Done.
-parsing GTF file: /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.ldzfF6eIHp/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.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.sortedByCoord.out.bam
23:38:35 : INFO : Done.
-parsing GTF file: /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.gtf
-parsing /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam

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[950000]   -done parsing /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 6,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 44,
          'per_id < 96' => 4578,
          ' ** passed ** ' => 22574,
          'exons hit < 2' => 5,
          'low complexity anchor region' => 63,
          'excessive soft clipping' => 5605,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 8,
          'seq-similar region overlap' => 319,
          'small anchor length' => 186,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 10,
          'num genes matched < 2' => 5,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
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[3000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[76000]   
[77000]   -fusion SPANNING read extraction for scaff: AC124944.2--SDHAP1

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[11000]   
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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: AGAP12P--FRMPD2

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[39000]   -fusion SPANNING read extraction for scaff: ATIC--AC092844.1
-fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

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[19000]   -fusion SPANNING read extraction for scaff: CDK19--RPF2

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[36000]   
[37000]   -fusion SPANNING read extraction for scaff: CFLAR-AS1--PIP5K1B

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[26000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

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[111000]   
[112000]   -fusion SPANNING read extraction for scaff: ETV6--FAR2

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[8000]   
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[12000]   -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1

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[22000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

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[62000]   
[63000]   -fusion SPANNING read extraction for scaff: HGD--GTF2E1

[1000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
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[3000]   -fusion SPANNING read extraction for scaff: LINC00993--PVT1

[1000]   
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[7000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

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[7000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

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[7000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

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[27000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

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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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[17000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

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[20000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

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[33000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA11

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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[26000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[7000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[14000]   
[15000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[30000]   
[31000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[15000]   
[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[14000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[18000]   
[19000]   -fusion SPANNING read extraction for scaff: RPF2--CDK19

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[45000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[27000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[27000]   -fusion SPANNING read extraction for scaff: TLK2--LINC01347

