Done.
-parsing GTF file: /tmp/nxf.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.kcRalF6c4R/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.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.kcRalF6c4R/fi_workdir/659_dRe-T1-TRNA-1_B23MHV2LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.kcRalF6c4R/fi_workdir/659_dRe-T1-TRNA-1_B23MHV2LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_dRe-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_dRe-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
11:01:22 : INFO : Done.
-parsing GTF file: /tmp/nxf.kcRalF6c4R/fi_workdir/659_dRe-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.kcRalF6c4R/fi_workdir/659_dRe-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam
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[3480000] -done parsing /tmp/nxf.kcRalF6c4R/fi_workdir/659_dRe-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 81,
'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 10,
'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 12,
'num genes matched < 2' => 38,
'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 9,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
'seq-similar region overlap' => 180,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 27,
'excessive soft clipping' => 17564,
'low complexity anchor region' => 191,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 182,
'small anchor length' => 163,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 760,
'exons hit < 2' => 10,
'per_id < 96' => 11669,
' ** passed ** ' => 16155,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 48,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 12
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.kcRalF6c4R/fi_workdir/659_dRe-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
[1000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L
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[1000] -fusion SPANNING read extraction for scaff: AC096582.2--SEPTIN14
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[56000] -fusion SPANNING read extraction for scaff: AGAP4--FRMPD2
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[18000] -fusion SPANNING read extraction for scaff: BMS1P7--AGAP14P
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[38000] -fusion SPANNING read extraction for scaff: BTBD9--DNAH8
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[152000] -fusion SPANNING read extraction for scaff: ETV6--DLG2
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[365000] -fusion SPANNING read extraction for scaff: LLGL2--SEPTIN9
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[179000] -fusion SPANNING read extraction for scaff: NPEPPS--AC243829.5
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[37000] -fusion SPANNING read extraction for scaff: NPHP3--ACAD11
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[99000] -fusion SPANNING read extraction for scaff: NSF--LRRC37A
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[263000] -fusion SPANNING read extraction for scaff: OLFM2--FBXL20
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[61000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13
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[83000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1
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[73000] -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2
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[43000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[64000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[55000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[6000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[11000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[7000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[21000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[9000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[10000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[31000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[200000] -fusion SPANNING read extraction for scaff: SEC31A--ATXN1
