Done.
-parsing GTF file: /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.NMeURXWyeZ/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.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_rd-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_rd-T1-TRNA-1_B23WHTKLT4_1.star.sortedByCoord.out.bam
11:37:47 : INFO : Done.
-parsing GTF file: /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.gtf
-parsing /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam

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[3160000]   -done parsing /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 48,
          'per_id < 96' => 11571,
          'num_hits: 8 != num_counted_on_fusion_contigs 6 ' => 48,
          ' ** passed ** ' => 92895,
          'num_hits: 8 != num_counted_on_fusion_contigs 4 ' => 8,
          'exons hit < 2' => 6,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 32,
          'seq-similar region overlap' => 1260,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 3686,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 66,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 24,
          'num_hits: 8 != num_counted_on_fusion_contigs 2 ' => 4,
          'excessive soft clipping' => 18028,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 4,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 242,
          'low complexity anchor region' => 254,
          'num genes matched < 2' => 521,
          'small anchor length' => 404
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[3000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

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[1177000]   
[1178000]   
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[1180000]   
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[1188000]   
[1189000]   
[1190000]   
[1191000]   
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[1195000]   
[1196000]   
[1197000]   
[1198000]   
[1199000]   
[1200000]   
[1201000]   
[1202000]   -fusion SPANNING read extraction for scaff: NAB2--STAT6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
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[20000]   
[21000]   
[22000]   
[23000]   
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[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
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[60000]   
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[70000]   
[71000]   
[72000]   
[73000]   
[74000]   
[75000]   
[76000]   
[77000]   
[78000]   
[79000]   
[80000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
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[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   -fusion SPANNING read extraction for scaff: PCDHGA2--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC5

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   
[40000]   
[41000]   
[42000]   
[43000]   
[44000]   
[45000]   
[46000]   
[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   
[60000]   
[61000]   
[62000]   
[63000]   
[64000]   
[65000]   
[66000]   
[67000]   
[68000]   
[69000]   
[70000]   
[71000]   
[72000]   
[73000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGC3

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGA6--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
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[33000]   -fusion SPANNING read extraction for scaff: SOGA3--KIAA0408

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[1191000]   -fusion SPANNING read extraction for scaff: STAT6--NAB2

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[21000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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[141000]   -fusion SPANNING read extraction for scaff: TMEM106B--THSD7A