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[21000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 31195,
          'lacks exon overlap' => 10568
        };
EM: Starting log likelihood: -7641.278033
EM: Round [1] log likelihood: -7629.279192
EM: Round [2] log likelihood: -7626.130149
EM: Round [3] log likelihood: -7623.537641
EM: Round [4] log likelihood: -7621.367491
EM: Round [5] log likelihood: -7619.532791
EM: Round [6] log likelihood: -7617.968805
EM: Round [7] log likelihood: -7616.626142
EM: Round [8] log likelihood: -7615.466392
EM: Round [9] log likelihood: -7614.459208
EM: Round [10] log likelihood: -7613.580276
EM: Round [11] log likelihood: -7612.809882
EM: Round [12] log likelihood: -7612.131867
EM: Round [13] log likelihood: -7611.532860
EM: Round [14] log likelihood: -7611.001704
EM: Round [15] log likelihood: -7610.529024
EM: Round [16] log likelihood: -7610.106891
EM: Round [17] log likelihood: -7609.728562
EM: Round [18] log likelihood: -7609.388282
EM: Round [19] log likelihood: -7609.081117
EM: Round [20] log likelihood: -7608.802825
EM: Round [21] log likelihood: -7608.549751
EM: Round [22] log likelihood: -7608.318737
EM: Round [23] log likelihood: -7608.107053
EM: Round [24] log likelihood: -7607.912331
EM: Round [25] log likelihood: -7607.732521
EM: Round [26] log likelihood: -7607.565841
EM: Round [27] log likelihood: -7607.410743
EM: Round [28] log likelihood: -7607.265881
EM: Round [29] log likelihood: -7607.130085
EM: Round [30] log likelihood: -7607.002334
EM: Round [31] log likelihood: -7606.881741
EM: Round [32] log likelihood: -7606.767531
EM: Round [33] log likelihood: -7606.659027
EM: Round [34] log likelihood: -7606.555640
EM: Round [35] log likelihood: -7606.456853
EM: Round [36] log likelihood: -7606.362216
EM: Round [37] log likelihood: -7606.271332
EM: Round [38] log likelihood: -7606.183856
EM: Round [39] log likelihood: -7606.099483
EM: Round [40] log likelihood: -7606.017945
EM: Round [41] log likelihood: -7605.939007
EM: Round [42] log likelihood: -7605.862460
EM: Round [43] log likelihood: -7605.788122
EM: Round [44] log likelihood: -7605.715829
EM: Round [45] log likelihood: -7605.645438
EM: Round [46] log likelihood: -7605.576820
EM: Round [47] log likelihood: -7605.509860
EM: Round [48] log likelihood: -7605.444458
EM: Round [49] log likelihood: -7605.380520
EM: Round [50] log likelihood: -7605.317965
EM: Round [51] log likelihood: -7605.256720
EM: Round [52] log likelihood: -7605.196716
EM: Round [53] log likelihood: -7605.137894
EM: Round [54] log likelihood: -7605.080198
EM: Round [55] log likelihood: -7605.023579
EM: Round [56] log likelihood: -7604.967989
EM: Round [57] log likelihood: -7604.913389
EM: Round [58] log likelihood: -7604.859737
EM: Round [59] log likelihood: -7604.807000
EM: Round [60] log likelihood: -7604.755144
EM: Round [61] log likelihood: -7604.704137
EM: Round [62] log likelihood: -7604.653952
EM: Round [63] log likelihood: -7604.604562
EM: Round [64] log likelihood: -7604.555942
EM: Round [65] log likelihood: -7604.508069
EM: Round [66] log likelihood: -7604.460919
EM: Round [67] log likelihood: -7604.414474
EM: Round [68] log likelihood: -7604.368712
EM: Round [69] log likelihood: -7604.323616
EM: Round [70] log likelihood: -7604.279168
EM: Round [71] log likelihood: -7604.235351
EM: Round [72] log likelihood: -7604.192149
EM: Round [73] log likelihood: -7604.149547
EM: Round [74] log likelihood: -7604.107530
EM: Round [75] log likelihood: -7604.066084
EM: Round [76] log likelihood: -7604.025197
EM: Round [77] log likelihood: -7603.984854
EM: Round [78] log likelihood: -7603.945045
EM: Round [79] log likelihood: -7603.905757
EM: Round [80] log likelihood: -7603.866978
EM: Round [81] log likelihood: -7603.828698
EM: Round [82] log likelihood: -7603.790907
EM: Round [83] log likelihood: -7603.753593
EM: Round [84] log likelihood: -7603.716747
EM: Round [85] log likelihood: -7603.680360
EM: Round [86] log likelihood: -7603.644423
EM: Round [87] log likelihood: -7603.608926
EM: Round [88] log likelihood: -7603.573860
EM: Round [89] log likelihood: -7603.539218
EM: Round [90] log likelihood: -7603.504992
