Done.
-parsing GTF file: /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.aLTRApY6Xv/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.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.aLTRApY6Xv/fi_workdir/tih_rna_sample_00626_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.aLTRApY6Xv/fi_workdir/tih_rna_sample_00626_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00626_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00626_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:47:41 : INFO : Done.
-parsing GTF file: /tmp/nxf.aLTRApY6Xv/fi_workdir/tih_rna_sample_00626_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.aLTRApY6Xv/fi_workdir/tih_rna_sample_00626_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

[10000]   
[20000]   
[30000]   
[40000]   
[50000]   
[60000]   
[70000]   
[80000]   
[90000]   
[100000]   
[110000]   
[120000]   
[130000]   
[140000]   
[150000]   
[160000]   
[170000]   
[180000]   
[190000]   
[200000]   
[210000]   
[220000]   
[230000]   -done parsing /tmp/nxf.aLTRApY6Xv/fi_workdir/tih_rna_sample_00626_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num genes matched < 2' => 2,
          'per_id < 96' => 684,
          'excessive soft clipping' => 896,
          'seq-similar region overlap' => 55,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 3,
          ' ** passed ** ' => 3028,
          'small anchor length' => 10,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 24
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.aLTRApY6Xv/fi_workdir/tih_rna_sample_00626_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

[1000]   
[2000]   
[3000]   
[4000]   -fusion SPANNING read extraction for scaff: KRT8P10--KRT6B

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHAC2

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHA10--PCDHA13

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   -fusion SPANNING read extraction for scaff: PCDHGB2--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]   
[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]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[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: PCDHGB2--PCDHGA12