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[16000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 37899,
          'lacks exon overlap' => 88552
        };
EM: Starting log likelihood: -26595.931124
EM: Round [1] log likelihood: -26504.739775
EM: Round [2] log likelihood: -26494.323491
EM: Round [3] log likelihood: -26485.957770
EM: Round [4] log likelihood: -26479.046297
EM: Round [5] log likelihood: -26473.287262
EM: Round [6] log likelihood: -26468.452261
EM: Round [7] log likelihood: -26464.364515
EM: Round [8] log likelihood: -26460.885438
EM: Round [9] log likelihood: -26457.905153
EM: Round [10] log likelihood: -26455.335680
EM: Round [11] log likelihood: -26453.105982
EM: Round [12] log likelihood: -26451.158306
EM: Round [13] log likelihood: -26449.445444
EM: Round [14] log likelihood: -26447.928644
EM: Round [15] log likelihood: -26446.575998
EM: Round [16] log likelihood: -26445.361163
EM: Round [17] log likelihood: -26444.262360
EM: Round [18] log likelihood: -26443.261552
EM: Round [19] log likelihood: -26442.343789
EM: Round [20] log likelihood: -26441.496665
EM: Round [21] log likelihood: -26440.709878
EM: Round [22] log likelihood: -26439.974864
EM: Round [23] log likelihood: -26439.284497
EM: Round [24] log likelihood: -26438.632839
EM: Round [25] log likelihood: -26438.014937
EM: Round [26] log likelihood: -26437.426652
EM: Round [27] log likelihood: -26436.864517
EM: Round [28] log likelihood: -26436.325623
EM: Round [29] log likelihood: -26435.807521
EM: Round [30] log likelihood: -26435.308144
EM: Round [31] log likelihood: -26434.825741
EM: Round [32] log likelihood: -26434.358823
EM: Round [33] log likelihood: -26433.906118
EM: Round [34] log likelihood: -26433.466535
EM: Round [35] log likelihood: -26433.039132
EM: Round [36] log likelihood: -26432.623091
EM: Round [37] log likelihood: -26432.217702
EM: Round [38] log likelihood: -26431.822338
EM: Round [39] log likelihood: -26431.436447
EM: Round [40] log likelihood: -26431.059539
EM: Round [41] log likelihood: -26430.691175
EM: Round [42] log likelihood: -26430.330960
EM: Round [43] log likelihood: -26429.978537
EM: Round [44] log likelihood: -26429.633579
EM: Round [45] log likelihood: -26429.295789
EM: Round [46] log likelihood: -26428.964892
EM: Round [47] log likelihood: -26428.640635
EM: Round [48] log likelihood: -26428.322781
EM: Round [49] log likelihood: -26428.011111
EM: Round [50] log likelihood: -26427.705417
EM: Round [51] log likelihood: -26427.405505
EM: Round [52] log likelihood: -26427.111193
EM: Round [53] log likelihood: -26426.822308
EM: Round [54] log likelihood: -26426.538685
EM: Round [55] log likelihood: -26426.260168
EM: Round [56] log likelihood: -26425.986610
EM: Round [57] log likelihood: -26425.717867
EM: Round [58] log likelihood: -26425.453805
EM: Round [59] log likelihood: -26425.194294
EM: Round [60] log likelihood: -26424.939210
EM: Round [61] log likelihood: -26424.688434
EM: Round [62] log likelihood: -26424.441852
EM: Round [63] log likelihood: -26424.199354
EM: Round [64] log likelihood: -26423.960835
EM: Round [65] log likelihood: -26423.726192
EM: Round [66] log likelihood: -26423.495327
EM: Round [67] log likelihood: -26423.268148
EM: Round [68] log likelihood: -26423.044562
EM: Round [69] log likelihood: -26422.824481
EM: Round [70] log likelihood: -26422.607822
EM: Round [71] log likelihood: -26422.394502
EM: Round [72] log likelihood: -26422.184443
EM: Round [73] log likelihood: -26421.977567
EM: Round [74] log likelihood: -26421.773802
EM: Round [75] log likelihood: -26421.573075
