Done.
-parsing GTF file: /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.vuGnvWu9DD/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.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00658_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00658_B23MVV7LT4_1.star.sortedByCoord.out.bam
12:31:33 : INFO : Done.
-parsing GTF file: /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[1590000]   -done parsing /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'per_id < 96' => 4475,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 24,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 86,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 24,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 8,
          'low complexity anchor region' => 6,
          'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 6,
          'seq-similar region overlap' => 68,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 52,
          'excessive soft clipping' => 7667,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2,
          ' ** passed ** ' => 29722,
          'small anchor length' => 90,
          'num genes matched < 2' => 12,
          'num_hits: 10 != num_counted_on_fusion_contigs 8 ' => 16
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[5000]   -fusion SPANNING read extraction for scaff: AC013268.1--MALL

[1000]   
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[5000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

[1000]   -fusion SPANNING read extraction for scaff: CCDC169--SOHLH2

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[74000]   -fusion SPANNING read extraction for scaff: LINC02204--TLE3

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[71000]   -fusion SPANNING read extraction for scaff: NPHP3--ACAD11

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[27000]   -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC1

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[26000]   -fusion SPANNING read extraction for scaff: PCDHA2--PCDHAC2

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[28000]   -fusion SPANNING read extraction for scaff: PCDHA2--PCDHA13

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[47000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13

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[46000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1

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[44000]   -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA8

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA10

[1000]   
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[13000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB6

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC4

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[15000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC5

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[29000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA9

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGA12

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[44000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGB7

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[145000]   -fusion SPANNING read extraction for scaff: PCDHGA5--PCDHGC3

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

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[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[30000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[24000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[44000]   
[45000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[145000]   
[146000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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[146000]   
[147000]   -fusion SPANNING read extraction for scaff: SS18--SSX1

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[25000]   -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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[19000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[11000]   -fusion SPANNING read extraction for scaff: UBE2E2--AC027229.1

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[135000]   -fusion SPANNING read extraction for scaff: UBE2E2--SS18

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[11000]   -fusion SPANNING read extraction for scaff: UBE2E2--RN7SL97P

