM: Round [35] log likelihood: -16115.058091
EM: Round [36] log likelihood: -16114.915401
EM: Round [37] log likelihood: -16114.778261
EM: Round [38] log likelihood: -16114.646271
EM: Round [39] log likelihood: -16114.519078
EM: Round [40] log likelihood: -16114.396360
EM: Round [41] log likelihood: -16114.277830
EM: Round [42] log likelihood: -16114.163230
EM: Round [43] log likelihood: -16114.052324
EM: Round [44] log likelihood: -16113.944901
EM: Round [45] log likelihood: -16113.840768
EM: Round [46] log likelihood: -16113.739748
EM: Round [47] log likelihood: -16113.641683
EM: Round [48] log likelihood: -16113.546424
EM: Round [49] log likelihood: -16113.453837
EM: Round [50] log likelihood: -16113.363797
EM: Round [51] log likelihood: -16113.276190
EM: Round [52] log likelihood: -16113.190910
EM: Round [53] log likelihood: -16113.107856
EM: Round [54] log likelihood: -16113.026938
EM: Round [55] log likelihood: -16112.948069
EM: Round [56] log likelihood: -16112.871168
EM: Round [57] log likelihood: -16112.796161
EM: Round [58] log likelihood: -16112.722975
EM: Round [59] log likelihood: -16112.651544
EM: Round [60] log likelihood: -16112.581803
EM: Round [61] log likelihood: -16112.513694
EM: Round [62] log likelihood: -16112.447159
EM: Round [63] log likelihood: -16112.382143
EM: Round [64] log likelihood: -16112.318596
EM: Round [65] log likelihood: -16112.256467
EM: Round [66] log likelihood: -16112.195709
EM: Round [67] log likelihood: -16112.136279
EM: Round [68] log likelihood: -16112.078132
EM: Round [69] log likelihood: -16112.021228
EM: Round [70] log likelihood: -16111.965527
EM: Round [71] log likelihood: -16111.910990
EM: Round [72] log likelihood: -16111.857582
EM: Round [73] log likelihood: -16111.805268
EM: Round [74] log likelihood: -16111.754012
EM: Round [75] log likelihood: -16111.703784
EM: Round [76] log likelihood: -16111.654552
EM: Round [77] log likelihood: -16111.606286
EM: Round [78] log likelihood: -16111.558956
EM: Round [79] log likelihood: -16111.512535
EM: Round [80] log likelihood: -16111.466996
EM: Round [81] log likelihood: -16111.422312
EM: Round [82] log likelihood: -16111.378459
EM: Round [83] log likelihood: -16111.335413
EM: Round [84] log likelihood: -16111.293149
EM: Round [85] log likelihood: -16111.251646
EM: Round [86] log likelihood: -16111.210881
EM: Round [87] log likelihood: -16111.170833
EM: Round [88] log likelihood: -16111.131483
EM: Round [89] log likelihood: -16111.092811
EM: Round [90] log likelihood: -16111.054797
EM: Round [91] log likelihood: -16111.017424
EM: Round [92] log likelihood: -16110.980673
EM: Round [93] log likelihood: -16110.944528
EM: Round [94] log likelihood: -16110.908972
EM: Round [95] log likelihood: -16110.873989
EM: Round [96] log likelihood: -16110.839564
EM: Round [97] log likelihood: -16110.805682
EM: Round [98] log likelihood: -16110.772328
EM: Round [99] log likelihood: -16110.739489
EM: Round [100] log likelihood: -16110.707152
EM: Round [101] log likelihood: -16110.675302
EM: Round [102] log likelihood: -16110.643929
EM: Round [103] log likelihood: -16110.613019
EM: Round [104] log likelihood: -16110.582561
EM: Round [105] log likelihood: -16110.552544
EM: Round [106] log likelihood: -16110.522957
EM: Round [107] log likelihood: -16110.493788
EM: Round [108] log likelihood: -16110.465029
EM: Round [109] log likelihood: -16110.436669
EM: Round [110] log likelihood: -16110.408698
EM: Round [111] log likelihood: -16110.381108