EM: Round [91] log likelihood: -7603.471173
EM: Round [92] log likelihood: -7603.437753
EM: Round [93] log likelihood: -7603.404726
EM: Round [94] log likelihood: -7603.372084
EM: Round [95] log likelihood: -7603.339821
EM: Round [96] log likelihood: -7603.307928
EM: Round [97] log likelihood: -7603.276400
EM: Round [98] log likelihood: -7603.245231
EM: Round [99] log likelihood: -7603.214413
EM: Round [100] log likelihood: -7603.183941
EM: Round [101] log likelihood: -7603.153809
EM: Round [102] log likelihood: -7603.124012
EM: Round [103] log likelihood: -7603.094542
EM: Round [104] log likelihood: -7603.065395
EM: Round [105] log likelihood: -7603.036566
EM: Round [106] log likelihood: -7603.008050
EM: Round [107] log likelihood: -7602.979840
EM: Round [108] log likelihood: -7602.951932
EM: Round [109] log likelihood: -7602.924322
EM: Round [110] log likelihood: -7602.897004
EM: Round [111] log likelihood: -7602.869975
EM: Round [112] log likelihood: -7602.843228
EM: Round [113] log likelihood: -7602.816760
EM: Round [114] log likelihood: -7602.790567
EM: Round [115] log likelihood: -7602.764644
EM: Round [116] log likelihood: -7602.738988
EM: Round [117] log likelihood: -7602.713593
EM: Round [118] log likelihood: -7602.688457
EM: Round [119] log likelihood: -7602.663575
EM: Round [120] log likelihood: -7602.638943
EM: Round [121] log likelihood: -7602.614559
EM: Round [122] log likelihood: -7602.590417
EM: Round [123] log likelihood: -7602.566515
EM: Round [124] log likelihood: -7602.542849
EM: Round [125] log likelihood: -7602.519416
EM: Round [126] log likelihood: -7602.496212
EM: Round [127] log likelihood: -7602.473234
EM: Round [128] log likelihood: -7602.450480
EM: Round [129] log likelihood: -7602.427945
EM: Round [130] log likelihood: -7602.405627
EM: Round [131] log likelihood: -7602.383522
EM: Round [132] log likelihood: -7602.361628
EM: Round [133] log likelihood: -7602.339942
EM: Round [134] log likelihood: -7602.318462
EM: Round [135] log likelihood: -7602.297183
EM: Round [136] log likelihood: -7602.276104
EM: Round [137] log likelihood: -7602.255222
EM: Round [138] log likelihood: -7602.234534
EM: Round [139] log likelihood: -7602.214037
EM: Round [140] log likelihood: -7602.193730
EM: Round [141] log likelihood: -7602.173609
EM: Round [142] log likelihood: -7602.153673
EM: Round [143] log likelihood: -7602.133918
EM: Round [144] log likelihood: -7602.114343
EM: Round [145] log likelihood: -7602.094945
EM: Round [146] log likelihood: -7602.075722
EM: Round [147] log likelihood: -7602.056672
EM: Round [148] log likelihood: -7602.037792
EM: Round [149] log likelihood: -7602.019081
EM: Round [150] log likelihood: -7602.000536
EM: Round [151] log likelihood: -7601.982155
EM: Round [152] log likelihood: -7601.963936
EM: Round [153] log likelihood: -7601.945878
EM: Round [154] log likelihood: -7601.927978
EM: Round [155] log likelihood: -7601.910234
EM: Round [156] log likelihood: -7601.892644
EM: Round [157] log likelihood: -7601.875207
EM: Round [158] log likelihood: -7601.857921
EM: Round [159] log likelihood: -7601.840784
EM: Round [160] log likelihood: -7601.823794
EM: Round [161] log likelihood: -7601.806949
EM: Round [162] log likelihood: -7601.790248
EM: Round [163] log likelihood: -7601.773689
EM: Round [164] log likelihood: -7601.757270
EM: Round [165] log likelihood: -7601.740990
EM: Round [166] log likelihood: -7601.724848
EM: Round [167] log likelihood: -7601.708840
EM: Round [168] log likelihood: -7601.692967
EM: Round [169] log likelihood: -7601.677227
EM: Round [170] log likelihood: -7601.661617
EM: Round [171] log likelihood: -7601.646137
EM: Round [172] log likelihood: -7601.630785
EM: Round [173] log likelihood: -7601.615559
EM: Round [174] log likelihood: -7601.600459
EM: Round [175] log likelihood: -7601.585483
EM: Round [176] log likelihood: -7601.570629
EM: Round [177] log likelihood: -7601.555896
EM: Round [178] log likelihood: -7601.541283
EM: Round [179] log likelihood: -7601.526788
EM: Round [180] log likelihood: -7601.512411
EM: Round [181] log likelihood: -7601.498149
EM: Round [182] log likelihood: -7601.484002
EM: Round [183] log likelihood: -7601.469969
EM: Round [184] log likelihood: -7601.456048