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[147000]   -fusion SPANNING read extraction for scaff: UBE2E2--ZNF521
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 46366,
          'lacks exon overlap' => 3125
        };
EM: Starting log likelihood: -10046.725348
EM: Round [1] log likelihood: -10045.997359
EM: Round [2] log likelihood: -10045.760535
EM: Round [3] log likelihood: -10045.523241
EM: Round [4] log likelihood: -10045.285225
EM: Round [5] log likelihood: -10045.046912
EM: Round [6] log likelihood: -10044.808894
EM: Round [7] log likelihood: -10044.571858
EM: Round [8] log likelihood: -10044.336539
EM: Round [9] log likelihood: -10044.103680
EM: Round [10] log likelihood: -10043.874001
EM: Round [11] log likelihood: -10043.648176
EM: Round [12] log likelihood: -10043.426814
EM: Round [13] log likelihood: -10043.210451
EM: Round [14] log likelihood: -10042.999546
EM: Round [15] log likelihood: -10042.794474
EM: Round [16] log likelihood: -10042.595531
EM: Round [17] log likelihood: -10042.402937
EM: Round [18] log likelihood: -10042.216838
EM: Round [19] log likelihood: -10042.037317
EM: Round [20] log likelihood: -10041.864398
EM: Round [21] log likelihood: -10041.698054
EM: Round [22] log likelihood: -10041.538214
EM: Round [23] log likelihood: -10041.384768
EM: Round [24] log likelihood: -10041.237578
EM: Round [25] log likelihood: -10041.096480
EM: Round [26] log likelihood: -10040.961290
EM: Round [27] log likelihood: -10040.831809
EM: Round [28] log likelihood: -10040.707830
EM: Round [29] log likelihood: -10040.589136
EM: Round [30] log likelihood: -10040.475510
EM: Round [31] log likelihood: -10040.366731
EM: Round [32] log likelihood: -10040.262581
EM: Round [33] log likelihood: -10040.162845
EM: Round [34] log likelihood: -10040.067310
EM: Round [35] log likelihood: -10039.975773
EM: Round [36] log likelihood: -10039.888033
EM: Round [37] log likelihood: -10039.803900
EM: Round [38] log likelihood: -10039.723188
EM: Round [39] log likelihood: -10039.645723
EM: Round [40] log likelihood: -10039.571336
EM: Round [41] log likelihood: -10039.499867
EM: Round [42] log likelihood: -10039.431163
EM: Round [43] log likelihood: -10039.365081
EM: Round [44] log likelihood: -10039.301484
EM: Round [45] log likelihood: -10039.240244
EM: Round [46] log likelihood: -10039.181238
EM: Round [47] log likelihood: -10039.124351
EM: Round [48] log likelihood: -10039.069476
EM: Round [49] log likelihood: -10039.016510
EM: Round [50] log likelihood: -10038.965358
EM: Round [51] log likelihood: -10038.915929
EM: Round [52] log likelihood: -10038.868139
EM: Round [53] log likelihood: -10038.821908
EM: Round [54] log likelihood: -10038.777160
EM: Round [55] log likelihood: -10038.733825
EM: Round [56] log likelihood: -10038.691837
EM: Round [57] log likelihood: -10038.651133
EM: Round [58] log likelihood: -10038.611655
EM: Round [59] log likelihood: -10038.573347
EM: Round [60] log likelihood: -10038.536157
EM: Round [61] log likelihood: -10038.500037
EM: Round [62] log likelihood: -10038.464940
EM: Round [63] log likelihood: -10038.430823
EM: Round [64] log likelihood: -10038.397644
EM: Round [65] log likelihood: -10038.365365
EM: Round [66] log likelihood: -10038.333950
EM: Round [67] log likelihood: -10038.303363
EM: Round [68] log likelihood: -10038.273572
EM: Round [69] log likelihood: -10038.244546
EM: Round [70] log likelihood: -10038.216256
EM: Round [71] log likelihood: -10038.188674
EM: Round [72] log likelihood: -10038.161773
EM: Round [73] log likelihood: -10038.135529
EM: Round [74] log likelihood: -10038.109918
EM: Round [75] log likelihood: -10038.084917
EM: Round [76] log likelihood: -10038.060504
EM: Round [77] log likelihood: -10038.036660
EM: Round [78] log likelihood: -10038.013364
EM: Round [79] log likelihood: -10037.990599
EM: Round [80] log likelihood: -10037.968346
EM: Round [81] log likelihood: -10037.946588
EM: Round [82] log likelihood: -10037.925310
EM: Round [83] log likelihood: -10037.904496
EM: Round [84] log likelihood: -10037.884130
EM: Round [85] log likelihood: -10037.864199
EM: Round [86] log likelihood: -10037.844690
EM: Round [87] log likelihood: -10037.825589
EM: Round [88] log likelihood: -10037.806883
EM: Round [89] log likelihood: -10037.788562
EM: Round [90] log likelihood: -10037.770612
EM: Round [91] log likelihood: -10037.753024
EM: Round [92] log likelihood: -10037.735786
EM: Round [93] log likelihood: -10037.718889
EM: Round [94] log likelihood: -10037.702322
EM: Round [95] log likelihood: -10037.686076
EM: Round [96] log likelihood: -10037.670142
EM: Round [97] log likelihood: -10037.654510
EM: Round [98] log likelihood: -10037.639174
EM: Round [99] log likelihood: -10037.624124
EM: Round [100] log likelihood: -10037.609352
EM: Round [101] log likelihood: -10037.594851
EM: Round [102] log likelihood: -10037.580614
EM: Round [103] log likelihood: -10037.566633
EM: Round [104] log likelihood: -10037.552902
EM: Round [105] log likelihood: -10037.539413
EM: Round [106] log likelihood: -10037.526161
EM: Round [107] log likelihood: -10037.513139
EM: Round [108] log likelihood: -10037.500342
EM: Round [109] log likelihood: -10037.487762
EM: Round [110] log likelihood: -10037.475396
EM: Round [111] log likelihood: -10037.463237
EM: Round [112] log likelihood: -10037.451279
EM: Round [113] log likelihood: -10037.439519
EM: Round [114] log likelihood: -10037.427951
EM: Round [115] log likelihood: -10037.416569
EM: Round [116] log likelihood: -10037.405371
EM: Round [117] log likelihood: -10037.394350
EM: Round [118] log likelihood: -10037.383502
EM: Round [119] log likelihood: -10037.372824
EM: Round [120] log likelihood: -10037.362311
EM: Round [121] log likelihood: -10037.351959
EM: Round [122] log likelihood: -10037.341765
EM: Round [123] log likelihood: -10037.331724
EM: Round [124] log likelihood: -10037.321832
EM: Round [125] log likelihood: -10037.312087