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[8000] -fusion SPANNING read extraction for scaff: SMURF2P1--LRRC37B
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[47000] -fusion SPANNING read extraction for scaff: SNU13--LLPH
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[42000] -fusion SPANNING read extraction for scaff: SPIDR--AC091096.1
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[36000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[6000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[23000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2
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[13000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[1228000] -fusion SPANNING read extraction for scaff: ZEB1--GRB7
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 16272,
'seq similar region alignment' => 65060
};
EM: Starting log likelihood: -17819.529029
EM: Round [1] log likelihood: -17802.272283
EM: Round [2] log likelihood: -17797.867958
EM: Round [3] log likelihood: -17794.518200
EM: Round [4] log likelihood: -17791.891178
EM: Round [5] log likelihood: -17789.813068
EM: Round [6] log likelihood: -17788.158780
EM: Round [7] log likelihood: -17786.835195
EM: Round [8] log likelihood: -17785.771763
EM: Round [9] log likelihood: -17784.914300
EM: Round [10] log likelihood: -17784.220746
EM: Round [11] log likelihood: -17783.658158
EM: Round [12] log likelihood: -17783.200564
EM: Round [13] log likelihood: -17782.827366
EM: Round [14] log likelihood: -17782.522156
EM: Round [15] log likelihood: -17782.271818
EM: Round [16] log likelihood: -17782.065834
EM: Round [17] log likelihood: -17781.895750
EM: Round [18] log likelihood: -17781.754757
EM: Round [19] log likelihood: -17781.637365
EM: Round [20] log likelihood: -17781.539136
EM: Round [21] log likelihood: -17781.456485
EM: Round [22] log likelihood: -17781.386509
EM: Round [23] log likelihood: -17781.326857
EM: Round [24] log likelihood: -17781.275624
EM: Round [25] log likelihood: -17781.231264
EM: Round [26] log likelihood: -17781.192525
EM: Round [27] log likelihood: -17781.158390
EM: Round [28] log likelihood: -17781.128031
EM: Round [29] log likelihood: -17781.100778
EM: Round [30] log likelihood: -17781.076086
EM: Round [31] log likelihood: -17781.053511
EM: Round [32] log likelihood: -17781.032691
EM: Round [33] log likelihood: -17781.013335
EM: Round [34] log likelihood: -17780.995201
EM: Round [35] log likelihood: -17780.978096
EM: Round [36] log likelihood: -17780.961860
EM: Round [37] log likelihood: -17780.946363
EM: Round [38] log likelihood: -17780.931500
EM: Round [39] log likelihood: -17780.917182
EM: Round [40] log likelihood: -17780.903340
EM: Round [41] log likelihood: -17780.889914
EM: Round [42] log likelihood: -17780.876857
EM: Round [43] log likelihood: -17780.864127
EM: Round [44] log likelihood: -17780.851694
EM: Round [45] log likelihood: -17780.839529
EM: Round [46] log likelihood: -17780.827610
EM: Round [47] log likelihood: -17780.815917
EM: Round [48] log likelihood: -17780.804435
EM: Round [49] log likelihood: -17780.793150
EM: Round [50] log likelihood: -17780.782051
EM: Round [51] log likelihood: -17780.771127
EM: Round [52] log likelihood: -17780.760371
EM: Round [53] log likelihood: -17780.749775
EM: Round [54] log likelihood: -17780.739332
EM: Round [55] log likelihood: -17780.729037
EM: Round [56] log likelihood: -17780.718886
EM: Round [57] log likelihood: -17780.708872
EM: Round [58] log likelihood: -17780.698993
EM: Round [59] log likelihood: -17780.689245
EM: Round [60] log likelihood: -17780.679623
EM: Round [61] log likelihood: -17780.670126
EM: Round [62] log likelihood: -17780.660750
EM: Round [63] log likelihood: -17780.651492
EM: Round [64] log likelihood: -17780.642351
EM: Round [65] log likelihood: -17780.633322
EM: Round [66] log likelihood: -17780.624405
EM: Round [67] log likelihood: -17780.615596
EM: Round [68] log likelihood: -17780.606895
EM: Round [69] log likelihood: -17780.598298
EM: Round [70] log likelihood: -17780.589804
EM: Round [71] log likelihood: -17780.581411
EM: Round [72] log likelihood: -17780.573117
EM: Round [73] log likelihood: -17780.564921