EM: Round [112] log likelihood: -16110.353889
EM: Round [113] log likelihood: -16110.327032
EM: Round [114] log likelihood: -16110.300530
EM: Round [115] log likelihood: -16110.274375
EM: Round [116] log likelihood: -16110.248557
EM: Round [117] log likelihood: -16110.223071
EM: Round [118] log likelihood: -16110.197908
EM: Round [119] log likelihood: -16110.173062
EM: Round [120] log likelihood: -16110.148525
EM: Round [121] log likelihood: -16110.124291
EM: Round [122] log likelihood: -16110.100353
EM: Round [123] log likelihood: -16110.076706
EM: Round [124] log likelihood: -16110.053343
EM: Round [125] log likelihood: -16110.030258
EM: Round [126] log likelihood: -16110.007446
EM: Round [127] log likelihood: -16109.984901
EM: Round [128] log likelihood: -16109.962618
EM: Round [129] log likelihood: -16109.940591
EM: Round [130] log likelihood: -16109.918816
EM: Round [131] log likelihood: -16109.897288
EM: Round [132] log likelihood: -16109.876002
EM: Round [133] log likelihood: -16109.854953
EM: Round [134] log likelihood: -16109.834137
EM: Round [135] log likelihood: -16109.813550
EM: Round [136] log likelihood: -16109.793187
EM: Round [137] log likelihood: -16109.773045
EM: Round [138] log likelihood: -16109.753119
EM: Round [139] log likelihood: -16109.733405
EM: Round [140] log likelihood: -16109.713901
EM: Round [141] log likelihood: -16109.694601
EM: Round [142] log likelihood: -16109.675504
EM: Round [143] log likelihood: -16109.656604
EM: Round [144] log likelihood: -16109.637900
EM: Round [145] log likelihood: -16109.619387
EM: Round [146] log likelihood: -16109.601062
EM: Round [147] log likelihood: -16109.582923
EM: Round [148] log likelihood: -16109.564966
EM: Round [149] log likelihood: -16109.547189
EM: Round [150] log likelihood: -16109.529588
EM: Round [151] log likelihood: -16109.512161
EM: Round [152] log likelihood: -16109.494905
EM: Round [153] log likelihood: -16109.477818
EM: Round [154] log likelihood: -16109.460896
EM: Round [155] log likelihood: -16109.444138
EM: Round [156] log likelihood: -16109.427541
EM: Round [157] log likelihood: -16109.411102
EM: Round [158] log likelihood: -16109.394820
EM: Round [159] log likelihood: -16109.378691
EM: Round [160] log likelihood: -16109.362715
EM: Round [161] log likelihood: -16109.346887
EM: Round [162] log likelihood: -16109.331207
EM: Round [163] log likelihood: -16109.315673
EM: Round [164] log likelihood: -16109.300281
EM: Round [165] log likelihood: -16109.285032
EM: Round [166] log likelihood: -16109.269921
EM: Round [167] log likelihood: -16109.254948
EM: Round [168] log likelihood: -16109.240110
EM: Round [169] log likelihood: -16109.225407
EM: Round [170] log likelihood: -16109.210835
EM: Round [171] log likelihood: -16109.196394
EM: Round [172] log likelihood: -16109.182081
EM: Round [173] log likelihood: -16109.167895
EM: Round [174] log likelihood: -16109.153835
EM: Round [175] log likelihood: -16109.139898
EM: Round [176] log likelihood: -16109.126083
EM: Round [177] log likelihood: -16109.112389
EM: Round [178] log likelihood: -16109.098814
EM: Round [179] log likelihood: -16109.085357
EM: Round [180] log likelihood: -16109.072015
EM: Round [181] log likelihood: -16109.058789
EM: Round [182] log likelihood: -16109.045676
EM: Round [183] log likelihood: -16109.032674
EM: Round [184] log likelihood: -16109.019784
EM: Round [185] log likelihood: -16109.007002
EM: Round [186] log likelihood: -16108.994329
EM: Round [187] log likelihood: -16108.981762