EM: Round [126] log likelihood: -10037.302485
EM: Round [127] log likelihood: -10037.293022
EM: Round [128] log likelihood: -10037.283695
EM: Round [129] log likelihood: -10037.274501
EM: Round [130] log likelihood: -10037.265437
EM: Round [131] log likelihood: -10037.256500
EM: Round [132] log likelihood: -10037.247687
EM: Round [133] log likelihood: -10037.238995
EM: Round [134] log likelihood: -10037.230422
EM: Round [135] log likelihood: -10037.221964
EM: Round [136] log likelihood: -10037.213619
EM: Round [137] log likelihood: -10037.205384
EM: Round [138] log likelihood: -10037.197258
EM: Round [139] log likelihood: -10037.189238
EM: Round [140] log likelihood: -10037.181320
EM: Round [141] log likelihood: -10037.173504
EM: Round [142] log likelihood: -10037.165787
EM: Round [143] log likelihood: -10037.158166
EM: Round [144] log likelihood: -10037.150640
EM: Round [145] log likelihood: -10037.143207
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EM: Round [621] log likelihood: -10036.023848
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EM: Round [630] log likelihood: -10036.016236
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EM: Round [750] log likelihood: -10035.931818
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EM: Round [1000] log likelihood: -10035.825914
EM: Round [1001] log likelihood: -10035.825620
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter  --genome_lib_dir ctat_genome_lib_build_dir  --max_promiscuity 10  --min_pct_dom_promiscuity 50 
CMD: cp /tmp/nxf.vuGnvWu9DD/fi_workdir/tih_rna_sample_00658_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -7640.985514
EM: Round [1] log likelihood: -7640.775431
EM: Round [2] log likelihood: -7640.760313
EM: Round [3] log likelihood: -7640.745555
EM: Round [4] log likelihood: -7640.730942
EM: Round [5] log likelihood: -7640.716472
EM: Round [6] log likelihood: -7640.702142
EM: Round [7] log likelihood: -7640.687951
EM: Round [8] log likelihood: -7640.673895
EM: Round [9] log likelihood: -7640.659973
EM: Round [10] log likelihood: -7640.646182
EM: Round [11] log likelihood: -7640.632520
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EM: Round [932] log likelihood: -7638.177212
EM: Round [933] log likelihood: -7638.176831
EM: Round [934] log likelihood: -7638.176452
EM: Round [935] log likelihood: -7638.176073
EM: Round [936] log likelihood: -7638.175695
EM: Round [937] log likelihood: -7638.175319
EM: Round [938] log likelihood: -7638.174943
EM: Round [939] log likelihood: -7638.174569
EM: Round [940] log likelihood: -7638.174195
EM: Round [941] log likelihood: -7638.173822
EM: Round [942] log likelihood: -7638.173451
EM: Round [943] log likelihood: -7638.173080
EM: Round [944] log likelihood: -7638.172711
EM: Round [945] log likelihood: -7638.172343
EM: Round [946] log likelihood: -7638.171975
EM: Round [947] log likelihood: -7638.171609
EM: Round [948] log likelihood: -7638.171243
EM: Round [949] log likelihood: -7638.170879
EM: Round [950] log likelihood: -7638.170515
EM: Round [951] log likelihood: -7638.170153
EM: Round [952] log likelihood: -7638.169791
EM: Round [953] log likelihood: -7638.169431
EM: Round [954] log likelihood: -7638.169071
EM: Round [955] log likelihood: -7638.168713
EM: Round [956] log likelihood: -7638.168355
EM: Round [957] log likelihood: -7638.167999
EM: Round [958] log likelihood: -7638.167643
EM: Round [959] log likelihood: -7638.167288
EM: Round [960] log likelihood: -7638.166935
EM: Round [961] log likelihood: -7638.166582
EM: Round [962] log likelihood: -7638.166230
EM: Round [963] log likelihood: -7638.165879
EM: Round [964] log likelihood: -7638.165529
EM: Round [965] log likelihood: -7638.165181
EM: Round [966] log likelihood: -7638.164833
EM: Round [967] log likelihood: -7638.164486
EM: Round [968] log likelihood: -7638.164140
EM: Round [969] log likelihood: -7638.163794
EM: Round [970] log likelihood: -7638.163450
EM: Round [971] log likelihood: -7638.163107
EM: Round [972] log likelihood: -7638.162765
EM: Round [973] log likelihood: -7638.162423
EM: Round [974] log likelihood: -7638.162083
EM: Round [975] log likelihood: -7638.161743
EM: Round [976] log likelihood: -7638.161405
EM: Round [977] log likelihood: -7638.161067
EM: Round [978] log likelihood: -7638.160730
EM: Round [979] log likelihood: -7638.160394
EM: Round [980] log likelihood: -7638.160059
EM: Round [981] log likelihood: -7638.159725
EM: Round [982] log likelihood: -7638.159392
EM: Round [983] log likelihood: -7638.159060
EM: Round [984] log likelihood: -7638.158729
EM: Round [985] log likelihood: -7638.158398
EM: Round [986] log likelihood: -7638.158069
EM: Round [987] log likelihood: -7638.157740
EM: Round [988] log likelihood: -7638.157412
EM: Round [989] log likelihood: -7638.157085
EM: Round [990] log likelihood: -7638.156759
EM: Round [991] log likelihood: -7638.156434
EM: Round [992] log likelihood: -7638.156110
EM: Round [993] log likelihood: -7638.155787
EM: Round [994] log likelihood: -7638.155464
EM: Round [995] log likelihood: -7638.155142
EM: Round [996] log likelihood: -7638.154822
EM: Round [997] log likelihood: -7638.154502
EM: Round [998] log likelihood: -7638.154183
EM: Round [999] log likelihood: -7638.153865
EM: Round [1000] log likelihood: -7638.153547
EM: Round [1001] log likelihood: -7638.153231
-total frags in /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1_1.fastp.fastq.gz: 229586432
Warning - not locating file: /tmp/nxf.vuGnvWu9DD/tih_rna_sample_00658_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [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 [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000282057.1]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000186148.13]
WARNING, no entry stored in dbm for [ENSG00000280639.1]
WARNING, no entry stored in dbm for [ENSG00000280639.1]
ls: cannot access 'IGV_inputs': No such file or directory