EM: Round [74] log likelihood: -17780.556820
EM: Round [75] log likelihood: -17780.548813
EM: Round [76] log likelihood: -17780.540899
EM: Round [77] log likelihood: -17780.533076
EM: Round [78] log likelihood: -17780.525342
EM: Round [79] log likelihood: -17780.517696
EM: Round [80] log likelihood: -17780.510137
EM: Round [81] log likelihood: -17780.502662
EM: Round [82] log likelihood: -17780.495272
EM: Round [83] log likelihood: -17780.487963
EM: Round [84] log likelihood: -17780.480736
EM: Round [85] log likelihood: -17780.473589
EM: Round [86] log likelihood: -17780.466520
EM: Round [87] log likelihood: -17780.459528
EM: Round [88] log likelihood: -17780.452613
EM: Round [89] log likelihood: -17780.445773
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EM: Round [91] log likelihood: -17780.432313
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EM: Round [94] log likelihood: -17780.412657
EM: Round [95] log likelihood: -17780.406244
EM: Round [96] log likelihood: -17780.399898
EM: Round [97] log likelihood: -17780.393618
EM: Round [98] log likelihood: -17780.387405
EM: Round [99] log likelihood: -17780.381256
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EM: Round [101] log likelihood: -17780.369147
EM: Round [102] log likelihood: -17780.363187
EM: Round [103] log likelihood: -17780.357287
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EM: Round [106] log likelihood: -17780.339946
EM: Round [107] log likelihood: -17780.334282
EM: Round [108] log likelihood: -17780.328676
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EM: Round [110] log likelihood: -17780.317630
EM: Round [111] log likelihood: -17780.312189
EM: Round [112] log likelihood: -17780.306803
EM: Round [113] log likelihood: -17780.301469
EM: Round [114] log likelihood: -17780.296188
EM: Round [115] log likelihood: -17780.290959
EM: Round [116] log likelihood: -17780.285781
EM: Round [117] log likelihood: -17780.280654
EM: Round [118] log likelihood: -17780.275576
EM: Round [119] log likelihood: -17780.270548
EM: Round [120] log likelihood: -17780.265568
EM: Round [121] log likelihood: -17780.260636
EM: Round [122] log likelihood: -17780.255752
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EM: Round [124] log likelihood: -17780.246122
EM: Round [125] log likelihood: -17780.241376
EM: Round [126] log likelihood: -17780.236674
EM: Round [127] log likelihood: -17780.232017
EM: Round [128] log likelihood: -17780.227404
EM: Round [129] log likelihood: -17780.222835
EM: Round [130] log likelihood: -17780.218308
EM: Round [131] log likelihood: -17780.213823
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EM: Round [133] log likelihood: -17780.204978
EM: Round [134] log likelihood: -17780.200617
EM: Round [135] log likelihood: -17780.196297
EM: Round [136] log likelihood: -17780.192016
EM: Round [137] log likelihood: -17780.187774
EM: Round [138] log likelihood: -17780.183571
EM: Round [139] log likelihood: -17780.179407
EM: Round [140] log likelihood: -17780.175280
EM: Round [141] log likelihood: -17780.171191
EM: Round [142] log likelihood: -17780.167139
EM: Round [143] log likelihood: -17780.163123
EM: Round [144] log likelihood: -17780.159144
EM: Round [145] log likelihood: -17780.155200
EM: Round [146] log likelihood: -17780.151292
EM: Round [147] log likelihood: -17780.147419
EM: Round [148] log likelihood: -17780.143580
EM: Round [149] log likelihood: -17780.139775
EM: Round [150] log likelihood: -17780.136004
EM: Round [151] log likelihood: -17780.132267
EM: Round [152] log likelihood: -17780.128562
EM: Round [153] log likelihood: -17780.124890
EM: Round [154] log likelihood: -17780.121250
EM: Round [155] log likelihood: -17780.117642
EM: Round [156] log likelihood: -17780.114066
EM: Round [157] log likelihood: -17780.110521
EM: Round [158] log likelihood: -17780.107007
EM: Round [159] log likelihood: -17780.103523
EM: Round [160] log likelihood: -17780.100069
EM: Round [161] log likelihood: -17780.096645
EM: Round [162] log likelihood: -17780.093251
EM: Round [163] log likelihood: -17780.089886
EM: Round [164] log likelihood: -17780.086550
EM: Round [165] log likelihood: -17780.083242