EM: Round [188] log likelihood: -16108.969301
EM: Round [189] log likelihood: -16108.956944
EM: Round [190] log likelihood: -16108.944691
EM: Round [191] log likelihood: -16108.932539
EM: Round [192] log likelihood: -16108.920487
EM: Round [193] log likelihood: -16108.908536
EM: Round [194] log likelihood: -16108.896683
EM: Round [195] log likelihood: -16108.884927
EM: Round [196] log likelihood: -16108.873267
EM: Round [197] log likelihood: -16108.861703
EM: Round [198] log likelihood: -16108.850232
EM: Round [199] log likelihood: -16108.838855
EM: Round [200] log likelihood: -16108.827570
EM: Round [201] log likelihood: -16108.816376
EM: Round [202] log likelihood: -16108.805272
EM: Round [203] log likelihood: -16108.794257
EM: Round [204] log likelihood: -16108.783330
EM: Round [205] log likelihood: -16108.772490
EM: Round [206] log likelihood: -16108.761737
EM: Round [207] log likelihood: -16108.751069
EM: Round [208] log likelihood: -16108.740486
EM: Round [209] log likelihood: -16108.729986
EM: Round [210] log likelihood: -16108.719569
EM: Round [211] log likelihood: -16108.709234
EM: Round [212] log likelihood: -16108.698980
EM: Round [213] log likelihood: -16108.688806
EM: Round [214] log likelihood: -16108.678712
EM: Round [215] log likelihood: -16108.668696
EM: Round [216] log likelihood: -16108.658758
EM: Round [217] log likelihood: -16108.648896
EM: Round [218] log likelihood: -16108.639111
EM: Round [219] log likelihood: -16108.629402
EM: Round [220] log likelihood: -16108.619767
EM: Round [221] log likelihood: -16108.610206
EM: Round [222] log likelihood: -16108.600718
EM: Round [223] log likelihood: -16108.591303
EM: Round [224] log likelihood: -16108.581960
EM: Round [225] log likelihood: -16108.572688
EM: Round [226] log likelihood: -16108.563486
EM: Round [227] log likelihood: -16108.554353
EM: Round [228] log likelihood: -16108.545290
EM: Round [229] log likelihood: -16108.536295
EM: Round [230] log likelihood: -16108.527368
EM: Round [231] log likelihood: -16108.518508
EM: Round [232] log likelihood: -16108.509714
EM: Round [233] log likelihood: -16108.500986
EM: Round [234] log likelihood: -16108.492323
EM: Round [235] log likelihood: -16108.483725
EM: Round [236] log likelihood: -16108.475191
EM: Round [237] log likelihood: -16108.466720
EM: Round [238] log likelihood: -16108.458312
EM: Round [239] log likelihood: -16108.449965
EM: Round [240] log likelihood: -16108.441681
EM: Round [241] log likelihood: -16108.433457
EM: Round [242] log likelihood: -16108.425294
EM: Round [243] log likelihood: -16108.417191
EM: Round [244] log likelihood: -16108.409147
EM: Round [245] log likelihood: -16108.401162
EM: Round [246] log likelihood: -16108.393235
EM: Round [247] log likelihood: -16108.385366
EM: Round [248] log likelihood: -16108.377554
EM: Round [249] log likelihood: -16108.369798
EM: Round [250] log likelihood: -16108.362099
EM: Round [251] log likelihood: -16108.354455
EM: Round [252] log likelihood: -16108.346867
EM: Round [253] log likelihood: -16108.339333
EM: Round [254] log likelihood: -16108.331854
EM: Round [255] log likelihood: -16108.324428
EM: Round [256] log likelihood: -16108.317055
EM: Round [257] log likelihood: -16108.309735
EM: Round [258] log likelihood: -16108.302467
EM: Round [259] log likelihood: -16108.295251
EM: Round [260] log likelihood: -16108.288087
EM: Round [261] log likelihood: -16108.280973
EM: Round [262] log likelihood: -16108.273910
EM: Round [263] log likelihood: -16108.266897