EM: Round [185] log likelihood: -7601.442238
EM: Round [186] log likelihood: -7601.428538
EM: Round [187] log likelihood: -7601.414946
EM: Round [188] log likelihood: -7601.401462
EM: Round [189] log likelihood: -7601.388085
EM: Round [190] log likelihood: -7601.374812
EM: Round [191] log likelihood: -7601.361645
EM: Round [192] log likelihood: -7601.348580
EM: Round [193] log likelihood: -7601.335617
EM: Round [194] log likelihood: -7601.322755
EM: Round [195] log likelihood: -7601.309994
EM: Round [196] log likelihood: -7601.297331
EM: Round [197] log likelihood: -7601.284766
EM: Round [198] log likelihood: -7601.272299
EM: Round [199] log likelihood: -7601.259927
EM: Round [200] log likelihood: -7601.247650
EM: Round [201] log likelihood: -7601.235468
EM: Round [202] log likelihood: -7601.223379
EM: Round [203] log likelihood: -7601.211382
EM: Round [204] log likelihood: -7601.199476
EM: Round [205] log likelihood: -7601.187660
EM: Round [206] log likelihood: -7601.175935
EM: Round [207] log likelihood: -7601.164297
EM: Round [208] log likelihood: -7601.152748
EM: Round [209] log likelihood: -7601.141286
EM: Round [210] log likelihood: -7601.129909
EM: Round [211] log likelihood: -7601.118618
EM: Round [212] log likelihood: -7601.107412
EM: Round [213] log likelihood: -7601.096289
EM: Round [214] log likelihood: -7601.085248
EM: Round [215] log likelihood: -7601.074290
EM: Round [216] log likelihood: -7601.063414
EM: Round [217] log likelihood: -7601.052617
EM: Round [218] log likelihood: -7601.041901
EM: Round [219] log likelihood: -7601.031263
EM: Round [220] log likelihood: -7601.020704
EM: Round [221] log likelihood: -7601.010222
EM: Round [222] log likelihood: -7600.999817
EM: Round [223] log likelihood: -7600.989488
EM: Round [224] log likelihood: -7600.979234
EM: Round [225] log likelihood: -7600.969055
EM: Round [226] log likelihood: -7600.958950
EM: Round [227] log likelihood: -7600.948918
EM: Round [228] log likelihood: -7600.938959
EM: Round [229] log likelihood: -7600.929072
EM: Round [230] log likelihood: -7600.919257
EM: Round [231] log likelihood: -7600.909512
EM: Round [232] log likelihood: -7600.899837
EM: Round [233] log likelihood: -7600.890231
EM: Round [234] log likelihood: -7600.880694
EM: Round [235] log likelihood: -7600.871226
EM: Round [236] log likelihood: -7600.861825
EM: Round [237] log likelihood: -7600.852491
EM: Round [238] log likelihood: -7600.843223
EM: Round [239] log likelihood: -7600.834021
EM: Round [240] log likelihood: -7600.824884
EM: Round [241] log likelihood: -7600.815812
EM: Round [242] log likelihood: -7600.806804
EM: Round [243] log likelihood: -7600.797859
EM: Round [244] log likelihood: -7600.788977
EM: Round [245] log likelihood: -7600.780158
EM: Round [246] log likelihood: -7600.771401
EM: Round [247] log likelihood: -7600.762705
EM: Round [248] log likelihood: -7600.754069
EM: Round [249] log likelihood: -7600.745494
EM: Round [250] log likelihood: -7600.736979
EM: Round [251] log likelihood: -7600.728523
EM: Round [252] log likelihood: -7600.720125
EM: Round [253] log likelihood: -7600.711786
EM: Round [254] log likelihood: -7600.703505
EM: Round [255] log likelihood: -7600.695280
EM: Round [256] log likelihood: -7600.687113
EM: Round [257] log likelihood: -7600.679002
EM: Round [258] log likelihood: -7600.670946
EM: Round [259] log likelihood: -7600.662946
EM: Round [260] log likelihood: -7600.655001
EM: Round [261] log likelihood: -7600.647110
EM: Round [262] log likelihood: -7600.639274
EM: Round [263] log likelihood: -7600.631490
EM: Round [264] log likelihood: -7600.623760
EM: Round [265] log likelihood: -7600.616082
EM: Round [266] log likelihood: -7600.608457
EM: Round [267] log likelihood: -7600.600883
EM: Round [268] log likelihood: -7600.593361
EM: Round [269] log likelihood: -7600.585890
EM: Round [270] log likelihood: -7600.578469
EM: Round [271] log likelihood: -7600.571098
EM: Round [272] log likelihood: -7600.563777
EM: Round [273] log likelihood: -7600.556505
EM: Round [274] log likelihood: -7600.549282
EM: Round [275] log likelihood: -7600.542107
EM: Round [276] log likelihood: -7600.534981