EM: Round [166] log likelihood: -17780.079962
EM: Round [167] log likelihood: -17780.076711
EM: Round [168] log likelihood: -17780.073487
EM: Round [169] log likelihood: -17780.070291
EM: Round [170] log likelihood: -17780.067121
EM: Round [171] log likelihood: -17780.063978
EM: Round [172] log likelihood: -17780.060862
EM: Round [173] log likelihood: -17780.057772
EM: Round [174] log likelihood: -17780.054708
EM: Round [175] log likelihood: -17780.051670
EM: Round [176] log likelihood: -17780.048657
EM: Round [177] log likelihood: -17780.045669
EM: Round [178] log likelihood: -17780.042706
EM: Round [179] log likelihood: -17780.039768
EM: Round [180] log likelihood: -17780.036854
EM: Round [181] log likelihood: -17780.033964
EM: Round [182] log likelihood: -17780.031098
EM: Round [183] log likelihood: -17780.028256
EM: Round [184] log likelihood: -17780.025437
EM: Round [185] log likelihood: -17780.022641
EM: Round [186] log likelihood: -17780.019869
EM: Round [187] log likelihood: -17780.017118
EM: Round [188] log likelihood: -17780.014391
EM: Round [189] log likelihood: -17780.011685
EM: Round [190] log likelihood: -17780.009002
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EM: Round [192] log likelihood: -17780.003700
EM: Round [193] log likelihood: -17780.001081
EM: Round [194] log likelihood: -17779.998483
EM: Round [195] log likelihood: -17779.995907
EM: Round [196] log likelihood: -17779.993351
EM: Round [197] log likelihood: -17779.990815
EM: Round [198] log likelihood: -17779.988300
EM: Round [199] log likelihood: -17779.985805
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EM: Round [201] log likelihood: -17779.980875
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EM: Round [203] log likelihood: -17779.976022
EM: Round [204] log likelihood: -17779.973625
EM: Round [205] log likelihood: -17779.971247
EM: Round [206] log likelihood: -17779.968887
EM: Round [207] log likelihood: -17779.966546
EM: Round [208] log likelihood: -17779.964224
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EM: Round [210] log likelihood: -17779.959633
EM: Round [211] log likelihood: -17779.957365
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EM: Round [215] log likelihood: -17779.948468
EM: Round [216] log likelihood: -17779.946287
EM: Round [217] log likelihood: -17779.944123
EM: Round [218] log likelihood: -17779.941976
EM: Round [219] log likelihood: -17779.939845
EM: Round [220] log likelihood: -17779.937730
EM: Round [221] log likelihood: -17779.935632
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EM: Round [442] log likelihood: -17779.703799
EM: Round [443] log likelihood: -17779.703341
EM: Round [444] log likelihood: -17779.702885
EM: Round [445] log likelihood: -17779.702433
EM: Round [446] log likelihood: -17779.701983
EM: Round [447] log likelihood: -17779.701536
EM: Round [448] log likelihood: -17779.701092
EM: Round [449] log likelihood: -17779.700650
EM: Round [450] log likelihood: -17779.700212
EM: Round [451] log likelihood: -17779.699776
EM: Round [452] log likelihood: -17779.699343
EM: Round [453] log likelihood: -17779.698912
EM: Round [454] log likelihood: -17779.698484
EM: Round [455] log likelihood: -17779.698059
EM: Round [456] log likelihood: -17779.697637
EM: Round [457] log likelihood: -17779.697217
EM: Round [458] log likelihood: -17779.696799
EM: Round [459] log likelihood: -17779.696385
EM: Round [460] log likelihood: -17779.695973
EM: Round [461] log likelihood: -17779.695563
EM: Round [462] log likelihood: -17779.695156
EM: Round [463] log likelihood: -17779.694751
EM: Round [464] log likelihood: -17779.694349
EM: Round [465] log likelihood: -17779.693950
EM: Round [466] log likelihood: -17779.693553
EM: Round [467] log likelihood: -17779.693158
EM: Round [468] log likelihood: -17779.692766
EM: Round [469] log likelihood: -17779.692376
EM: Round [470] log likelihood: -17779.691988
EM: Round [471] log likelihood: -17779.691603
EM: Round [472] log likelihood: -17779.691221
EM: Round [473] log likelihood: -17779.690840
EM: Round [474] log likelihood: -17779.690462
EM: Round [475] log likelihood: -17779.690087
