Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 86347062 86347195 . - . gene_id "U8^ENSG00000202537.1"; transcript_id "ENST00000365667.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.9-201"; exon_number 1; exon_id "ENSE00001440430.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000202537.1"; orig_coord_info "chr2,86347062,86347195,-";
Error, chr discrepancy in gtf info for chr2 ENSEMBL exon 185661774 185661906 . + . gene_id "U8^ENSG00000212581.1"; transcript_id "ENST00000391279.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.16-201"; exon_number 1; exon_id "ENSE00001509063.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000212581.1"; orig_coord_info "chr2,185661774,185661906,+";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 41899111 41899253 . - . gene_id "U8^ENSG00000212145.2"; transcript_id "ENST00000390843.2"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.14-201"; exon_number 1; exon_id "ENSE00001508627.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000212145.2"; orig_coord_info "chr3,41899111,41899253,-";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 154007367 154007502 . - . gene_id "U8^ENSG00000201398.1"; transcript_id "ENST00000364528.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.5-201"; exon_number 1; exon_id "ENSE00001439291.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000201398.1"; orig_coord_info "chr3,154007367,154007502,-";
Error, chr discrepancy in gtf info for chr3 ENSEMBL exon 180542701 180542836 . + . gene_id "U8^ENSG00000201810.1"; transcript_id "ENST00000364940.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.7-201"; exon_number 1; exon_id "ENSE00001439703.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000201810.1"; orig_coord_info "chr3,180542701,180542836,+";
Error, chr discrepancy in gtf info for chr5 ENSEMBL exon 15110786 15110920 . - . gene_id "U8^ENSG00000202269.1"; transcript_id "ENST00000365399.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.8-201"; exon_number 1; exon_id "ENSE00001440162.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000202269.1"; orig_coord_info "chr5,15110786,15110920,-";
Error, chr discrepancy in gtf info for chr5 ENSEMBL exon 68873954 68874087 . + . gene_id "U8^ENSG00000212249.2"; transcript_id "ENST00000390947.2"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.15-201"; exon_number 1; exon_id "ENSE00001508731.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000212249.2"; orig_coord_info "chr5,68873954,68874087,+";
Error, chr discrepancy in gtf info for chr6 ENSEMBL exon 154905076 154905206 . - . gene_id "U8^ENSG00000238963.2"; transcript_id "ENST00000459445.2"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.20-201"; exon_number 1; exon_id "ENSE00001807926.2"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000238963.2"; orig_coord_info "chr6,154905076,154905206,-";
Error, chr discrepancy in gtf info for chr8 ENSEMBL exon 71815494 71815625 . - . gene_id "U8^ENSG00000200191.1"; transcript_id "ENST00000363321.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.3-201"; exon_number 1; exon_id "ENSE00001438084.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000200191.1"; orig_coord_info "chr8,71815494,71815625,-";
Error, chr discrepancy in gtf info for chr9 ENSEMBL exon 38147428 38147561 . + . gene_id "U8^ENSG00000200026.1"; transcript_id "ENST00000363156.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.2-201"; exon_number 1; exon_id "ENSE00001437919.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000200026.1"; orig_coord_info "chr9,38147428,38147561,+";
Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 4962436 4962568 . - . gene_id "U8^ENSG00000238840.1"; transcript_id "ENST00000459095.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.19-201"; exon_number 1; exon_id "ENSE00001808956.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000238840.1"; orig_coord_info "chr10,4962436,4962568,-";
Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 5004710 5004842 . + . gene_id "U8^ENSG00000239148.1"; transcript_id "ENST00000459141.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.22-201"; exon_number 1; exon_id "ENSE00001809269.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000239148.1"; orig_coord_info "chr10,5004710,5004842,+";
Error, chr discrepancy in gtf info for chr10 ENSEMBL exon 5093408 5093543 . - . gene_id "U8^ENSG00000239142.1"; transcript_id "ENST00000459536.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.21-201"; exon_number 1; exon_id "ENSE00001809201.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000239142.1"; orig_coord_info "chr10,5093408,5093543,-";
Error, chr discrepancy in gtf info for chr11 ENSEMBL exon 123301390 123301523 . + . gene_id "U8^ENSG00000200496.1"; transcript_id "ENST00000363626.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.4-201"; exon_number 1; exon_id "ENSE00001438389.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000200496.1"; orig_coord_info "chr11,123301390,123301523,+";
Error, chr discrepancy in gtf info for chr12 ENSEMBL exon 73764279 73764413 . - . gene_id "U8^ENSG00000201809.1"; transcript_id "ENST00000364939.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.6-201"; exon_number 1; exon_id "ENSE00001439702.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000201809.1"; orig_coord_info "chr12,73764279,73764413,-";
