Done.
-parsing GTF file: /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.3wPegTwVqQ/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.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_epG-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_epG-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
11:27:05 : INFO : Done.
-parsing GTF file: /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[5640000] -done parsing /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'exons hit < 2' => 5,
'num_hits: 7 != num_counted_on_fusion_contigs 5 ' => 10,
'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 200,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 124,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 275,
'num genes matched < 2' => 62,
' ** passed ** ' => 92233,
'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16,
'per_id < 96' => 16334,
'low complexity anchor region' => 224,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 12,
'small anchor length' => 348,
'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 48,
'num_hits: 7 != num_counted_on_fusion_contigs 2 ' => 10,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 42,
'num_hits: 6 != num_counted_on_fusion_contigs 1 ' => 2,
'excessive soft clipping' => 31220,
'seq-similar region overlap' => 435,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 4,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 3,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 45
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[51000] -fusion SPANNING read extraction for scaff: ABR--CHRNB3
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[8000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L
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[29000] -fusion SPANNING read extraction for scaff: BMPR1A--RNLS
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[33000] -fusion SPANNING read extraction for scaff: ELMO1--CC2D2B
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[29000] -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1
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[74000] -fusion SPANNING read extraction for scaff: GPATCH8--RGS9
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[66000] -fusion SPANNING read extraction for scaff: GPATCH8--LINC02563
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[29000] -fusion SPANNING read extraction for scaff: GRB2--RGS9
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[76000] -fusion SPANNING read extraction for scaff: JPX--GRHL2
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[20000] -fusion SPANNING read extraction for scaff: LIPA--TMEM106B
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[23000] -fusion SPANNING read extraction for scaff: MAP2K4--DHRS7B
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[9000] -fusion SPANNING read extraction for scaff: MAP2K4--LINC01563
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[608000] -fusion SPANNING read extraction for scaff: MBOAT2--KIDINS220
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[7000] -fusion SPANNING read extraction for scaff: MPDU1--AC022816.1
[1000]
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[9000] -fusion SPANNING read extraction for scaff: MPDU1--RPS18P12
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[83000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
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[179000] -fusion SPANNING read extraction for scaff: NTN1--MYH10
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[38000] -fusion SPANNING read extraction for scaff: PBX3--RGS9
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[43000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[48000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[46000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[53000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[55000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[50000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5
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[8000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4
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[27000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8
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[17000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11
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[12000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7
