Done.
-parsing GTF file: /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.njsCWyy5ep/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.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1_1.fastp.fastq.gz /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.njsCWyy5ep/fi_workdir/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.njsCWyy5ep/fi_workdir/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.star.sortedByCoord.out.bam
22:21:54 : INFO : Done.
-parsing GTF file: /tmp/nxf.njsCWyy5ep/fi_workdir/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.gtf
-parsing /tmp/nxf.njsCWyy5ep/fi_workdir/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam

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[2030000]   -done parsing /tmp/nxf.njsCWyy5ep/fi_workdir/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 384,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 1141,
          'num_hits: 7 != num_counted_on_fusion_contigs 4 ' => 4,
          'num_hits: 9 != num_counted_on_fusion_contigs 8 ' => 8,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 1088,
          'num_hits: 9 != num_counted_on_fusion_contigs 7 ' => 7,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 6,
          'num_hits: 5 != num_counted_on_fusion_contigs 2 ' => 48,
          'num_hits: 6 != num_counted_on_fusion_contigs 3 ' => 33,
          'small anchor length' => 109,
          'low complexity anchor region' => 5,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 112,
          'num_hits: 9 != num_counted_on_fusion_contigs 5 ' => 5,
          'seq-similar region overlap' => 128,
          'excessive soft clipping' => 20082,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 81,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 2300,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 436,
          'num_hits: 6 != num_counted_on_fusion_contigs 4 ' => 28,
          'per_id < 96' => 7970,
          ' ** passed ** ' => 12489,
          'exons hit < 2' => 2,
          'num_hits: 9 != num_counted_on_fusion_contigs 6 ' => 6,
          'num_hits: 6 != num_counted_on_fusion_contigs 5 ' => 30,
          'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 5,
          'num genes matched < 2' => 661
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.njsCWyy5ep/fi_workdir/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[13000]   -fusion SPANNING read extraction for scaff: AC005993.1--RGS6

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[5000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[52000]   -fusion SPANNING read extraction for scaff: AC114814.2--GIGYF2

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[11000]   -fusion SPANNING read extraction for scaff: AC114814.2--CHRNG

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[84000]   -fusion SPANNING read extraction for scaff: AGAP1--GIGYF2

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[43000]   -fusion SPANNING read extraction for scaff: AGAP1--CHRNG

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[25000]   -fusion SPANNING read extraction for scaff: AKAP10--TMIGD3

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[16000]   -fusion SPANNING read extraction for scaff: AKAP10--AQP4-AS1

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[16000]   -fusion SPANNING read extraction for scaff: AKAP10--CHST9

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[294000]   -fusion SPANNING read extraction for scaff: BCR--ARFGAP3

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[199000]   
[200000]   -fusion SPANNING read extraction for scaff: CABIN1--HIC2

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[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: CHRNG--AC114814.2

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[42000]   
[43000]   -fusion SPANNING read extraction for scaff: CHRNG--AGAP1

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[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   -fusion SPANNING read extraction for scaff: COX6CP1--COX6C

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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: CRYZL2P--SEC16B

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[6000]   
[7000]   
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[27000]   
[28000]   -fusion SPANNING read extraction for scaff: DNAJB6--PTPRN2

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[61000]   
[62000]   
[63000]   -fusion SPANNING read extraction for scaff: GIGYF2--CHRNG

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[48000]   
[49000]   
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[52000]   
[53000]   
[54000]   -fusion SPANNING read extraction for scaff: GIGYF2--SLC16A14

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[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   
[54000]   -fusion SPANNING read extraction for scaff: GIGYF2--AC009950.1

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

[1000]   
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[6000]   
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[8000]   
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[28000]   
[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   -fusion SPANNING read extraction for scaff: MTAP--CDKN2B-AS1

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[303000]   
[304000]   -fusion SPANNING read extraction for scaff: NBPF10--LARGE1

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[5000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC1

[1000]   
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[6000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHAC2

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[5000]   -fusion SPANNING read extraction for scaff: PCDHA11--PCDHA13

[1000]   
[2000]   
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[5000]   
[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC2

[1000]   
[2000]   
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[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHA13

[1000]   
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[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHA3--PCDHAC1

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[8000]   
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[14000]   
[15000]   
[16000]   
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[20000]   
[21000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

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[19000]   
[20000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

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[6000]   
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[8000]   
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[28000]   
[29000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

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

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[20000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

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[6000]   
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[8000]   
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[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

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[35000]   
[36000]   -fusion SPANNING read extraction for scaff: PRSS27--TPSB2

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[6000]   
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[8000]   
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[11000]   
[12000]   -fusion SPANNING read extraction for scaff: RGS6--AC005993.1

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[80000]   -fusion SPANNING read extraction for scaff: SFI1--FKBP5

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[76000]   
[77000]   -fusion SPANNING read extraction for scaff: SPECC1--LINC01750