EM: Round [76] log likelihood: -26421.375318
EM: Round [77] log likelihood: -26421.180464
EM: Round [78] log likelihood: -26420.988447
EM: Round [79] log likelihood: -26420.799207
EM: Round [80] log likelihood: -26420.612680
EM: Round [81] log likelihood: -26420.428810
EM: Round [82] log likelihood: -26420.247539
EM: Round [83] log likelihood: -26420.068810
EM: Round [84] log likelihood: -26419.892572
EM: Round [85] log likelihood: -26419.718772
EM: Round [86] log likelihood: -26419.547358
EM: Round [87] log likelihood: -26419.378284
EM: Round [88] log likelihood: -26419.211499
EM: Round [89] log likelihood: -26419.046960
EM: Round [90] log likelihood: -26418.884620
EM: Round [91] log likelihood: -26418.724436
EM: Round [92] log likelihood: -26418.566365
EM: Round [93] log likelihood: -26418.410367
EM: Round [94] log likelihood: -26418.256402
EM: Round [95] log likelihood: -26418.104430
EM: Round [96] log likelihood: -26417.954413
EM: Round [97] log likelihood: -26417.806315
EM: Round [98] log likelihood: -26417.660100
EM: Round [99] log likelihood: -26417.515733
EM: Round [100] log likelihood: -26417.373179
EM: Round [101] log likelihood: -26417.232406
EM: Round [102] log likelihood: -26417.093382
EM: Round [103] log likelihood: -26416.956075
EM: Round [104] log likelihood: -26416.820454
EM: Round [105] log likelihood: -26416.686490
EM: Round [106] log likelihood: -26416.554153
EM: Round [107] log likelihood: -26416.423416
EM: Round [108] log likelihood: -26416.294249
EM: Round [109] log likelihood: -26416.166628
EM: Round [110] log likelihood: -26416.040524
EM: Round [111] log likelihood: -26415.915913
EM: Round [112] log likelihood: -26415.792769
EM: Round [113] log likelihood: -26415.671068
EM: Round [114] log likelihood: -26415.550786
EM: Round [115] log likelihood: -26415.431899
EM: Round [116] log likelihood: -26415.314385
EM: Round [117] log likelihood: -26415.198222
EM: Round [118] log likelihood: -26415.083388
EM: Round [119] log likelihood: -26414.969861
EM: Round [120] log likelihood: -26414.857621
EM: Round [121] log likelihood: -26414.746647
EM: Round [122] log likelihood: -26414.636919
EM: Round [123] log likelihood: -26414.528419
EM: Round [124] log likelihood: -26414.421126
EM: Round [125] log likelihood: -26414.315023
EM: Round [126] log likelihood: -26414.210092
EM: Round [127] log likelihood: -26414.106313
EM: Round [128] log likelihood: -26414.003671
EM: Round [129] log likelihood: -26413.902148
EM: Round [130] log likelihood: -26413.801726
EM: Round [131] log likelihood: -26413.702391
EM: Round [132] log likelihood: -26413.604126
EM: Round [133] log likelihood: -26413.506915
EM: Round [134] log likelihood: -26413.410742
EM: Round [135] log likelihood: -26413.315593
EM: Round [136] log likelihood: -26413.221454
EM: Round [137] log likelihood: -26413.128309
EM: Round [138] log likelihood: -26413.036144
EM: Round [139] log likelihood: -26412.944946
EM: Round [140] log likelihood: -26412.854700
EM: Round [141] log likelihood: -26412.765394
EM: Round [142] log likelihood: -26412.677015
EM: Round [143] log likelihood: -26412.589549
EM: Round [144] log likelihood: -26412.502984
EM: Round [145] log likelihood: -26412.417307
EM: Round [146] log likelihood: -26412.332507
EM: Round [147] log likelihood: -26412.248572
EM: Round [148] log likelihood: -26412.165489
EM: Round [149] log likelihood: -26412.083248
EM: Round [150] log likelihood: -26412.001837
EM: Round [151] log likelihood: -26411.921245
EM: Round [152] log likelihood: -26411.841462
EM: Round [153] log likelihood: -26411.762476
EM: Round [154] log likelihood: -26411.684277
EM: Round [155] log likelihood: -26411.606855
EM: Round [156] log likelihood: -26411.530199