EM: Round [264] log likelihood: -16108.259933
EM: Round [265] log likelihood: -16108.253019
EM: Round [266] log likelihood: -16108.246153
EM: Round [267] log likelihood: -16108.239336
EM: Round [268] log likelihood: -16108.232566
EM: Round [269] log likelihood: -16108.225844
EM: Round [270] log likelihood: -16108.219169
EM: Round [271] log likelihood: -16108.212541
EM: Round [272] log likelihood: -16108.205958
EM: Round [273] log likelihood: -16108.199422
EM: Round [274] log likelihood: -16108.192932
EM: Round [275] log likelihood: -16108.186486
EM: Round [276] log likelihood: -16108.180085
EM: Round [277] log likelihood: -16108.173728
EM: Round [278] log likelihood: -16108.167416
EM: Round [279] log likelihood: -16108.161147
EM: Round [280] log likelihood: -16108.154921
EM: Round [281] log likelihood: -16108.148738
EM: Round [282] log likelihood: -16108.142597
EM: Round [283] log likelihood: -16108.136499
EM: Round [284] log likelihood: -16108.130443
EM: Round [285] log likelihood: -16108.124428
EM: Round [286] log likelihood: -16108.118454
EM: Round [287] log likelihood: -16108.112520
EM: Round [288] log likelihood: -16108.106628
EM: Round [289] log likelihood: -16108.100775
EM: Round [290] log likelihood: -16108.094962
EM: Round [291] log likelihood: -16108.089189
EM: Round [292] log likelihood: -16108.083455
EM: Round [293] log likelihood: -16108.077759
EM: Round [294] log likelihood: -16108.072102
EM: Round [295] log likelihood: -16108.066483
EM: Round [296] log likelihood: -16108.060902
EM: Round [297] log likelihood: -16108.055359
EM: Round [298] log likelihood: -16108.049853
EM: Round [299] log likelihood: -16108.044384
EM: Round [300] log likelihood: -16108.038951
EM: Round [301] log likelihood: -16108.033555
EM: Round [302] log likelihood: -16108.028195
EM: Round [303] log likelihood: -16108.022871
EM: Round [304] log likelihood: -16108.017582
EM: Round [305] log likelihood: -16108.012328
EM: Round [306] log likelihood: -16108.007110
EM: Round [307] log likelihood: -16108.001926
EM: Round [308] log likelihood: -16107.996776
EM: Round [309] log likelihood: -16107.991660
EM: Round [310] log likelihood: -16107.986579
EM: Round [311] log likelihood: -16107.981531
EM: Round [312] log likelihood: -16107.976516
EM: Round [313] log likelihood: -16107.971534
EM: Round [314] log likelihood: -16107.966585
EM: Round [315] log likelihood: -16107.961669
EM: Round [316] log likelihood: -16107.956785
EM: Round [317] log likelihood: -16107.951933
EM: Round [318] log likelihood: -16107.947112
EM: Round [319] log likelihood: -16107.942323
EM: Round [320] log likelihood: -16107.937566
EM: Round [321] log likelihood: -16107.932839
EM: Round [322] log likelihood: -16107.928144
EM: Round [323] log likelihood: -16107.923479
EM: Round [324] log likelihood: -16107.918844
EM: Round [325] log likelihood: -16107.914239
EM: Round [326] log likelihood: -16107.909664
EM: Round [327] log likelihood: -16107.905119
EM: Round [328] log likelihood: -16107.900603
EM: Round [329] log likelihood: -16107.896117
EM: Round [330] log likelihood: -16107.891659
EM: Round [331] log likelihood: -16107.887230
EM: Round [332] log likelihood: -16107.882830
EM: Round [333] log likelihood: -16107.878458
EM: Round [334] log likelihood: -16107.874114
EM: Round [335] log likelihood: -16107.869798
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EM: Round [795] log likelihood: -16107.175183
EM: Round [796] log likelihood: -16107.174791