EM: Round [277] log likelihood: -7600.527902
EM: Round [278] log likelihood: -7600.520871
EM: Round [279] log likelihood: -7600.513887
EM: Round [280] log likelihood: -7600.506949
EM: Round [281] log likelihood: -7600.500057
EM: Round [282] log likelihood: -7600.493211
EM: Round [283] log likelihood: -7600.486411
EM: Round [284] log likelihood: -7600.479656
EM: Round [285] log likelihood: -7600.472945
EM: Round [286] log likelihood: -7600.466279
EM: Round [287] log likelihood: -7600.459657
EM: Round [288] log likelihood: -7600.453079
EM: Round [289] log likelihood: -7600.446544
EM: Round [290] log likelihood: -7600.440052
EM: Round [291] log likelihood: -7600.433603
EM: Round [292] log likelihood: -7600.427196
EM: Round [293] log likelihood: -7600.420831
EM: Round [294] log likelihood: -7600.414508
EM: Round [295] log likelihood: -7600.408226
EM: Round [296] log likelihood: -7600.401985
EM: Round [297] log likelihood: -7600.395785
EM: Round [298] log likelihood: -7600.389626
EM: Round [299] log likelihood: -7600.383506
EM: Round [300] log likelihood: -7600.377427
EM: Round [301] log likelihood: -7600.371387
EM: Round [302] log likelihood: -7600.365386
EM: Round [303] log likelihood: -7600.359424
EM: Round [304] log likelihood: -7600.353500
EM: Round [305] log likelihood: -7600.347615
EM: Round [306] log likelihood: -7600.341768
EM: Round [307] log likelihood: -7600.335959
EM: Round [308] log likelihood: -7600.330187
EM: Round [309] log likelihood: -7600.324452
EM: Round [310] log likelihood: -7600.318755
EM: Round [311] log likelihood: -7600.313093
EM: Round [312] log likelihood: -7600.307469
EM: Round [313] log likelihood: -7600.301880
EM: Round [314] log likelihood: -7600.296327
EM: Round [315] log likelihood: -7600.290809
EM: Round [316] log likelihood: -7600.285327
EM: Round [317] log likelihood: -7600.279880
EM: Round [318] log likelihood: -7600.274468
EM: Round [319] log likelihood: -7600.269090
EM: Round [320] log likelihood: -7600.263746
EM: Round [321] log likelihood: -7600.258437
EM: Round [322] log likelihood: -7600.253161
EM: Round [323] log likelihood: -7600.247918
EM: Round [324] log likelihood: -7600.242709
EM: Round [325] log likelihood: -7600.237533
EM: Round [326] log likelihood: -7600.232390
EM: Round [327] log likelihood: -7600.227279
EM: Round [328] log likelihood: -7600.222200
EM: Round [329] log likelihood: -7600.217154
EM: Round [330] log likelihood: -7600.212139
EM: Round [331] log likelihood: -7600.207156
EM: Round [332] log likelihood: -7600.202204
EM: Round [333] log likelihood: -7600.197283
EM: Round [334] log likelihood: -7600.192393
EM: Round [335] log likelihood: -7600.187534
EM: Round [336] log likelihood: -7600.182706
EM: Round [337] log likelihood: -7600.177907
EM: Round [338] log likelihood: -7600.173139
EM: Round [339] log likelihood: -7600.168401
EM: Round [340] log likelihood: -7600.163692
EM: Round [341] log likelihood: -7600.159012
EM: Round [342] log likelihood: -7600.154362
EM: Round [343] log likelihood: -7600.149741
EM: Round [344] log likelihood: -7600.145148
EM: Round [345] log likelihood: -7600.140584
EM: Round [346] log likelihood: -7600.136048
EM: Round [347] log likelihood: -7600.131541
EM: Round [348] log likelihood: -7600.127061
EM: Round [349] log likelihood: -7600.122610
EM: Round [350] log likelihood: -7600.118185
EM: Round [351] log likelihood: -7600.113789
EM: Round [352] log likelihood: -7600.109419
EM: Round [353] log likelihood: -7600.105076
EM: Round [354] log likelihood: -7600.100761
EM: Round [355] log likelihood: -7600.096471
EM: Round [356] log likelihood: -7600.092209
EM: Round [357] log likelihood: -7600.087972
EM: Round [358] log likelihood: -7600.083762
EM: Round [359] log likelihood: -7600.079577
EM: Round [360] log likelihood: -7600.075418
EM: Round [361] log likelihood: -7600.071285
EM: Round [362] log likelihood: -7600.067177
EM: Round [363] log likelihood: -7600.063094
EM: Round [364] log likelihood: -7600.059037
EM: Round [365] log likelihood: -7600.055004
EM: Round [366] log likelihood: -7600.050995
EM: Round [367] log likelihood: -7600.047012
EM: Round [368] log likelihood: -7600.043052
EM: Round [369] log likelihood: -7600.039117