EM: Round [157] log likelihood: -26411.454301
EM: Round [158] log likelihood: -26411.379150
EM: Round [159] log likelihood: -26411.304736
EM: Round [160] log likelihood: -26411.231050
EM: Round [161] log likelihood: -26411.158083
EM: Round [162] log likelihood: -26411.085826
EM: Round [163] log likelihood: -26411.014270
EM: Round [164] log likelihood: -26410.943406
EM: Round [165] log likelihood: -26410.873226
EM: Round [166] log likelihood: -26410.803720
EM: Round [167] log likelihood: -26410.734881
EM: Round [168] log likelihood: -26410.666700
EM: Round [169] log likelihood: -26410.599170
EM: Round [170] log likelihood: -26410.532282
EM: Round [171] log likelihood: -26410.466028
EM: Round [172] log likelihood: -26410.400402
EM: Round [173] log likelihood: -26410.335395
EM: Round [174] log likelihood: -26410.270999
EM: Round [175] log likelihood: -26410.207208
EM: Round [176] log likelihood: -26410.144015
EM: Round [177] log likelihood: -26410.081412
EM: Round [178] log likelihood: -26410.019392
EM: Round [179] log likelihood: -26409.957948
EM: Round [180] log likelihood: -26409.897074
EM: Round [181] log likelihood: -26409.836763
EM: Round [182] log likelihood: -26409.777008
EM: Round [183] log likelihood: -26409.717804
EM: Round [184] log likelihood: -26409.659143
EM: Round [185] log likelihood: -26409.601019
EM: Round [186] log likelihood: -26409.543426
EM: Round [187] log likelihood: -26409.486359
EM: Round [188] log likelihood: -26409.429810
EM: Round [189] log likelihood: -26409.373775
EM: Round [190] log likelihood: -26409.318247
EM: Round [191] log likelihood: -26409.263221
EM: Round [192] log likelihood: -26409.208691
EM: Round [193] log likelihood: -26409.154651
EM: Round [194] log likelihood: -26409.101097
EM: Round [195] log likelihood: -26409.048022
EM: Round [196] log likelihood: -26408.995421
EM: Round [197] log likelihood: -26408.943289
EM: Round [198] log likelihood: -26408.891622
EM: Round [199] log likelihood: -26408.840413
EM: Round [200] log likelihood: -26408.789658
EM: Round [201] log likelihood: -26408.739351
EM: Round [202] log likelihood: -26408.689489
EM: Round [203] log likelihood: -26408.640066
EM: Round [204] log likelihood: -26408.591077
EM: Round [205] log likelihood: -26408.542518
EM: Round [206] log likelihood: -26408.494384
EM: Round [207] log likelihood: -26408.446670
EM: Round [208] log likelihood: -26408.399373
EM: Round [209] log likelihood: -26408.352487
EM: Round [210] log likelihood: -26408.306009
EM: Round [211] log likelihood: -26408.259933
EM: Round [212] log likelihood: -26408.214257
EM: Round [213] log likelihood: -26408.168974
EM: Round [214] log likelihood: -26408.124083
EM: Round [215] log likelihood: -26408.079577
EM: Round [216] log likelihood: -26408.035454
EM: Round [217] log likelihood: -26407.991709
EM: Round [218] log likelihood: -26407.948339
EM: Round [219] log likelihood: -26407.905339
EM: Round [220] log likelihood: -26407.862706
EM: Round [221] log likelihood: -26407.820436
EM: Round [222] log likelihood: -26407.778525
EM: Round [223] log likelihood: -26407.736969
EM: Round [224] log likelihood: -26407.695766
EM: Round [225] log likelihood: -26407.654911
EM: Round [226] log likelihood: -26407.614401
EM: Round [227] log likelihood: -26407.574232
EM: Round [228] log likelihood: -26407.534401
EM: Round [229] log likelihood: -26407.494904
EM: Round [230] log likelihood: -26407.455739
EM: Round [231] log likelihood: -26407.416902
EM: Round [232] log likelihood: -26407.378389
EM: Round [233] log likelihood: -26407.340198
EM: Round [234] log likelihood: -26407.302324
EM: Round [235] log likelihood: -26407.264766
EM: Round [236] log likelihood: -26407.227520
EM: Round [237] log likelihood: -26407.190582