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[31000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3
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[18000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6
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[16000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12
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[20000] -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[8000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[27000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[32000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[16000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[279000] -fusion SPANNING read extraction for scaff: PDLIM5--MT-RNR2
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[49000] -fusion SPANNING read extraction for scaff: PKD2--CLUAP1
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[33000] -fusion SPANNING read extraction for scaff: PRKCA--QRICH2
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[67000] -fusion SPANNING read extraction for scaff: PTEN--RBM20
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[149000] -fusion SPANNING read extraction for scaff: QRICH2--ACTN1
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[88000] -fusion SPANNING read extraction for scaff: STX16--NPEPL1
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[41000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[8000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[1759000] -fusion SPANNING read extraction for scaff: TMPRSS2--ERG
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[26000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[184000] -fusion SPANNING read extraction for scaff: ZZEF1--PIK3R5
[1000]
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[168000] -fusion SPANNING read extraction for scaff: ZZEF1--AC002091.1
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[178000] -fusion SPANNING read extraction for scaff: ZZEF1--NTN1
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 30682,
'seq similar region alignment' => 125814
};
EM: Starting log likelihood: -76210.677926
EM: Round [1] log likelihood: -76186.606325
EM: Round [2] log likelihood: -76179.806826
EM: Round [3] log likelihood: -76174.211985
EM: Round [4] log likelihood: -76169.455397
EM: Round [5] log likelihood: -76165.327201
EM: Round [6] log likelihood: -76161.696940
EM: Round [7] log likelihood: -76158.478619
EM: Round [8] log likelihood: -76155.611999
EM: Round [9] log likelihood: -76153.052146
EM: Round [10] log likelihood: -76150.763469
EM: Round [11] log likelihood: -76148.716323
EM: Round [12] log likelihood: -76146.885074
EM: Round [13] log likelihood: -76145.247022
EM: Round [14] log likelihood: -76143.781785
EM: Round [15] log likelihood: -76142.470957
EM: Round [16] log likelihood: -76141.297885
EM: Round [17] log likelihood: -76140.247523
EM: Round [18] log likelihood: -76139.306315
EM: Round [19] log likelihood: -76138.462080
EM: Round [20] log likelihood: -76137.703912
EM: Round [21] log likelihood: -76137.022074
EM: Round [22] log likelihood: -76136.407900
EM: Round [23] log likelihood: -76135.853693
EM: Round [24] log likelihood: -76135.352631
EM: Round [25] log likelihood: -76134.898681
EM: Round [26] log likelihood: -76134.486511
EM: Round [27] log likelihood: -76134.111416
EM: Round [28] log likelihood: -76133.769248
EM: Round [29] log likelihood: -76133.456349
EM: Round [30] log likelihood: -76133.169499
EM: Round [31] log likelihood: -76132.905858
EM: Round [32] log likelihood: -76132.662927
EM: Round [33] log likelihood: -76132.438501
EM: Round [34] log likelihood: -76132.230638
EM: Round [35] log likelihood: -76132.037622
EM: Round [36] log likelihood: -76131.857942
EM: Round [37] log likelihood: -76131.690261
EM: Round [38] log likelihood: -76131.533396
EM: Round [39] log likelihood: -76131.386301
EM: Round [40] log likelihood: -76131.248050
EM: Round [41] log likelihood: -76131.117819
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EM: Round [504] log likelihood: -76126.046425
EM: Round [505] log likelihood: -76126.045761
EM: Round [506] log likelihood: -76126.045102
EM: Round [507] log likelihood: -76126.044448
EM: Round [508] log likelihood: -76126.043798
EM: Round [509] log likelihood: -76126.043152
EM: Round [510] log likelihood: -76126.042511
EM: Round [511] log likelihood: -76126.041874