Error, chr discrepancy in gtf info for chr12 ENSEMBL exon 103592112 103592243 . + . gene_id "U8^ENSG00000212594.1"; transcript_id "ENST00000391292.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.17-201"; exon_number 1; exon_id "ENSE00001509076.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000212594.1"; orig_coord_info "chr12,103592112,103592243,+";
Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 30112198 30112330 . + . gene_id "U8^ENSG00000207432.1"; transcript_id "ENST00000384701.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.12-201"; exon_number 1; exon_id "ENSE00001807133.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000207432.1"; orig_coord_info "chr15,30112198,30112330,+";
Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 30384959 30385091 . - . gene_id "U8^ENSG00000238519.1"; transcript_id "ENST00000459285.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.18-201"; exon_number 1; exon_id "ENSE00001807694.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000238519.1"; orig_coord_info "chr15,30384959,30385091,-";
Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 30581184 30581316 . + . gene_id "U8^ENSG00000207430.1"; transcript_id "ENST00000384699.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.11-201"; exon_number 1; exon_id "ENSE00001808585.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000207430.1"; orig_coord_info "chr15,30581184,30581316,+";
Error, chr discrepancy in gtf info for chr15 ENSEMBL exon 32426288 32426420 . - . gene_id "U8^ENSG00000206987.1"; transcript_id "ENST00000384260.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.10-201"; exon_number 1; exon_id "ENSE00001808229.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000206987.1"; orig_coord_info "chr15,32426288,32426420,-";
Error, chr discrepancy in gtf info for chr18 ENSEMBL exon 58818883 58819016 . - . gene_id "U8^ENSG00000199713.1"; transcript_id "ENST00000362843.1"; gene_type "snoRNA"; gene_name "U8"; transcript_type "snoRNA"; transcript_name "U8.1-201"; exon_number 1; exon_id "ENSE00001437606.1"; level 3; transcript_support_level "NA"; tag "basic"; FI_gene_label "U8^ENSG00000199713.1"; orig_coord_info "chr18,58818883,58819016,-";
Done.
-parsing GTF file: /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.DmBSvM3QcW/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.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.DmBSvM3QcW/fi_workdir/tih_rna_sample_00639_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.DmBSvM3QcW/fi_workdir/tih_rna_sample_00639_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00639_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00639_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:30:49 : INFO : Done.
-parsing GTF file: /tmp/nxf.DmBSvM3QcW/fi_workdir/tih_rna_sample_00639_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.DmBSvM3QcW/fi_workdir/tih_rna_sample_00639_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[2710000] -done parsing /tmp/nxf.DmBSvM3QcW/fi_workdir/tih_rna_sample_00639_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
' ** passed ** ' => 6566,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 25,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 600,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1413,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 18,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 50,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 14,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 88,
'exons hit < 2' => 12,
'seq-similar region overlap' => 145,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 635,
'num genes matched < 2' => 86,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 9,
'excessive soft clipping' => 21220,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2500,
'per_id < 96' => 15991,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 117,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 36,
'small anchor length' => 4,
'low complexity anchor region' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 54
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.DmBSvM3QcW/fi_workdir/tih_rna_sample_00639_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[363000] -fusion SPANNING read extraction for scaff: ADGRG1--ADGRG5
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[14000] -fusion SPANNING read extraction for scaff: AL357874.3--GLIPR2
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[31000] -fusion SPANNING read extraction for scaff: ANKH--AC016575.2
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[31000] -fusion SPANNING read extraction for scaff: ANKH--U8
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[139000] -fusion SPANNING read extraction for scaff: CCSER1--REXO1
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[34000] -fusion SPANNING read extraction for scaff: CSMD1--AC019176.1
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[167000] -fusion SPANNING read extraction for scaff: EPRS1--H2BC18