EM: Round [238] log likelihood: -26407.153951
EM: Round [239] log likelihood: -26407.117622
EM: Round [240] log likelihood: -26407.081593
EM: Round [241] log likelihood: -26407.045860
EM: Round [242] log likelihood: -26407.010422
EM: Round [243] log likelihood: -26406.975275
EM: Round [244] log likelihood: -26406.940417
EM: Round [245] log likelihood: -26406.905844
EM: Round [246] log likelihood: -26406.871553
EM: Round [247] log likelihood: -26406.837543
EM: Round [248] log likelihood: -26406.803811
EM: Round [249] log likelihood: -26406.770353
EM: Round [250] log likelihood: -26406.737167
EM: Round [251] log likelihood: -26406.704251
EM: Round [252] log likelihood: -26406.671601
EM: Round [253] log likelihood: -26406.639216
EM: Round [254] log likelihood: -26406.607093
EM: Round [255] log likelihood: -26406.575230
EM: Round [256] log likelihood: -26406.543623
EM: Round [257] log likelihood: -26406.512271
EM: Round [258] log likelihood: -26406.481172
EM: Round [259] log likelihood: -26406.450322
EM: Round [260] log likelihood: -26406.419720
EM: Round [261] log likelihood: -26406.389363
EM: Round [262] log likelihood: -26406.359248
EM: Round [263] log likelihood: -26406.329375
EM: Round [264] log likelihood: -26406.299740
EM: Round [265] log likelihood: -26406.270341
EM: Round [266] log likelihood: -26406.241176
EM: Round [267] log likelihood: -26406.212243
EM: Round [268] log likelihood: -26406.183540
EM: Round [269] log likelihood: -26406.155065
EM: Round [270] log likelihood: -26406.126815
EM: Round [271] log likelihood: -26406.098788
EM: Round [272] log likelihood: -26406.070983
EM: Round [273] log likelihood: -26406.043398
EM: Round [274] log likelihood: -26406.016030
EM: Round [275] log likelihood: -26405.988878
EM: Round [276] log likelihood: -26405.961939
EM: Round [277] log likelihood: -26405.935211
EM: Round [278] log likelihood: -26405.908694
EM: Round [279] log likelihood: -26405.882384
EM: Round [280] log likelihood: -26405.856280
EM: Round [281] log likelihood: -26405.830380
EM: Round [282] log likelihood: -26405.804683
EM: Round [283] log likelihood: -26405.779186
EM: Round [284] log likelihood: -26405.753888
EM: Round [285] log likelihood: -26405.728786
EM: Round [286] log likelihood: -26405.703880
EM: Round [287] log likelihood: -26405.679168
EM: Round [288] log likelihood: -26405.654647
EM: Round [289] log likelihood: -26405.630316
EM: Round [290] log likelihood: -26405.606173
EM: Round [291] log likelihood: -26405.582217
EM: Round [292] log likelihood: -26405.558446
EM: Round [293] log likelihood: -26405.534859
EM: Round [294] log likelihood: -26405.511453
EM: Round [295] log likelihood: -26405.488228
EM: Round [296] log likelihood: -26405.465181
EM: Round [297] log likelihood: -26405.442312
EM: Round [298] log likelihood: -26405.419618
EM: Round [299] log likelihood: -26405.397098
EM: Round [300] log likelihood: -26405.374751
EM: Round [301] log likelihood: -26405.352574
EM: Round [302] log likelihood: -26405.330567
EM: Round [303] log likelihood: -26405.308729
EM: Round [304] log likelihood: -26405.287057
EM: Round [305] log likelihood: -26405.265550
EM: Round [306] log likelihood: -26405.244207
EM: Round [307] log likelihood: -26405.223026
EM: Round [308] log likelihood: -26405.202007
EM: Round [309] log likelihood: -26405.181147
EM: Round [310] log likelihood: -26405.160445
EM: Round [311] log likelihood: -26405.139900
EM: Round [312] log likelihood: -26405.119511
EM: Round [313] log likelihood: -26405.099276
EM: Round [314] log likelihood: -26405.079194
EM: Round [315] log likelihood: -26405.059264
EM: Round [316] log likelihood: -26405.039484
EM: Round [317] log likelihood: -26405.019853