EM: Round [512] log likelihood: -76126.041242
EM: Round [513] log likelihood: -76126.040614
EM: Round [514] log likelihood: -76126.039990
EM: Round [515] log likelihood: -76126.039371
EM: Round [516] log likelihood: -76126.038756
EM: Round [517] log likelihood: -76126.038145
EM: Round [518] log likelihood: -76126.037538
EM: Round [519] log likelihood: -76126.036935
EM: Round [520] log likelihood: -76126.036336
EM: Round [521] log likelihood: -76126.035742
EM: Round [522] log likelihood: -76126.035151
EM: Round [523] log likelihood: -76126.034565
EM: Round [524] log likelihood: -76126.033983
EM: Round [525] log likelihood: -76126.033404
EM: Round [526] log likelihood: -76126.032830
EM: Round [527] log likelihood: -76126.032259
EM: Round [528] log likelihood: -76126.031693
EM: Round [529] log likelihood: -76126.031130
EM: Round [530] log likelihood: -76126.030571
EM: Round [531] log likelihood: -76126.030016
EM: Round [532] log likelihood: -76126.029465
EM: Round [533] log likelihood: -76126.028917
EM: Round [534] log likelihood: -76126.028373
EM: Round [535] log likelihood: -76126.027833
EM: Round [536] log likelihood: -76126.027297
EM: Round [537] log likelihood: -76126.026764
EM: Round [538] log likelihood: -76126.026235
EM: Round [539] log likelihood: -76126.025709
EM: Round [540] log likelihood: -76126.025187
EM: Round [541] log likelihood: -76126.024669
EM: Round [542] log likelihood: -76126.024154
EM: Round [543] log likelihood: -76126.023642
EM: Round [544] log likelihood: -76126.023134
EM: Round [545] log likelihood: -76126.022630
EM: Round [546] log likelihood: -76126.022129
EM: Round [547] log likelihood: -76126.021631
EM: Round [548] log likelihood: -76126.021137
EM: Round [549] log likelihood: -76126.020646
EM: Round [550] log likelihood: -76126.020159
EM: Round [551] log likelihood: -76126.019674
EM: Round [552] log likelihood: -76126.019193
EM: Round [553] log likelihood: -76126.018716
EM: Round [554] log likelihood: -76126.018241
EM: Round [555] log likelihood: -76126.017770
EM: Round [556] log likelihood: -76126.017302
EM: Round [557] log likelihood: -76126.016837
EM: Round [558] log likelihood: -76126.016376
EM: Round [559] log likelihood: -76126.015917
EM: Round [560] log likelihood: -76126.015462
EM: Round [561] log likelihood: -76126.015009
EM: Round [562] log likelihood: -76126.014560
EM: Round [563] log likelihood: -76126.014114
EM: Round [564] log likelihood: -76126.013671
EM: Round [565] log likelihood: -76126.013230
EM: Round [566] log likelihood: -76126.012793
EM: Round [567] log likelihood: -76126.012359
EM: Round [568] log likelihood: -76126.011928
EM: Round [569] log likelihood: -76126.011499
EM: Round [570] log likelihood: -76126.011074
EM: Round [571] log likelihood: -76126.010651
EM: Round [572] log likelihood: -76126.010231
EM: Round [573] log likelihood: -76126.009814
EM: Round [574] log likelihood: -76126.009400
EM: Round [575] log likelihood: -76126.008989
EM: Round [576] log likelihood: -76126.008580
EM: Round [577] log likelihood: -76126.008175
EM: Round [578] log likelihood: -76126.007772
EM: Round [579] log likelihood: -76126.007371
EM: Round [580] log likelihood: -76126.006974
EM: Round [581] log likelihood: -76126.006579
EM: Round [582] log likelihood: -76126.006187
EM: Round [583] log likelihood: -76126.005797
EM: Round [584] log likelihood: -76126.005410
EM: Round [585] log likelihood: -76126.005026
EM: Round [586] log likelihood: -76126.004644
EM: Round [587] log likelihood: -76126.004265
EM: Round [588] log likelihood: -76126.003889
EM: Round [589] log likelihood: -76126.003515
EM: Round [590] log likelihood: -76126.003143
EM: Round [591] log likelihood: -76126.002774
EM: Round [592] log likelihood: -76126.002408
EM: Round [593] log likelihood: -76126.002044
EM: Round [594] log likelihood: -76126.001682
EM: Round [595] log likelihood: -76126.001323
EM: Round [596] log likelihood: -76126.000966
EM: Round [597] log likelihood: -76126.000612
EM: Round [598] log likelihood: -76126.000260
EM: Round [599] log likelihood: -76125.999910
EM: Round [600] log likelihood: -76125.999563
EM: Round [601] log likelihood: -76125.999218
EM: Round [602] log likelihood: -76125.998876
EM: Round [603] log likelihood: -76125.998536
EM: Round [604] log likelihood: -76125.998198
EM: Round [605] log likelihood: -76125.997862
EM: Round [606] log likelihood: -76125.997529
EM: Round [607] log likelihood: -76125.997198
EM: Round [608] log likelihood: -76125.996869