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[26000] -fusion SPANNING read extraction for scaff: FBXW11--AC008632.1
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[26000] -fusion SPANNING read extraction for scaff: FBXW11--AC008663.1
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[37000] -fusion SPANNING read extraction for scaff: NBPF11--SUSD4
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[56000] -fusion SPANNING read extraction for scaff: NBPF12--SUSD4
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[92000] -fusion SPANNING read extraction for scaff: OTUD7B--PIP5K1A
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[26000] -fusion SPANNING read extraction for scaff: PAPSS1--CYP2U1-AS1
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[34000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2
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[35000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1
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[34000] -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13
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[25000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[27000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[25000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[22000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC2
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[23000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHAC1
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[22000] -fusion SPANNING read extraction for scaff: PCDHA4--PCDHA13
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[277000] -fusion SPANNING read extraction for scaff: SCNN1A--C1RL-AS1
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[11000] -fusion SPANNING read extraction for scaff: SDE2--AC253572.1
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[11000] -fusion SPANNING read extraction for scaff: SDE2--RNVU1-19
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[12000] -fusion SPANNING read extraction for scaff: SDE2--PPIAL4A
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[7000] -fusion SPANNING read extraction for scaff: SNX30--AC131274.3
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[7000] -fusion SPANNING read extraction for scaff: SNX30--AC069061.1
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[39000] -fusion SPANNING read extraction for scaff: SUSD4--TRIM11
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[148000] -fusion SPANNING read extraction for scaff: TBC1D22A--RANBP1
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[92000] -fusion SPANNING read extraction for scaff: TBL1X--MID1
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[102000] -fusion SPANNING read extraction for scaff: TPTE--BAGE2
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[62000] -fusion SPANNING read extraction for scaff: TRIM11--HYDIN2
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[16000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[83000] -fusion SPANNING read extraction for scaff: UHMK1--DDR2
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[143000] -fusion SPANNING read extraction for scaff: ZC3H7B--L3MBTL2
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 38731,
'lacks exon overlap' => 33034
};
EM: Starting log likelihood: -7252.002015
EM: Round [1] log likelihood: -7250.493655
EM: Round [2] log likelihood: -7250.003120
EM: Round [3] log likelihood: -7249.621274
EM: Round [4] log likelihood: -7249.282881
EM: Round [5] log likelihood: -7248.977903
EM: Round [6] log likelihood: -7248.701676
EM: Round [7] log likelihood: -7248.450603
EM: Round [8] log likelihood: -7248.221675
EM: Round [9] log likelihood: -7248.012336
EM: Round [10] log likelihood: -7247.820399
EM: Round [11] log likelihood: -7247.643978
EM: Round [12] log likelihood: -7247.481443
EM: Round [13] log likelihood: -7247.331375
EM: Round [14] log likelihood: -7247.192530
EM: Round [15] log likelihood: -7247.063820
EM: Round [16] log likelihood: -7246.944281
EM: Round [17] log likelihood: -7246.833064
EM: Round [18] log likelihood: -7246.729412
EM: Round [19] log likelihood: -7246.632650
EM: Round [20] log likelihood: -7246.542179
EM: Round [21] log likelihood: -7246.457457
EM: Round [22] log likelihood: -7246.378000
EM: Round [23] log likelihood: -7246.303372
EM: Round [24] log likelihood: -7246.233179
EM: Round [25] log likelihood: -7246.167066
EM: Round [26] log likelihood: -7246.104709
EM: Round [27] log likelihood: -7246.045815
EM: Round [28] log likelihood: -7245.990119
EM: Round [29] log likelihood: -7245.937379
EM: Round [30] log likelihood: -7245.887373
EM: Round [31] log likelihood: -7245.839900
EM: Round [32] log likelihood: -7245.794777
EM: Round [33] log likelihood: -7245.751834
EM: Round [34] log likelihood: -7245.710918
EM: Round [35] log likelihood: -7245.671887
EM: Round [36] log likelihood: -7245.634612
EM: Round [37] log likelihood: -7245.598973
EM: Round [38] log likelihood: -7245.564861
EM: Round [39] log likelihood: -7245.532175
EM: Round [40] log likelihood: -7245.500823
EM: Round [41] log likelihood: -7245.470720
EM: Round [42] log likelihood: -7245.441787
EM: Round [43] log likelihood: -7245.413950
EM: Round [44] log likelihood: -7245.387145