EM: Round [318] log likelihood: -26405.000370
EM: Round [319] log likelihood: -26404.981034
EM: Round [320] log likelihood: -26404.961843
EM: Round [321] log likelihood: -26404.942796
EM: Round [322] log likelihood: -26404.923892
EM: Round [323] log likelihood: -26404.905130
EM: Round [324] log likelihood: -26404.886508
EM: Round [325] log likelihood: -26404.868026
EM: Round [326] log likelihood: -26404.849682
EM: Round [327] log likelihood: -26404.831475
EM: Round [328] log likelihood: -26404.813404
EM: Round [329] log likelihood: -26404.795468
EM: Round [330] log likelihood: -26404.777665
EM: Round [331] log likelihood: -26404.759995
EM: Round [332] log likelihood: -26404.742457
EM: Round [333] log likelihood: -26404.725049
EM: Round [334] log likelihood: -26404.707770
EM: Round [335] log likelihood: -26404.690620
EM: Round [336] log likelihood: -26404.673597
EM: Round [337] log likelihood: -26404.656700
EM: Round [338] log likelihood: -26404.639928
EM: Round [339] log likelihood: -26404.623280
EM: Round [340] log likelihood: -26404.606755
EM: Round [341] log likelihood: -26404.590353
EM: Round [342] log likelihood: -26404.574071
EM: Round [343] log likelihood: -26404.557909
EM: Round [344] log likelihood: -26404.541867
EM: Round [345] log likelihood: -26404.525943
EM: Round [346] log likelihood: -26404.510136
EM: Round [347] log likelihood: -26404.494445
EM: Round [348] log likelihood: -26404.478870
EM: Round [349] log likelihood: -26404.463409
EM: Round [350] log likelihood: -26404.448061
EM: Round [351] log likelihood: -26404.432826
EM: Round [352] log likelihood: -26404.417702
EM: Round [353] log likelihood: -26404.402690
EM: Round [354] log likelihood: -26404.387787
EM: Round [355] log likelihood: -26404.372993
EM: Round [356] log likelihood: -26404.358307
EM: Round [357] log likelihood: -26404.343728
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EM: Round [816] log likelihood: -26402.343211
EM: Round [817] log likelihood: -26402.342547
EM: Round [818] log likelihood: -26402.341887
EM: Round [819] log likelihood: -26402.341231
EM: Round [820] log likelihood: -26402.340580
EM: Round [821] log likelihood: -26402.339932
EM: Round [822] log likelihood: -26402.339289
EM: Round [823] log likelihood: -26402.338649
EM: Round [824] log likelihood: -26402.338014
EM: Round [825] log likelihood: -26402.337383
EM: Round [826] log likelihood: -26402.336755
EM: Round [827] log likelihood: -26402.336132
EM: Round [828] log likelihood: -26402.335512
EM: Round [829] log likelihood: -26402.334897
EM: Round [830] log likelihood: -26402.334285
EM: Round [831] log likelihood: -26402.333678
EM: Round [832] log likelihood: -26402.333074
EM: Round [833] log likelihood: -26402.332474
EM: Round [834] log likelihood: -26402.331878
EM: Round [835] log likelihood: -26402.331285
EM: Round [836] log likelihood: -26402.330696
EM: Round [837] log likelihood: -26402.330111
EM: Round [838] log likelihood: -26402.329530
EM: Round [839] log likelihood: -26402.328952
EM: Round [840] log likelihood: -26402.328378
EM: Round [841] log likelihood: -26402.327808
EM: Round [842] log likelihood: -26402.327241
EM: Round [843] log likelihood: -26402.326678
EM: Round [844] log likelihood: -26402.326118
EM: Round [845] log likelihood: -26402.325562
EM: Round [846] log likelihood: -26402.325009
EM: Round [847] log likelihood: -26402.324460
EM: Round [848] log likelihood: -26402.323915
EM: Round [849] log likelihood: -26402.323372
EM: Round [850] log likelihood: -26402.322833
EM: Round [851] log likelihood: -26402.322298
EM: Round [852] log likelihood: -26402.321766
EM: Round [853] log likelihood: -26402.321237
EM: Round [854] log likelihood: -26402.320712
EM: Round [855] log likelihood: -26402.320190