EM: Round [609] log likelihood: -76125.996542
EM: Round [610] log likelihood: -76125.996217
EM: Round [611] log likelihood: -76125.995895
EM: Round [612] log likelihood: -76125.995575
EM: Round [613] log likelihood: -76125.995257
EM: Round [614] log likelihood: -76125.994941
EM: Round [615] log likelihood: -76125.994628
EM: Round [616] log likelihood: -76125.994316
EM: Round [617] log likelihood: -76125.994006
EM: Round [618] log likelihood: -76125.993699
EM: Round [619] log likelihood: -76125.993394
EM: Round [620] log likelihood: -76125.993090
EM: Round [621] log likelihood: -76125.992789
EM: Round [622] log likelihood: -76125.992490
EM: Round [623] log likelihood: -76125.992193
EM: Round [624] log likelihood: -76125.991898
EM: Round [625] log likelihood: -76125.991604
EM: Round [626] log likelihood: -76125.991313
EM: Round [627] log likelihood: -76125.991024
EM: Round [628] log likelihood: -76125.990736
EM: Round [629] log likelihood: -76125.990451
EM: Round [630] log likelihood: -76125.990168
EM: Round [631] log likelihood: -76125.989886
EM: Round [632] log likelihood: -76125.989606
EM: Round [633] log likelihood: -76125.989328
EM: Round [634] log likelihood: -76125.989052
EM: Round [635] log likelihood: -76125.988778
EM: Round [636] log likelihood: -76125.988506
EM: Round [637] log likelihood: -76125.988236
EM: Round [638] log likelihood: -76125.987967
EM: Round [639] log likelihood: -76125.987700
EM: Round [640] log likelihood: -76125.987435
EM: Round [641] log likelihood: -76125.987172
EM: Round [642] log likelihood: -76125.986911
EM: Round [643] log likelihood: -76125.986651
EM: Round [644] log likelihood: -76125.986393
EM: Round [645] log likelihood: -76125.986137
EM: Round [646] log likelihood: -76125.985882
EM: Round [647] log likelihood: -76125.985629
EM: Round [648] log likelihood: -76125.985378
EM: Round [649] log likelihood: -76125.985129
EM: Round [650] log likelihood: -76125.984881
EM: Round [651] log likelihood: -76125.984635
EM: Round [652] log likelihood: -76125.984390
EM: Round [653] log likelihood: -76125.984148
EM: Round [654] log likelihood: -76125.983906
EM: Round [655] log likelihood: -76125.983667
EM: Round [656] log likelihood: -76125.983429
EM: Round [657] log likelihood: -76125.983193
EM: Round [658] log likelihood: -76125.982958
EM: Round [659] log likelihood: -76125.982725
EM: Round [660] log likelihood: -76125.982493
EM: Round [661] log likelihood: -76125.982263
EM: Round [662] log likelihood: -76125.982034
EM: Round [663] log likelihood: -76125.981807
EM: Round [664] log likelihood: -76125.981582
EM: Round [665] log likelihood: -76125.981358
EM: Round [666] log likelihood: -76125.981135
EM: Round [667] log likelihood: -76125.980914
EM: Round [668] log likelihood: -76125.980695
EM: Round [669] log likelihood: -76125.980477
EM: Round [670] log likelihood: -76125.980260
EM: Round [671] log likelihood: -76125.980045
EM: Round [672] log likelihood: -76125.979831
EM: Round [673] log likelihood: -76125.979619
EM: Round [674] log likelihood: -76125.979408
EM: Round [675] log likelihood: -76125.979199
EM: Round [676] log likelihood: -76125.978991
EM: Round [677] log likelihood: -76125.978784
EM: Round [678] log likelihood: -76125.978579
EM: Round [679] log likelihood: -76125.978375
EM: Round [680] log likelihood: -76125.978173
EM: Round [681] log likelihood: -76125.977972
EM: Round [682] log likelihood: -76125.977772
EM: Round [683] log likelihood: -76125.977573
EM: Round [684] log likelihood: -76125.977376
EM: Round [685] log likelihood: -76125.977180
EM: Round [686] log likelihood: -76125.976986
EM: Round [687] log likelihood: -76125.976793
EM: Round [688] log likelihood: -76125.976601
EM: Round [689] log likelihood: -76125.976410
EM: Round [690] log likelihood: -76125.976221
EM: Round [691] log likelihood: -76125.976033
EM: Round [692] log likelihood: -76125.975846
EM: Round [693] log likelihood: -76125.975660
EM: Round [694] log likelihood: -76125.975476
EM: Round [695] log likelihood: -76125.975293
EM: Round [696] log likelihood: -76125.975111
EM: Round [697] log likelihood: -76125.974930
EM: Round [698] log likelihood: -76125.974751
EM: Round [699] log likelihood: -76125.974573
EM: Round [700] log likelihood: -76125.974396
EM: Round [701] log likelihood: -76125.974220
EM: Round [702] log likelihood: -76125.974045
EM: Round [703] log likelihood: -76125.973871
EM: Round [704] log likelihood: -76125.973699