EM: Round [476] log likelihood: -17779.689713
EM: Round [477] log likelihood: -17779.689342
EM: Round [478] log likelihood: -17779.688973
EM: Round [479] log likelihood: -17779.688607
EM: Round [480] log likelihood: -17779.688242
EM: Round [481] log likelihood: -17779.687880
EM: Round [482] log likelihood: -17779.687520
EM: Round [483] log likelihood: -17779.687163
EM: Round [484] log likelihood: -17779.686807
EM: Round [485] log likelihood: -17779.686454
EM: Round [486] log likelihood: -17779.686103
EM: Round [487] log likelihood: -17779.685754
EM: Round [488] log likelihood: -17779.685407
EM: Round [489] log likelihood: -17779.685062
EM: Round [490] log likelihood: -17779.684720
EM: Round [491] log likelihood: -17779.684379
EM: Round [492] log likelihood: -17779.684041
EM: Round [493] log likelihood: -17779.683704
EM: Round [494] log likelihood: -17779.683370
EM: Round [495] log likelihood: -17779.683037
EM: Round [496] log likelihood: -17779.682707
EM: Round [497] log likelihood: -17779.682379
EM: Round [498] log likelihood: -17779.682052
EM: Round [499] log likelihood: -17779.681728
EM: Round [500] log likelihood: -17779.681406
EM: Round [501] log likelihood: -17779.681085
EM: Round [502] log likelihood: -17779.680767
EM: Round [503] log likelihood: -17779.680450
EM: Round [504] log likelihood: -17779.680136
EM: Round [505] log likelihood: -17779.679823
EM: Round [506] log likelihood: -17779.679512
EM: Round [507] log likelihood: -17779.679203
EM: Round [508] log likelihood: -17779.678896
EM: Round [509] log likelihood: -17779.678591
EM: Round [510] log likelihood: -17779.678287
EM: Round [511] log likelihood: -17779.677986
EM: Round [512] log likelihood: -17779.677686
EM: Round [513] log likelihood: -17779.677388
EM: Round [514] log likelihood: -17779.677092
EM: Round [515] log likelihood: -17779.676798
EM: Round [516] log likelihood: -17779.676505
EM: Round [517] log likelihood: -17779.676214
EM: Round [518] log likelihood: -17779.675925
EM: Round [519] log likelihood: -17779.675638
EM: Round [520] log likelihood: -17779.675352
EM: Round [521] log likelihood: -17779.675068
EM: Round [522] log likelihood: -17779.674786
EM: Round [523] log likelihood: -17779.674506
EM: Round [524] log likelihood: -17779.674227
EM: Round [525] log likelihood: -17779.673950
EM: Round [526] log likelihood: -17779.673674
EM: Round [527] log likelihood: -17779.673400
EM: Round [528] log likelihood: -17779.673128
EM: Round [529] log likelihood: -17779.672858
EM: Round [530] log likelihood: -17779.672589
EM: Round [531] log likelihood: -17779.672321
EM: Round [532] log likelihood: -17779.672056
EM: Round [533] log likelihood: -17779.671792
EM: Round [534] log likelihood: -17779.671529
EM: Round [535] log likelihood: -17779.671268
EM: Round [536] log likelihood: -17779.671009
EM: Round [537] log likelihood: -17779.670751
EM: Round [538] log likelihood: -17779.670495
EM: Round [539] log likelihood: -17779.670240
EM: Round [540] log likelihood: -17779.669986
EM: Round [541] log likelihood: -17779.669735
EM: Round [542] log likelihood: -17779.669484
EM: Round [543] log likelihood: -17779.669236
EM: Round [544] log likelihood: -17779.668988
EM: Round [545] log likelihood: -17779.668743
EM: Round [546] log likelihood: -17779.668498
EM: Round [547] log likelihood: -17779.668255
EM: Round [548] log likelihood: -17779.668014
EM: Round [549] log likelihood: -17779.667774
EM: Round [550] log likelihood: -17779.667535
EM: Round [551] log likelihood: -17779.667298
EM: Round [552] log likelihood: -17779.667062
EM: Round [553] log likelihood: -17779.666828
EM: Round [554] log likelihood: -17779.666595
EM: Round [555] log likelihood: -17779.666363
EM: Round [556] log likelihood: -17779.666133
EM: Round [557] log likelihood: -17779.665904
EM: Round [558] log likelihood: -17779.665677
EM: Round [559] log likelihood: -17779.665451
EM: Round [560] log likelihood: -17779.665226
EM: Round [561] log likelihood: -17779.665002
EM: Round [562] log likelihood: -17779.664780
EM: Round [563] log likelihood: -17779.664559
EM: Round [564] log likelihood: -17779.664340
EM: Round [565] log likelihood: -17779.664122