EM: Round [856] log likelihood: -26402.319671
EM: Round [857] log likelihood: -26402.319155
EM: Round [858] log likelihood: -26402.318643
EM: Round [859] log likelihood: -26402.318134
EM: Round [860] log likelihood: -26402.317628
EM: Round [861] log likelihood: -26402.317125
EM: Round [862] log likelihood: -26402.316626
EM: Round [863] log likelihood: -26402.316130
EM: Round [864] log likelihood: -26402.315636
EM: Round [865] log likelihood: -26402.315146
EM: Round [866] log likelihood: -26402.314659
EM: Round [867] log likelihood: -26402.314175
EM: Round [868] log likelihood: -26402.313694
EM: Round [869] log likelihood: -26402.313216
EM: Round [870] log likelihood: -26402.312741
EM: Round [871] log likelihood: -26402.312269
EM: Round [872] log likelihood: -26402.311800
EM: Round [873] log likelihood: -26402.311334
EM: Round [874] log likelihood: -26402.310871
EM: Round [875] log likelihood: -26402.310411
EM: Round [876] log likelihood: -26402.309953
EM: Round [877] log likelihood: -26402.309499
EM: Round [878] log likelihood: -26402.309047
EM: Round [879] log likelihood: -26402.308598
EM: Round [880] log likelihood: -26402.308152
EM: Round [881] log likelihood: -26402.307709
EM: Round [882] log likelihood: -26402.307269
EM: Round [883] log likelihood: -26402.306831
EM: Round [884] log likelihood: -26402.306396
EM: Round [885] log likelihood: -26402.305964
EM: Round [886] log likelihood: -26402.305534
EM: Round [887] log likelihood: -26402.305107
EM: Round [888] log likelihood: -26402.304683
EM: Round [889] log likelihood: -26402.304262
EM: Round [890] log likelihood: -26402.303843
EM: Round [891] log likelihood: -26402.303426
EM: Round [892] log likelihood: -26402.303013
EM: Round [893] log likelihood: -26402.302602
EM: Round [894] log likelihood: -26402.302193
EM: Round [895] log likelihood: -26402.301787
EM: Round [896] log likelihood: -26402.301384
EM: Round [897] log likelihood: -26402.300983
EM: Round [898] log likelihood: -26402.300585
EM: Round [899] log likelihood: -26402.300189
EM: Round [900] log likelihood: -26402.299795
EM: Round [901] log likelihood: -26402.299404
EM: Round [902] log likelihood: -26402.299016
EM: Round [903] log likelihood: -26402.298630
EM: Round [904] log likelihood: -26402.298246
EM: Round [905] log likelihood: -26402.297865
EM: Round [906] log likelihood: -26402.297486
EM: Round [907] log likelihood: -26402.297109
EM: Round [908] log likelihood: -26402.296735
EM: Round [909] log likelihood: -26402.296363
EM: Round [910] log likelihood: -26402.295993
EM: Round [911] log likelihood: -26402.295626
EM: Round [912] log likelihood: -26402.295261
EM: Round [913] log likelihood: -26402.294898
EM: Round [914] log likelihood: -26402.294538
EM: Round [915] log likelihood: -26402.294180
EM: Round [916] log likelihood: -26402.293824
EM: Round [917] log likelihood: -26402.293470
EM: Round [918] log likelihood: -26402.293118
EM: Round [919] log likelihood: -26402.292769
EM: Round [920] log likelihood: -26402.292422
EM: Round [921] log likelihood: -26402.292076
EM: Round [922] log likelihood: -26402.291734
EM: Round [923] log likelihood: -26402.291393
EM: Round [924] log likelihood: -26402.291054
EM: Round [925] log likelihood: -26402.290717
EM: Round [926] log likelihood: -26402.290383
EM: Round [927] log likelihood: -26402.290051
EM: Round [928] log likelihood: -26402.289720
EM: Round [929] log likelihood: -26402.289392
EM: Round [930] log likelihood: -26402.289066
EM: Round [931] log likelihood: -26402.288741
EM: Round [932] log likelihood: -26402.288419
EM: Round [933] log likelihood: -26402.288099
EM: Round [934] log likelihood: -26402.287781
EM: Round [935] log likelihood: -26402.287464