EM: Round [705] log likelihood: -76125.973528
EM: Round [706] log likelihood: -76125.973358
EM: Round [707] log likelihood: -76125.973189
EM: Round [708] log likelihood: -76125.973021
EM: Round [709] log likelihood: -76125.972854
EM: Round [710] log likelihood: -76125.972689
EM: Round [711] log likelihood: -76125.972524
EM: Round [712] log likelihood: -76125.972361
EM: Round [713] log likelihood: -76125.972199
EM: Round [714] log likelihood: -76125.972037
EM: Round [715] log likelihood: -76125.971877
EM: Round [716] log likelihood: -76125.971718
EM: Round [717] log likelihood: -76125.971560
EM: Round [718] log likelihood: -76125.971403
EM: Round [719] log likelihood: -76125.971247
EM: Round [720] log likelihood: -76125.971093
EM: Round [721] log likelihood: -76125.970939
EM: Round [722] log likelihood: -76125.970786
EM: Round [723] log likelihood: -76125.970634
EM: Round [724] log likelihood: -76125.970483
EM: Round [725] log likelihood: -76125.970334
EM: Round [726] log likelihood: -76125.970185
EM: Round [727] log likelihood: -76125.970037
EM: Round [728] log likelihood: -76125.969890
EM: Round [729] log likelihood: -76125.969745
EM: Round [730] log likelihood: -76125.969600
EM: Round [731] log likelihood: -76125.969456
EM: Round [732] log likelihood: -76125.969313
EM: Round [733] log likelihood: -76125.969171
EM: Round [734] log likelihood: -76125.969030
EM: Round [735] log likelihood: -76125.968890
EM: Round [736] log likelihood: -76125.968751
EM: Round [737] log likelihood: -76125.968613
EM: Round [738] log likelihood: -76125.968476
EM: Round [739] log likelihood: -76125.968339
EM: Round [740] log likelihood: -76125.968204
EM: Round [741] log likelihood: -76125.968069
EM: Round [742] log likelihood: -76125.967936
EM: Round [743] log likelihood: -76125.967803
EM: Round [744] log likelihood: -76125.967671
EM: Round [745] log likelihood: -76125.967540
EM: Round [746] log likelihood: -76125.967410
EM: Round [747] log likelihood: -76125.967281
EM: Round [748] log likelihood: -76125.967152
EM: Round [749] log likelihood: -76125.967025
EM: Round [750] log likelihood: -76125.966898
EM: Round [751] log likelihood: -76125.966772
EM: Round [752] log likelihood: -76125.966647
EM: Round [753] log likelihood: -76125.966523
EM: Round [754] log likelihood: -76125.966400
EM: Round [755] log likelihood: -76125.966277
EM: Round [756] log likelihood: -76125.966156
EM: Round [757] log likelihood: -76125.966035
EM: Round [758] log likelihood: -76125.965915
EM: Round [759] log likelihood: -76125.965796
EM: Round [760] log likelihood: -76125.965677
EM: Round [761] log likelihood: -76125.965559
EM: Round [762] log likelihood: -76125.965443
EM: Round [763] log likelihood: -76125.965326
EM: Round [764] log likelihood: -76125.965211
EM: Round [765] log likelihood: -76125.965097
EM: Round [766] log likelihood: -76125.964983
EM: Round [767] log likelihood: -76125.964870
EM: Round [768] log likelihood: -76125.964757
EM: Round [769] log likelihood: -76125.964646
EM: Round [770] log likelihood: -76125.964535
EM: Round [771] log likelihood: -76125.964425
EM: Round [772] log likelihood: -76125.964316
EM: Round [773] log likelihood: -76125.964207
EM: Round [774] log likelihood: -76125.964099
EM: Round [775] log likelihood: -76125.963992
EM: Round [776] log likelihood: -76125.963886
EM: Round [777] log likelihood: -76125.963780
EM: Round [778] log likelihood: -76125.963675
EM: Round [779] log likelihood: -76125.963570
EM: Round [780] log likelihood: -76125.963467
EM: Round [781] log likelihood: -76125.963364
EM: Round [782] log likelihood: -76125.963262
EM: Round [783] log likelihood: -76125.963160
EM: Round [784] log likelihood: -76125.963059
EM: Round [785] log likelihood: -76125.962959
EM: Round [786] log likelihood: -76125.962859
EM: Stopping iterations at round 786 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_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.3wPegTwVqQ/fi_workdir/659_epG-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -71928.906967
EM: Round [1] log likelihood: -71928.667971
EM: Round [2] log likelihood: -71928.667942
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 295912345
Warning - not locating file: /tmp/nxf.3wPegTwVqQ/659_epG-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [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 [ENSG00000210082.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000225470.8]
ls: cannot access 'IGV_inputs': No such file or directory