EM: Round [45] log likelihood: -7245.361307
EM: Round [46] log likelihood: -7245.336381
EM: Round [47] log likelihood: -7245.312314
EM: Round [48] log likelihood: -7245.289056
EM: Round [49] log likelihood: -7245.266563
EM: Round [50] log likelihood: -7245.244792
EM: Round [51] log likelihood: -7245.223704
EM: Round [52] log likelihood: -7245.203264
EM: Round [53] log likelihood: -7245.183437
EM: Round [54] log likelihood: -7245.164193
EM: Round [55] log likelihood: -7245.145503
EM: Round [56] log likelihood: -7245.127339
EM: Round [57] log likelihood: -7245.109677
EM: Round [58] log likelihood: -7245.092493
EM: Round [59] log likelihood: -7245.075765
EM: Round [60] log likelihood: -7245.059473
EM: Round [61] log likelihood: -7245.043598
EM: Round [62] log likelihood: -7245.028122
EM: Round [63] log likelihood: -7245.013028
EM: Round [64] log likelihood: -7244.998300
EM: Round [65] log likelihood: -7244.983925
EM: Round [66] log likelihood: -7244.969887
EM: Round [67] log likelihood: -7244.956175
EM: Round [68] log likelihood: -7244.942776
EM: Round [69] log likelihood: -7244.929678
EM: Round [70] log likelihood: -7244.916872
EM: Round [71] log likelihood: -7244.904346
EM: Round [72] log likelihood: -7244.892090
EM: Round [73] log likelihood: -7244.880097
EM: Round [74] log likelihood: -7244.868357
EM: Round [75] log likelihood: -7244.856862
EM: Round [76] log likelihood: -7244.845605
EM: Round [77] log likelihood: -7244.834578
EM: Round [78] log likelihood: -7244.823774
EM: Round [79] log likelihood: -7244.813186
EM: Round [80] log likelihood: -7244.802809
EM: Round [81] log likelihood: -7244.792635
EM: Round [82] log likelihood: -7244.782661
EM: Round [83] log likelihood: -7244.772879
EM: Round [84] log likelihood: -7244.763284
EM: Round [85] log likelihood: -7244.753873
EM: Round [86] log likelihood: -7244.744639
EM: Round [87] log likelihood: -7244.735579
EM: Round [88] log likelihood: -7244.726688
EM: Round [89] log likelihood: -7244.717961
EM: Round [90] log likelihood: -7244.709394
EM: Round [91] log likelihood: -7244.700985
EM: Round [92] log likelihood: -7244.692728
EM: Round [93] log likelihood: -7244.684620
EM: Round [94] log likelihood: -7244.676659
EM: Round [95] log likelihood: -7244.668839
EM: Round [96] log likelihood: -7244.661158
EM: Round [97] log likelihood: -7244.653614
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EM: Round [99] log likelihood: -7244.638920
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EM: Round [114] log likelihood: -7244.543514
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EM: Round [313] log likelihood: -7244.178652
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EM: Round [326] log likelihood: -7244.173149
EM: Round [327] log likelihood: -7244.172753
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EM: Round [330] log likelihood: -7244.171587
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EM: Round [401] log likelihood: -7244.151451
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EM: Round [447] log likelihood: -7244.143585
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EM: Round [465] log likelihood: -7244.141220
EM: Round [466] log likelihood: -7244.141099
EM: Round [467] log likelihood: -7244.140978
EM: Round [468] log likelihood: -7244.140858
EM: Round [469] log likelihood: -7244.140740
EM: Round [470] log likelihood: -7244.140622
EM: Round [471] log likelihood: -7244.140505
EM: Round [472] log likelihood: -7244.140389
EM: Round [473] log likelihood: -7244.140274
EM: Round [474] log likelihood: -7244.140159
EM: Round [475] log likelihood: -7244.140046
EM: Round [476] log likelihood: -7244.139934
EM: Round [477] log likelihood: -7244.139822
EM: Round [478] log likelihood: -7244.139711
EM: Round [479] log likelihood: -7244.139602
EM: Round [480] log likelihood: -7244.139493
EM: Round [481] log likelihood: -7244.139385
EM: Round [482] log likelihood: -7244.139277
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EM: Round [484] log likelihood: -7244.139065
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EM: Round [487] log likelihood: -7244.138754
EM: Round [488] log likelihood: -7244.138651
EM: Round [489] log likelihood: -7244.138550
EM: Round [490] log likelihood: -7244.138449
EM: Round [491] log likelihood: -7244.138349
EM: Stopping iterations at round 491 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.DmBSvM3QcW/fi_workdir/tih_rna_sample_00639_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.DmBSvM3QcW/fi_workdir/tih_rna_sample_00639_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.DmBSvM3QcW/fi_workdir/tih_rna_sample_00639_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6444.105917
EM: Round [1] log likelihood: -6444.105917
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1_1.fastp.fastq.gz: 295868572
Warning - not locating file: /tmp/nxf.DmBSvM3QcW/tih_rna_sample_00639_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000276975.3]
WARNING, no entry stored in dbm for [ENSG00000245293.3]
WARNING, no entry stored in dbm for [ENSG00000245293.3]
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 [ENSG00000288586.1]
ls: cannot access 'IGV_inputs': No such file or directory