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[116000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[47000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[19000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 33549,
          'seq similar region alignment' => 27328
        };
EM: Starting log likelihood: -8515.401448
EM: Round [1] log likelihood: -8508.700638
EM: Round [2] log likelihood: -8508.120529
EM: Round [3] log likelihood: -8507.731475
EM: Round [4] log likelihood: -8507.452905
EM: Round [5] log likelihood: -8507.249063
EM: Round [6] log likelihood: -8507.096753
EM: Round [7] log likelihood: -8506.980497
EM: Round [8] log likelihood: -8506.889762
EM: Round [9] log likelihood: -8506.817284
EM: Round [10] log likelihood: -8506.757999
EM: Round [11] log likelihood: -8506.708351
EM: Round [12] log likelihood: -8506.665830
EM: Round [13] log likelihood: -8506.628650
EM: Round [14] log likelihood: -8506.595537
EM: Round [15] log likelihood: -8506.565578
EM: Round [16] log likelihood: -8506.538113
EM: Round [17] log likelihood: -8506.512661
EM: Round [18] log likelihood: -8506.488873
EM: Round [19] log likelihood: -8506.466490
EM: Round [20] log likelihood: -8506.445316
EM: Round [21] log likelihood: -8506.425205
EM: Round [22] log likelihood: -8506.406043
EM: Round [23] log likelihood: -8506.387742
EM: Round [24] log likelihood: -8506.370230
EM: Round [25] log likelihood: -8506.353450
EM: Round [26] log likelihood: -8506.337352
EM: Round [27] log likelihood: -8506.321895
EM: Round [28] log likelihood: -8506.307044
EM: Round [29] log likelihood: -8506.292766
EM: Round [30] log likelihood: -8506.279034
EM: Round [31] log likelihood: -8506.265822
EM: Round [32] log likelihood: -8506.253105
EM: Round [33] log likelihood: -8506.240862
EM: Round [34] log likelihood: -8506.229073
EM: Round [35] log likelihood: -8506.217719
EM: Round [36] log likelihood: -8506.206781
EM: Round [37] log likelihood: -8506.196242
EM: Round [38] log likelihood: -8506.186086
EM: Round [39] log likelihood: -8506.176298
EM: Round [40] log likelihood: -8506.166864
EM: Round [41] log likelihood: -8506.157769
EM: Round [42] log likelihood: -8506.149000
EM: Round [43] log likelihood: -8506.140545
EM: Round [44] log likelihood: -8506.132391
EM: Round [45] log likelihood: -8506.124527
EM: Round [46] log likelihood: -8506.116941
EM: Round [47] log likelihood: -8506.109624
EM: Round [48] log likelihood: -8506.102566
EM: Round [49] log likelihood: -8506.095755
EM: Round [50] log likelihood: -8506.089184
EM: Round [51] log likelihood: -8506.082844
EM: Round [52] log likelihood: -8506.076725
EM: Round [53] log likelihood: -8506.070819
EM: Round [54] log likelihood: -8506.065119
EM: Round [55] log likelihood: -8506.059618
EM: Round [56] log likelihood: -8506.054307
EM: Round [57] log likelihood: -8506.049181
EM: Round [58] log likelihood: -8506.044231
EM: Round [59] log likelihood: -8506.039453
EM: Round [60] log likelihood: -8506.034839
EM: Round [61] log likelihood: -8506.030385
EM: Round [62] log likelihood: -8506.026083
EM: Round [63] log likelihood: -8506.021929
EM: Round [64] log likelihood: -8506.017918
EM: Round [65] log likelihood: -8506.014043
EM: Round [66] log likelihood: -8506.010302
EM: Round [67] log likelihood: -8506.006688
EM: Round [68] log likelihood: -8506.003197
EM: Round [69] log likelihood: -8505.999825
EM: Round [70] log likelihood: -8505.996568
EM: Round [71] log likelihood: -8505.993422
EM: Round [72] log likelihood: -8505.990383
EM: Round [73] log likelihood: -8505.987447
EM: Round [74] log likelihood: -8505.984610
EM: Round [75] log likelihood: -8505.981869
EM: Round [76] log likelihood: -8505.979221
EM: Round [77] log likelihood: -8505.976663
EM: Round [78] log likelihood: -8505.974191
EM: Round [79] log likelihood: -8505.971802
EM: Round [80] log likelihood: -8505.969494
EM: Round [81] log likelihood: -8505.967264
EM: Round [82] log likelihood: -8505.965109
EM: Round [83] log likelihood: -8505.963026
EM: Round [84] log likelihood: -8505.961014
EM: Round [85] log likelihood: -8505.959069
EM: Round [86] log likelihood: -8505.957189
EM: Round [87] log likelihood: -8505.955373
EM: Round [88] log likelihood: -8505.953617
EM: Round [89] log likelihood: -8505.951920
EM: Round [90] log likelihood: -8505.950280
EM: Round [91] log likelihood: -8505.948695
EM: Round [92] log likelihood: -8505.947163
EM: Round [93] log likelihood: -8505.945683
EM: Round [94] log likelihood: -8505.944252
EM: Round [95] log likelihood: -8505.942868
EM: Round [96] log likelihood: -8505.941531
EM: Round [97] log likelihood: -8505.940239
EM: Round [98] log likelihood: -8505.938989
EM: Round [99] log likelihood: -8505.937782
EM: Round [100] log likelihood: -8505.936614
EM: Round [101] log likelihood: -8505.935486