EM: Round [797] log likelihood: -16107.174400
EM: Round [798] log likelihood: -16107.174011
EM: Round [799] log likelihood: -16107.173624
EM: Round [800] log likelihood: -16107.173239
EM: Round [801] log likelihood: -16107.172855
EM: Round [802] log likelihood: -16107.172472
EM: Round [803] log likelihood: -16107.172091
EM: Round [804] log likelihood: -16107.171712
EM: Round [805] log likelihood: -16107.171334
EM: Round [806] log likelihood: -16107.170958
EM: Round [807] log likelihood: -16107.170583
EM: Round [808] log likelihood: -16107.170210
EM: Round [809] log likelihood: -16107.169838
EM: Round [810] log likelihood: -16107.169468
EM: Round [811] log likelihood: -16107.169100
EM: Round [812] log likelihood: -16107.168732
EM: Round [813] log likelihood: -16107.168367
EM: Round [814] log likelihood: -16107.168003
EM: Round [815] log likelihood: -16107.167640
EM: Round [816] log likelihood: -16107.167279
EM: Round [817] log likelihood: -16107.166919
EM: Round [818] log likelihood: -16107.166560
EM: Round [819] log likelihood: -16107.166203
EM: Round [820] log likelihood: -16107.165848
EM: Round [821] log likelihood: -16107.165494
EM: Round [822] log likelihood: -16107.165141
EM: Round [823] log likelihood: -16107.164790
EM: Round [824] log likelihood: -16107.164440
EM: Round [825] log likelihood: -16107.164092
EM: Round [826] log likelihood: -16107.163745
EM: Round [827] log likelihood: -16107.163399
EM: Round [828] log likelihood: -16107.163055
EM: Round [829] log likelihood: -16107.162712
EM: Round [830] log likelihood: -16107.162370
EM: Round [831] log likelihood: -16107.162030
EM: Round [832] log likelihood: -16107.161691
EM: Round [833] log likelihood: -16107.161354
EM: Round [834] log likelihood: -16107.161017
EM: Round [835] log likelihood: -16107.160683
EM: Round [836] log likelihood: -16107.160349
EM: Round [837] log likelihood: -16107.160017
EM: Round [838] log likelihood: -16107.159686
EM: Round [839] log likelihood: -16107.159356
EM: Round [840] log likelihood: -16107.159028
EM: Round [841] log likelihood: -16107.158701
EM: Round [842] log likelihood: -16107.158375
EM: Round [843] log likelihood: -16107.158051
EM: Round [844] log likelihood: -16107.157728
EM: Round [845] log likelihood: -16107.157406
EM: Round [846] log likelihood: -16107.157085
EM: Round [847] log likelihood: -16107.156766
EM: Round [848] log likelihood: -16107.156447
EM: Round [849] log likelihood: -16107.156130
EM: Round [850] log likelihood: -16107.155815
EM: Round [851] log likelihood: -16107.155500
EM: Round [852] log likelihood: -16107.155187
EM: Round [853] log likelihood: -16107.154875
EM: Round [854] log likelihood: -16107.154564
EM: Round [855] log likelihood: -16107.154254
EM: Round [856] log likelihood: -16107.153946
EM: Round [857] log likelihood: -16107.153639
EM: Round [858] log likelihood: -16107.153333
EM: Round [859] log likelihood: -16107.153028
EM: Round [860] log likelihood: -16107.152724
EM: Round [861] log likelihood: -16107.152421
EM: Round [862] log likelihood: -16107.152120
EM: Round [863] log likelihood: -16107.151820
EM: Round [864] log likelihood: -16107.151521
EM: Round [865] log likelihood: -16107.151223
EM: Round [866] log likelihood: -16107.150926
EM: Round [867] log likelihood: -16107.150630
EM: Round [868] log likelihood: -16107.150336
EM: Round [869] log likelihood: -16107.150042
EM: Round [870] log likelihood: -16107.149750
EM: Round [871] log likelihood: -16107.149459
EM: Round [872] log likelihood: -16107.149168