EM: Round [936] log likelihood: -26402.287150
EM: Round [937] log likelihood: -26402.286838
EM: Round [938] log likelihood: -26402.286527
EM: Round [939] log likelihood: -26402.286219
EM: Round [940] log likelihood: -26402.285912
EM: Round [941] log likelihood: -26402.285607
EM: Round [942] log likelihood: -26402.285305
EM: Round [943] log likelihood: -26402.285004
EM: Round [944] log likelihood: -26402.284705
EM: Round [945] log likelihood: -26402.284407
EM: Round [946] log likelihood: -26402.284112
EM: Round [947] log likelihood: -26402.283818
EM: Round [948] log likelihood: -26402.283527
EM: Round [949] log likelihood: -26402.283237
EM: Round [950] log likelihood: -26402.282948
EM: Round [951] log likelihood: -26402.282662
EM: Round [952] log likelihood: -26402.282377
EM: Round [953] log likelihood: -26402.282095
EM: Round [954] log likelihood: -26402.281814
EM: Round [955] log likelihood: -26402.281534
EM: Round [956] log likelihood: -26402.281256
EM: Round [957] log likelihood: -26402.280981
EM: Round [958] log likelihood: -26402.280706
EM: Round [959] log likelihood: -26402.280434
EM: Round [960] log likelihood: -26402.280163
EM: Round [961] log likelihood: -26402.279894
EM: Round [962] log likelihood: -26402.279626
EM: Round [963] log likelihood: -26402.279360
EM: Round [964] log likelihood: -26402.279096
EM: Round [965] log likelihood: -26402.278833
EM: Round [966] log likelihood: -26402.278572
EM: Round [967] log likelihood: -26402.278313
EM: Round [968] log likelihood: -26402.278055
EM: Round [969] log likelihood: -26402.277799
EM: Round [970] log likelihood: -26402.277544
EM: Round [971] log likelihood: -26402.277291
EM: Round [972] log likelihood: -26402.277040
EM: Round [973] log likelihood: -26402.276790
EM: Round [974] log likelihood: -26402.276541
EM: Round [975] log likelihood: -26402.276294
EM: Round [976] log likelihood: -26402.276049
EM: Round [977] log likelihood: -26402.275805
EM: Round [978] log likelihood: -26402.275563
EM: Round [979] log likelihood: -26402.275322
EM: Round [980] log likelihood: -26402.275082
EM: Round [981] log likelihood: -26402.274844
EM: Round [982] log likelihood: -26402.274608
EM: Round [983] log likelihood: -26402.274373
EM: Round [984] log likelihood: -26402.274139
EM: Round [985] log likelihood: -26402.273907
EM: Round [986] log likelihood: -26402.273676
EM: Round [987] log likelihood: -26402.273447
EM: Round [988] log likelihood: -26402.273219
EM: Round [989] log likelihood: -26402.272993
EM: Round [990] log likelihood: -26402.272767
EM: Round [991] log likelihood: -26402.272544
EM: Round [992] log likelihood: -26402.272321
EM: Round [993] log likelihood: -26402.272100
EM: Round [994] log likelihood: -26402.271881
EM: Round [995] log likelihood: -26402.271662
EM: Round [996] log likelihood: -26402.271445
EM: Round [997] log likelihood: -26402.271230
EM: Round [998] log likelihood: -26402.271015
EM: Round [999] log likelihood: -26402.270802
EM: Round [1000] log likelihood: -26402.270590
EM: Round [1001] log likelihood: -26402.270380
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam into /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords > /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.NMeURXWyeZ/fi_workdir/659_rd-T1-TRNA-1_B23WHTKLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -15107.140015
EM: Round [1] log likelihood: -15076.718302
EM: Round [2] log likelihood: -15076.681118
EM: Round [3] log likelihood: -15076.681027
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1_1.fastp.fastq.gz: 295903958
Warning - not locating file: /tmp/nxf.NMeURXWyeZ/659_rd-T1-TRNA-1_B23WHTKLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
ls: cannot access 'IGV_inputs': No such file or directory