EM: Round [566] log likelihood: -17779.663905
EM: Round [567] log likelihood: -17779.663689
EM: Round [568] log likelihood: -17779.663475
EM: Round [569] log likelihood: -17779.663262
EM: Round [570] log likelihood: -17779.663050
EM: Round [571] log likelihood: -17779.662839
EM: Round [572] log likelihood: -17779.662630
EM: Round [573] log likelihood: -17779.662422
EM: Round [574] log likelihood: -17779.662215
EM: Round [575] log likelihood: -17779.662009
EM: Round [576] log likelihood: -17779.661805
EM: Round [577] log likelihood: -17779.661601
EM: Round [578] log likelihood: -17779.661399
EM: Round [579] log likelihood: -17779.661198
EM: Round [580] log likelihood: -17779.660999
EM: Round [581] log likelihood: -17779.660800
EM: Round [582] log likelihood: -17779.660603
EM: Round [583] log likelihood: -17779.660406
EM: Round [584] log likelihood: -17779.660211
EM: Round [585] log likelihood: -17779.660018
EM: Round [586] log likelihood: -17779.659825
EM: Round [587] log likelihood: -17779.659633
EM: Round [588] log likelihood: -17779.659443
EM: Round [589] log likelihood: -17779.659253
EM: Round [590] log likelihood: -17779.659065
EM: Round [591] log likelihood: -17779.658878
EM: Round [592] log likelihood: -17779.658692
EM: Round [593] log likelihood: -17779.658507
EM: Round [594] log likelihood: -17779.658323
EM: Round [595] log likelihood: -17779.658140
EM: Round [596] log likelihood: -17779.657958
EM: Round [597] log likelihood: -17779.657778
EM: Round [598] log likelihood: -17779.657598
EM: Round [599] log likelihood: -17779.657419
EM: Round [600] log likelihood: -17779.657242
EM: Round [601] log likelihood: -17779.657065
EM: Round [602] log likelihood: -17779.656890
EM: Round [603] log likelihood: -17779.656715
EM: Round [604] log likelihood: -17779.656542
EM: Round [605] log likelihood: -17779.656369
EM: Round [606] log likelihood: -17779.656198
EM: Round [607] log likelihood: -17779.656028
EM: Round [608] log likelihood: -17779.655858
EM: Round [609] log likelihood: -17779.655690
EM: Round [610] log likelihood: -17779.655522
EM: Round [611] log likelihood: -17779.655356
EM: Round [612] log likelihood: -17779.655190
EM: Round [613] log likelihood: -17779.655026
EM: Round [614] log likelihood: -17779.654862
EM: Round [615] log likelihood: -17779.654700
EM: Round [616] log likelihood: -17779.654538
EM: Round [617] log likelihood: -17779.654377
EM: Round [618] log likelihood: -17779.654217
EM: Round [619] log likelihood: -17779.654059
EM: Round [620] log likelihood: -17779.653901
EM: Round [621] log likelihood: -17779.653744
EM: Round [622] log likelihood: -17779.653587
EM: Round [623] log likelihood: -17779.653432
EM: Round [624] log likelihood: -17779.653278
EM: Round [625] log likelihood: -17779.653124
EM: Round [626] log likelihood: -17779.652972
EM: Round [627] log likelihood: -17779.652820
EM: Round [628] log likelihood: -17779.652670
EM: Round [629] log likelihood: -17779.652520
EM: Round [630] log likelihood: -17779.652371
EM: Round [631] log likelihood: -17779.652222
EM: Round [632] log likelihood: -17779.652075
EM: Round [633] log likelihood: -17779.651929
EM: Round [634] log likelihood: -17779.651783
EM: Round [635] log likelihood: -17779.651638
EM: Round [636] log likelihood: -17779.651495
EM: Round [637] log likelihood: -17779.651351
EM: Round [638] log likelihood: -17779.651209
EM: Round [639] log likelihood: -17779.651068
EM: Round [640] log likelihood: -17779.650927
EM: Round [641] log likelihood: -17779.650787
EM: Round [642] log likelihood: -17779.650648
EM: Round [643] log likelihood: -17779.650510
EM: Round [644] log likelihood: -17779.650373
EM: Round [645] log likelihood: -17779.650236
EM: Round [646] log likelihood: -17779.650100
EM: Round [647] log likelihood: -17779.649965
EM: Round [648] log likelihood: -17779.649831
EM: Round [649] log likelihood: -17779.649698
EM: Round [650] log likelihood: -17779.649565
EM: Round [651] log likelihood: -17779.649433
EM: Round [652] log likelihood: -17779.649302
EM: Round [653] log likelihood: -17779.649171
EM: Round [654] log likelihood: -17779.649042
EM: Round [655] log likelihood: -17779.648913
EM: Round [656] log likelihood: -17779.648785