EM: Round [873] log likelihood: -16107.148879
EM: Round [874] log likelihood: -16107.148592
EM: Round [875] log likelihood: -16107.148305
EM: Round [876] log likelihood: -16107.148019
EM: Round [877] log likelihood: -16107.147734
EM: Round [878] log likelihood: -16107.147451
EM: Round [879] log likelihood: -16107.147168
EM: Round [880] log likelihood: -16107.146887
EM: Round [881] log likelihood: -16107.146606
EM: Round [882] log likelihood: -16107.146327
EM: Round [883] log likelihood: -16107.146049
EM: Round [884] log likelihood: -16107.145771
EM: Round [885] log likelihood: -16107.145495
EM: Round [886] log likelihood: -16107.145220
EM: Round [887] log likelihood: -16107.144946
EM: Round [888] log likelihood: -16107.144673
EM: Round [889] log likelihood: -16107.144401
EM: Round [890] log likelihood: -16107.144129
EM: Round [891] log likelihood: -16107.143859
EM: Round [892] log likelihood: -16107.143590
EM: Round [893] log likelihood: -16107.143322
EM: Round [894] log likelihood: -16107.143055
EM: Round [895] log likelihood: -16107.142789
EM: Round [896] log likelihood: -16107.142524
EM: Round [897] log likelihood: -16107.142260
EM: Round [898] log likelihood: -16107.141996
EM: Round [899] log likelihood: -16107.141734
EM: Round [900] log likelihood: -16107.141473
EM: Round [901] log likelihood: -16107.141213
EM: Round [902] log likelihood: -16107.140953
EM: Round [903] log likelihood: -16107.140695
EM: Round [904] log likelihood: -16107.140437
EM: Round [905] log likelihood: -16107.140181
EM: Round [906] log likelihood: -16107.139925
EM: Round [907] log likelihood: -16107.139671
EM: Round [908] log likelihood: -16107.139417
EM: Round [909] log likelihood: -16107.139164
EM: Round [910] log likelihood: -16107.138912
EM: Round [911] log likelihood: -16107.138661
EM: Round [912] log likelihood: -16107.138411
EM: Round [913] log likelihood: -16107.138162
EM: Round [914] log likelihood: -16107.137914
EM: Round [915] log likelihood: -16107.137667
EM: Round [916] log likelihood: -16107.137420
EM: Round [917] log likelihood: -16107.137175
EM: Round [918] log likelihood: -16107.136930
EM: Round [919] log likelihood: -16107.136686
EM: Round [920] log likelihood: -16107.136443
EM: Round [921] log likelihood: -16107.136201
EM: Round [922] log likelihood: -16107.135960
EM: Round [923] log likelihood: -16107.135720
EM: Round [924] log likelihood: -16107.135481
EM: Round [925] log likelihood: -16107.135242
EM: Round [926] log likelihood: -16107.135004
EM: Round [927] log likelihood: -16107.134767
EM: Round [928] log likelihood: -16107.134531
EM: Round [929] log likelihood: -16107.134296
EM: Round [930] log likelihood: -16107.134062
EM: Round [931] log likelihood: -16107.133828
EM: Round [932] log likelihood: -16107.133596
EM: Round [933] log likelihood: -16107.133364
EM: Round [934] log likelihood: -16107.133133
EM: Round [935] log likelihood: -16107.132903
EM: Round [936] log likelihood: -16107.132673
EM: Round [937] log likelihood: -16107.132445
EM: Round [938] log likelihood: -16107.132217
EM: Round [939] log likelihood: -16107.131990
EM: Round [940] log likelihood: -16107.131764
EM: Round [941] log likelihood: -16107.131538
EM: Round [942] log likelihood: -16107.131314
EM: Round [943] log likelihood: -16107.131090
EM: Round [944] log likelihood: -16107.130867
EM: Round [945] log likelihood: -16107.130645
EM: Round [946] log likelihood: -16107.130423
EM: Round [947] log likelihood: -16107.130202
EM: Round [948] log likelihood: -16107.129983