EM: Round [370] log likelihood: -7600.035206
EM: Round [371] log likelihood: -7600.031318
EM: Round [372] log likelihood: -7600.027454
EM: Round [373] log likelihood: -7600.023614
EM: Round [374] log likelihood: -7600.019797
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EM: Round [376] log likelihood: -7600.012233
EM: Round [377] log likelihood: -7600.008485
EM: Round [378] log likelihood: -7600.004760
EM: Round [379] log likelihood: -7600.001057
EM: Round [380] log likelihood: -7599.997377
EM: Round [381] log likelihood: -7599.993719
EM: Round [382] log likelihood: -7599.990084
EM: Round [383] log likelihood: -7599.986470
EM: Round [384] log likelihood: -7599.982878
EM: Round [385] log likelihood: -7599.979308
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EM: Round [387] log likelihood: -7599.972231
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EM: Round [389] log likelihood: -7599.965240
EM: Round [390] log likelihood: -7599.961776
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EM: Round [397] log likelihood: -7599.938103
EM: Round [398] log likelihood: -7599.934801
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EM: Round [400] log likelihood: -7599.928258
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EM: Round [421] log likelihood: -7599.864065
EM: Round [422] log likelihood: -7599.861203
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EM: Round [883] log likelihood: -7599.396126
EM: Round [884] log likelihood: -7599.395908
EM: Round [885] log likelihood: -7599.395691
EM: Round [886] log likelihood: -7599.395475
EM: Round [887] log likelihood: -7599.395260
EM: Round [888] log likelihood: -7599.395046
EM: Round [889] log likelihood: -7599.394833
EM: Round [890] log likelihood: -7599.394622
EM: Round [891] log likelihood: -7599.394412
EM: Round [892] log likelihood: -7599.394202
EM: Round [893] log likelihood: -7599.393994
EM: Round [894] log likelihood: -7599.393787
EM: Round [895] log likelihood: -7599.393582
EM: Round [896] log likelihood: -7599.393377
EM: Round [897] log likelihood: -7599.393173
EM: Round [898] log likelihood: -7599.392971
EM: Round [899] log likelihood: -7599.392769
EM: Round [900] log likelihood: -7599.392569
EM: Round [901] log likelihood: -7599.392370
EM: Round [902] log likelihood: -7599.392172
EM: Round [903] log likelihood: -7599.391975
EM: Round [904] log likelihood: -7599.391779
EM: Round [905] log likelihood: -7599.391584
EM: Round [906] log likelihood: -7599.391390
EM: Round [907] log likelihood: -7599.391197
EM: Round [908] log likelihood: -7599.391005
EM: Round [909] log likelihood: -7599.390814
EM: Round [910] log likelihood: -7599.390625
EM: Round [911] log likelihood: -7599.390436
EM: Round [912] log likelihood: -7599.390248
EM: Round [913] log likelihood: -7599.390061
EM: Round [914] log likelihood: -7599.389876
EM: Round [915] log likelihood: -7599.389691
EM: Round [916] log likelihood: -7599.389507
EM: Round [917] log likelihood: -7599.389325
EM: Round [918] log likelihood: -7599.389143
EM: Round [919] log likelihood: -7599.388962
EM: Round [920] log likelihood: -7599.388782
EM: Round [921] log likelihood: -7599.388604
EM: Round [922] log likelihood: -7599.388426
EM: Round [923] log likelihood: -7599.388249
EM: Round [924] log likelihood: -7599.388073
EM: Round [925] log likelihood: -7599.387898
EM: Round [926] log likelihood: -7599.387724
EM: Round [927] log likelihood: -7599.387551
EM: Round [928] log likelihood: -7599.387379
EM: Round [929] log likelihood: -7599.387208
EM: Round [930] log likelihood: -7599.387037
EM: Round [931] log likelihood: -7599.386868
EM: Round [932] log likelihood: -7599.386700
EM: Round [933] log likelihood: -7599.386532
EM: Round [934] log likelihood: -7599.386365
EM: Round [935] log likelihood: -7599.386200
EM: Round [936] log likelihood: -7599.386035
EM: Round [937] log likelihood: -7599.385871
EM: Round [938] log likelihood: -7599.385708
EM: Round [939] log likelihood: -7599.385546
EM: Round [940] log likelihood: -7599.385384
EM: Round [941] log likelihood: -7599.385224
EM: Round [942] log likelihood: -7599.385064
EM: Round [943] log likelihood: -7599.384905
EM: Round [944] log likelihood: -7599.384748