EM: Round [102] log likelihood: -8505.934395
EM: Round [103] log likelihood: -8505.933340
EM: Round [104] log likelihood: -8505.932321
EM: Round [105] log likelihood: -8505.931335
EM: Round [106] log likelihood: -8505.930383
EM: Round [107] log likelihood: -8505.929462
EM: Round [108] log likelihood: -8505.928571
EM: Round [109] log likelihood: -8505.927710
EM: Round [110] log likelihood: -8505.926878
EM: Round [111] log likelihood: -8505.926074
EM: Round [112] log likelihood: -8505.925296
EM: Round [113] log likelihood: -8505.924544
EM: Round [114] log likelihood: -8505.923817
EM: Round [115] log likelihood: -8505.923114
EM: Round [116] log likelihood: -8505.922435
EM: Round [117] log likelihood: -8505.921778
EM: Round [118] log likelihood: -8505.921143
EM: Round [119] log likelihood: -8505.920529
EM: Round [120] log likelihood: -8505.919935
EM: Round [121] log likelihood: -8505.919361
EM: Round [122] log likelihood: -8505.918806
EM: Round [123] log likelihood: -8505.918269
EM: Round [124] log likelihood: -8505.917750
EM: Round [125] log likelihood: -8505.917249
EM: Round [126] log likelihood: -8505.916764
EM: Round [127] log likelihood: -8505.916295
EM: Round [128] log likelihood: -8505.915841
EM: Round [129] log likelihood: -8505.915403
EM: Round [130] log likelihood: -8505.914979
EM: Round [131] log likelihood: -8505.914569
EM: Round [132] log likelihood: -8505.914173
EM: Round [133] log likelihood: -8505.913790
EM: Round [134] log likelihood: -8505.913419
EM: Round [135] log likelihood: -8505.913061
EM: Round [136] log likelihood: -8505.912714
EM: Round [137] log likelihood: -8505.912379
EM: Round [138] log likelihood: -8505.912056
EM: Round [139] log likelihood: -8505.911742
EM: Round [140] log likelihood: -8505.911440
EM: Round [141] log likelihood: -8505.911147
EM: Round [142] log likelihood: -8505.910864
EM: Round [143] log likelihood: -8505.910590
EM: Round [144] log likelihood: -8505.910325
EM: Round [145] log likelihood: -8505.910069
EM: Round [146] log likelihood: -8505.909822
EM: Round [147] log likelihood: -8505.909582
EM: Round [148] log likelihood: -8505.909351
EM: Round [149] log likelihood: -8505.909127
EM: Round [150] log likelihood: -8505.908911
EM: Round [151] log likelihood: -8505.908702
EM: Round [152] log likelihood: -8505.908499
EM: Round [153] log likelihood: -8505.908304
EM: Round [154] log likelihood: -8505.908115
EM: Round [155] log likelihood: -8505.907932
EM: Round [156] log likelihood: -8505.907755
EM: Round [157] log likelihood: -8505.907584
EM: Round [158] log likelihood: -8505.907418
EM: Round [159] log likelihood: -8505.907258
EM: Round [160] log likelihood: -8505.907104
EM: Round [161] log likelihood: -8505.906954
EM: Round [162] log likelihood: -8505.906810
EM: Round [163] log likelihood: -8505.906670
EM: Round [164] log likelihood: -8505.906535
EM: Round [165] log likelihood: -8505.906404
EM: Round [166] log likelihood: -8505.906277
EM: Round [167] log likelihood: -8505.906155
EM: Round [168] log likelihood: -8505.906037
EM: Round [169] log likelihood: -8505.905923
EM: Round [170] log likelihood: -8505.905812
EM: Round [171] log likelihood: -8505.905705
EM: Round [172] log likelihood: -8505.905602
EM: Round [173] log likelihood: -8505.905502
EM: Stopping iterations at round 173 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.consolidated.bam into /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords > /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords > /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.njsCWyy5ep/fi_workdir/aih-tih-sc-89f3a3-R1_A23YTGFLT4_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.njsCWyy5ep/fi_workdir/aih-tih-sc-89f3a3-R1_A23YTGFLT4_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.njsCWyy5ep/fi_workdir/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -8067.905083
EM: Round [1] log likelihood: -8067.063517
EM: Round [2] log likelihood: -8067.062977
EM: Round [3] log likelihood: -8067.062977
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1_1.fastp.fastq.gz: 296942872
Warning - not locating file: /tmp/nxf.njsCWyy5ep/aih-tih-sc-89f3a3-R1_A23YTGFLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
WARNING, no entry stored in dbm for [ENSG00000266869.2]
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 [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000260318.1]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286065.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000240498.9]
WARNING, no entry stored in dbm for [ENSG00000240498.9]
WARNING, no entry stored in dbm for [ENSG00000240498.9]
WARNING, no entry stored in dbm for [ENSG00000240498.9]
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 [ENSG00000266869.2]
ls: cannot access 'IGV_inputs': No such file or directory