EM: Round [657] log likelihood: -17779.648657
EM: Round [658] log likelihood: -17779.648531
EM: Round [659] log likelihood: -17779.648405
EM: Round [660] log likelihood: -17779.648279
EM: Round [661] log likelihood: -17779.648155
EM: Round [662] log likelihood: -17779.648031
EM: Round [663] log likelihood: -17779.647908
EM: Round [664] log likelihood: -17779.647785
EM: Round [665] log likelihood: -17779.647664
EM: Round [666] log likelihood: -17779.647543
EM: Round [667] log likelihood: -17779.647422
EM: Round [668] log likelihood: -17779.647303
EM: Round [669] log likelihood: -17779.647184
EM: Round [670] log likelihood: -17779.647066
EM: Round [671] log likelihood: -17779.646948
EM: Round [672] log likelihood: -17779.646831
EM: Round [673] log likelihood: -17779.646715
EM: Round [674] log likelihood: -17779.646600
EM: Round [675] log likelihood: -17779.646485
EM: Round [676] log likelihood: -17779.646370
EM: Round [677] log likelihood: -17779.646257
EM: Round [678] log likelihood: -17779.646144
EM: Round [679] log likelihood: -17779.646032
EM: Round [680] log likelihood: -17779.645920
EM: Round [681] log likelihood: -17779.645809
EM: Round [682] log likelihood: -17779.645699
EM: Round [683] log likelihood: -17779.645589
EM: Round [684] log likelihood: -17779.645480
EM: Round [685] log likelihood: -17779.645372
EM: Round [686] log likelihood: -17779.645264
EM: Round [687] log likelihood: -17779.645156
EM: Round [688] log likelihood: -17779.645050
EM: Round [689] log likelihood: -17779.644944
EM: Round [690] log likelihood: -17779.644838
EM: Round [691] log likelihood: -17779.644734
EM: Round [692] log likelihood: -17779.644629
EM: Round [693] log likelihood: -17779.644526
EM: Round [694] log likelihood: -17779.644423
EM: Round [695] log likelihood: -17779.644320
EM: Round [696] log likelihood: -17779.644219
EM: Round [697] log likelihood: -17779.644117
EM: Round [698] log likelihood: -17779.644017
EM: Round [699] log likelihood: -17779.643917
EM: Round [700] log likelihood: -17779.643817
EM: Stopping iterations at round 700 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.kcRalF6c4R/659_dRe-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.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.kcRalF6c4R/659_dRe-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.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.kcRalF6c4R/659_dRe-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.kcRalF6c4R/fi_workdir/659_dRe-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.kcRalF6c4R/fi_workdir/659_dRe-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.kcRalF6c4R/fi_workdir/659_dRe-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -16710.025833
EM: Round [1] log likelihood: -16701.900955
EM: Round [2] log likelihood: -16701.896995
EM: Round [3] log likelihood: -16701.896979
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 271802730
Warning - not locating file: /tmp/nxf.kcRalF6c4R/659_dRe-T1-TRNA-1_B23MHV2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000278097.1]
WARNING, no entry stored in dbm for [ENSG00000278097.1]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000270025.2]
WARNING, no entry stored in dbm for [ENSG00000279058.2]
WARNING, no entry stored in dbm for [ENSG00000253396.1]
WARNING, no entry stored in dbm for [ENSG00000253396.1]
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 [ENSG00000253634.3]
WARNING, no entry stored in dbm for [ENSG00000253634.3]
WARNING, no entry stored in dbm for [ENSG00000253634.3]
WARNING, no entry stored in dbm for [ENSG00000253634.3]
WARNING, no entry stored in dbm for [ENSG00000253634.3]
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 [ENSG00000251378.1]
WARNING, no entry stored in dbm for [ENSG00000251378.1]
WARNING, no entry stored in dbm for [ENSG00000284634.1]
WARNING, no entry stored in dbm for [ENSG00000284634.1]
WARNING, no entry stored in dbm for [ENSG00000284634.1]
WARNING, no entry stored in dbm for [ENSG00000284634.1]
WARNING, no entry stored in dbm for [ENSG00000284634.1]
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]
ls: cannot access 'IGV_inputs': No such file or directory