EM: Round [945] log likelihood: -7599.384591
EM: Round [946] log likelihood: -7599.384434
EM: Round [947] log likelihood: -7599.384279
EM: Round [948] log likelihood: -7599.384125
EM: Round [949] log likelihood: -7599.383971
EM: Round [950] log likelihood: -7599.383818
EM: Round [951] log likelihood: -7599.383666
EM: Round [952] log likelihood: -7599.383515
EM: Round [953] log likelihood: -7599.383365
EM: Round [954] log likelihood: -7599.383215
EM: Round [955] log likelihood: -7599.383066
EM: Round [956] log likelihood: -7599.382918
EM: Round [957] log likelihood: -7599.382771
EM: Round [958] log likelihood: -7599.382625
EM: Round [959] log likelihood: -7599.382479
EM: Round [960] log likelihood: -7599.382334
EM: Round [961] log likelihood: -7599.382190
EM: Round [962] log likelihood: -7599.382047
EM: Round [963] log likelihood: -7599.381905
EM: Round [964] log likelihood: -7599.381763
EM: Round [965] log likelihood: -7599.381622
EM: Round [966] log likelihood: -7599.381482
EM: Round [967] log likelihood: -7599.381342
EM: Round [968] log likelihood: -7599.381204
EM: Round [969] log likelihood: -7599.381066
EM: Round [970] log likelihood: -7599.380929
EM: Round [971] log likelihood: -7599.380792
EM: Round [972] log likelihood: -7599.380657
EM: Round [973] log likelihood: -7599.380522
EM: Round [974] log likelihood: -7599.380387
EM: Round [975] log likelihood: -7599.380254
EM: Round [976] log likelihood: -7599.380121
EM: Round [977] log likelihood: -7599.379989
EM: Round [978] log likelihood: -7599.379858
EM: Round [979] log likelihood: -7599.379727
EM: Round [980] log likelihood: -7599.379597
EM: Round [981] log likelihood: -7599.379468
EM: Round [982] log likelihood: -7599.379339
EM: Round [983] log likelihood: -7599.379211
EM: Round [984] log likelihood: -7599.379084
EM: Round [985] log likelihood: -7599.378957
EM: Round [986] log likelihood: -7599.378832
EM: Round [987] log likelihood: -7599.378707
EM: Round [988] log likelihood: -7599.378582
EM: Round [989] log likelihood: -7599.378458
EM: Round [990] log likelihood: -7599.378335
EM: Round [991] log likelihood: -7599.378213
EM: Round [992] log likelihood: -7599.378091
EM: Round [993] log likelihood: -7599.377970
EM: Round [994] log likelihood: -7599.377849
EM: Round [995] log likelihood: -7599.377729
EM: Round [996] log likelihood: -7599.377610
EM: Round [997] log likelihood: -7599.377492
EM: Round [998] log likelihood: -7599.377374
EM: Round [999] log likelihood: -7599.377256
EM: Round [1000] log likelihood: -7599.377140
EM: Round [1001] log likelihood: -7599.377024
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam into /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.ldzfF6eIHp/659_b7Z-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.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.read_coords > /tmp/nxf.ldzfF6eIHp/659_b7Z-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.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.ldzfF6eIHp/659_b7Z-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.ldzfF6eIHp/fi_workdir/659_b7Z-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.ldzfF6eIHp/fi_workdir/659_b7Z-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.ldzfF6eIHp/fi_workdir/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -5270.044808
EM: Round [1] log likelihood: -5269.567155
EM: Round [2] log likelihood: -5269.566565
EM: Round [3] log likelihood: -5269.566563
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.ldzfF6eIHp/659_b7Z-T1-TRNA-1_B23MHV2LT4_1_1.fastp.fastq.gz: 296305715
Warning - not locating file: /tmp/nxf.ldzfF6eIHp/659_b7Z-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 [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000265018.6]
WARNING, no entry stored in dbm for [ENSG00000260261.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000260261.2]
WARNING, no entry stored in dbm for [ENSG00000185485.14]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
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 [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000242193.11]
WARNING, no entry stored in dbm for [ENSG00000226312.7]
ls: cannot access 'IGV_inputs': No such file or directory