EM: Round [949] log likelihood: -16107.129763
EM: Round [950] log likelihood: -16107.129545
EM: Round [951] log likelihood: -16107.129327
EM: Round [952] log likelihood: -16107.129111
EM: Round [953] log likelihood: -16107.128894
EM: Round [954] log likelihood: -16107.128679
EM: Round [955] log likelihood: -16107.128464
EM: Round [956] log likelihood: -16107.128251
EM: Round [957] log likelihood: -16107.128037
EM: Round [958] log likelihood: -16107.127825
EM: Round [959] log likelihood: -16107.127613
EM: Round [960] log likelihood: -16107.127402
EM: Round [961] log likelihood: -16107.127192
EM: Round [962] log likelihood: -16107.126983
EM: Round [963] log likelihood: -16107.126774
EM: Round [964] log likelihood: -16107.126566
EM: Round [965] log likelihood: -16107.126359
EM: Round [966] log likelihood: -16107.126152
EM: Round [967] log likelihood: -16107.125946
EM: Round [968] log likelihood: -16107.125741
EM: Round [969] log likelihood: -16107.125536
EM: Round [970] log likelihood: -16107.125333
EM: Round [971] log likelihood: -16107.125129
EM: Round [972] log likelihood: -16107.124927
EM: Round [973] log likelihood: -16107.124725
EM: Round [974] log likelihood: -16107.124524
EM: Round [975] log likelihood: -16107.124324
EM: Round [976] log likelihood: -16107.124124
EM: Round [977] log likelihood: -16107.123925
EM: Round [978] log likelihood: -16107.123727
EM: Round [979] log likelihood: -16107.123529
EM: Round [980] log likelihood: -16107.123332
EM: Round [981] log likelihood: -16107.123136
EM: Round [982] log likelihood: -16107.122940
EM: Round [983] log likelihood: -16107.122745
EM: Round [984] log likelihood: -16107.122551
EM: Round [985] log likelihood: -16107.122357
EM: Round [986] log likelihood: -16107.122164
EM: Round [987] log likelihood: -16107.121971
EM: Round [988] log likelihood: -16107.121780
EM: Round [989] log likelihood: -16107.121589
EM: Round [990] log likelihood: -16107.121398
EM: Round [991] log likelihood: -16107.121208
EM: Round [992] log likelihood: -16107.121019
EM: Round [993] log likelihood: -16107.120830
EM: Round [994] log likelihood: -16107.120642
EM: Round [995] log likelihood: -16107.120455
EM: Round [996] log likelihood: -16107.120268
EM: Round [997] log likelihood: -16107.120082
EM: Round [998] log likelihood: -16107.119897
EM: Round [999] log likelihood: -16107.119712
EM: Round [1000] log likelihood: -16107.119528
EM: Round [1001] log likelihood: -16107.119344
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam into /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords
CMD: touch /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords > /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.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.oDa2yAvfMx/fi_workdir/A673_FFPE_RNA_0001_B23LG7FLT4_3.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -7498.098323
EM: Round [1] log likelihood: -7496.217878
EM: Round [2] log likelihood: -7496.217867
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3_1.fastp.fastq.gz: 295197448
Warning - not locating file: /tmp/nxf.oDa2yAvfMx/A673_FFPE_RNA_0001_B23LG7FLT4_3.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000248121.8]
WARNING, no entry stored in dbm for [ENSG00000253554.7]
WARNING, no entry stored in dbm for [ENSG00000253554.7]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000286152.1]
WARNING, no entry stored in dbm for [IGH-.g@-ext]
ls: cannot access 'IGV_inputs': No such file or directory