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 519,
          'seq similar region alignment' => 24959
        };
EM: Starting log likelihood: -1196.917108
EM: Round [1] log likelihood: -1196.889171
EM: Round [2] log likelihood: -1196.862423
EM: Round [3] log likelihood: -1196.836801
EM: Round [4] log likelihood: -1196.812241
EM: Round [5] log likelihood: -1196.788690
EM: Round [6] log likelihood: -1196.766093
EM: Round [7] log likelihood: -1196.744402
EM: Round [8] log likelihood: -1196.723572
EM: Round [9] log likelihood: -1196.703559
EM: Round [10] log likelihood: -1196.684325
EM: Round [11] log likelihood: -1196.665832
EM: Round [12] log likelihood: -1196.648045
EM: Round [13] log likelihood: -1196.630931
EM: Round [14] log likelihood: -1196.614459
EM: Round [15] log likelihood: -1196.598601
EM: Round [16] log likelihood: -1196.583328
EM: Round [17] log likelihood: -1196.568615
EM: Round [18] log likelihood: -1196.554438
EM: Round [19] log likelihood: -1196.540773
EM: Round [20] log likelihood: -1196.527598
EM: Round [21] log likelihood: -1196.514894
EM: Round [22] log likelihood: -1196.502640
EM: Round [23] log likelihood: -1196.490818
EM: Round [24] log likelihood: -1196.479409
EM: Round [25] log likelihood: -1196.468399
EM: Round [26] log likelihood: -1196.457770
EM: Round [27] log likelihood: -1196.447507
EM: Round [28] log likelihood: -1196.437596
EM: Round [29] log likelihood: -1196.428023
EM: Round [30] log likelihood: -1196.418776
EM: Round [31] log likelihood: -1196.409841
EM: Round [32] log likelihood: -1196.401207
EM: Round [33] log likelihood: -1196.392862
EM: Round [34] log likelihood: -1196.384796
EM: Round [35] log likelihood: -1196.376999
EM: Round [36] log likelihood: -1196.369459
EM: Round [37] log likelihood: -1196.362168
EM: Round [38] log likelihood: -1196.355118
EM: Round [39] log likelihood: -1196.348298
EM: Round [40] log likelihood: -1196.341701
EM: Round [41] log likelihood: -1196.335318
EM: Round [42] log likelihood: -1196.329143
EM: Round [43] log likelihood: -1196.323168
EM: Round [44] log likelihood: -1196.317385
EM: Round [45] log likelihood: -1196.311789
EM: Round [46] log likelihood: -1196.306372
EM: Round [47] log likelihood: -1196.301128
EM: Round [48] log likelihood: -1196.296052
EM: Round [49] log likelihood: -1196.291137
EM: Round [50] log likelihood: -1196.286378
EM: Round [51] log likelihood: -1196.281770
EM: Round [52] log likelihood: -1196.277308
EM: Round [53] log likelihood: -1196.272987
EM: Round [54] log likelihood: -1196.268801
EM: Round [55] log likelihood: -1196.264747
EM: Round [56] log likelihood: -1196.260820
EM: Round [57] log likelihood: -1196.257016
EM: Round [58] log likelihood: -1196.253331
EM: Round [59] log likelihood: -1196.249760
EM: Round [60] log likelihood: -1196.246301
EM: Round [61] log likelihood: -1196.242949
EM: Round [62] log likelihood: -1196.239701
EM: Round [63] log likelihood: -1196.236554
EM: Round [64] log likelihood: -1196.233504
EM: Round [65] log likelihood: -1196.230548
EM: Round [66] log likelihood: -1196.227683
EM: Round [67] log likelihood: -1196.224906
EM: Round [68] log likelihood: -1196.222215
EM: Round [69] log likelihood: -1196.219606
EM: Round [70] log likelihood: -1196.217078
EM: Round [71] log likelihood: -1196.214626
EM: Round [72] log likelihood: -1196.212250
EM: Round [73] log likelihood: -1196.209946
EM: Round [74] log likelihood: -1196.207713
EM: Round [75] log likelihood: -1196.205547
EM: Round [76] log likelihood: -1196.203448
EM: Round [77] log likelihood: -1196.201412
EM: Round [78] log likelihood: -1196.199439
EM: Round [79] log likelihood: -1196.197525
EM: Round [80] log likelihood: -1196.195669
EM: Round [81] log likelihood: -1196.193870
EM: Round [82] log likelihood: -1196.192124
EM: Round [83] log likelihood: -1196.190432
EM: Round [84] log likelihood: -1196.188791
EM: Round [85] log likelihood: -1196.187199
EM: Round [86] log likelihood: -1196.185656
EM: Round [87] log likelihood: -1196.184159
EM: Round [88] log likelihood: -1196.182707
EM: Round [89] log likelihood: -1196.181299
EM: Round [90] log likelihood: -1196.179933
EM: Round [91] log likelihood: -1196.178608
EM: Round [92] log likelihood: -1196.177323
EM: Round [93] log likelihood: -1196.176077
EM: Round [94] log likelihood: -1196.174868
EM: Round [95] log likelihood: -1196.173695
EM: Round [96] log likelihood: -1196.172557
EM: Round [97] log likelihood: -1196.171454
EM: Round [98] log likelihood: -1196.170383
EM: Round [99] log likelihood: -1196.169345
EM: Round [100] log likelihood: -1196.168337
EM: Round [101] log likelihood: -1196.167360
EM: Round [102] log likelihood: -1196.166412
EM: Round [103] log likelihood: -1196.165492
EM: Round [104] log likelihood: -1196.164600
EM: Round [105] log likelihood: -1196.163734
EM: Round [106] log likelihood: -1196.162894
EM: Round [107] log likelihood: -1196.162080
EM: Round [108] log likelihood: -1196.161289
EM: Round [109] log likelihood: -1196.160522
EM: Round [110] log likelihood: -1196.159778
EM: Round [111] log likelihood: -1196.159056
EM: Round [112] log likelihood: -1196.158355
EM: Round [113] log likelihood: -1196.157676
EM: Round [114] log likelihood: -1196.157016
EM: Round [115] log likelihood: -1196.156376
EM: Round [116] log likelihood: -1196.155756
EM: Round [117] log likelihood: -1196.155153
EM: Round [118] log likelihood: -1196.154569
EM: Round [119] log likelihood: -1196.154001
EM: Round [120] log likelihood: -1196.153451
EM: Round [121] log likelihood: -1196.152917
EM: Round [122] log likelihood: -1196.152399
EM: Round [123] log likelihood: -1196.151896
EM: Round [124] log likelihood: -1196.151408
EM: Round [125] log likelihood: -1196.150935
EM: Round [126] log likelihood: -1196.150476
EM: Round [127] log likelihood: -1196.150030
EM: Round [128] log likelihood: -1196.149597
EM: Round [129] log likelihood: -1196.149177
EM: Round [130] log likelihood: -1196.148770
EM: Round [131] log likelihood: -1196.148375
EM: Round [132] log likelihood: -1196.147991
EM: Round [133] log likelihood: -1196.147619
EM: Round [134] log likelihood: -1196.147258
EM: Round [135] log likelihood: -1196.146907
EM: Round [136] log likelihood: -1196.146567
EM: Round [137] log likelihood: -1196.146237
EM: Round [138] log likelihood: -1196.145917
EM: Round [139] log likelihood: -1196.145606
EM: Round [140] log likelihood: -1196.145304
EM: Round [141] log likelihood: -1196.145012
EM: Round [142] log likelihood: -1196.144728
EM: Round [143] log likelihood: -1196.144452
EM: Round [144] log likelihood: -1196.144184
EM: Round [145] log likelihood: -1196.143925
EM: Round [146] log likelihood: -1196.143673
EM: Round [147] log likelihood: -1196.143428
EM: Round [148] log likelihood: -1196.143191
EM: Round [149] log likelihood: -1196.142960
EM: Round [150] log likelihood: -1196.142737
EM: Round [151] log likelihood: -1196.142520
EM: Round [152] log likelihood: -1196.142309
EM: Round [153] log likelihood: -1196.142105
EM: Round [154] log likelihood: -1196.141907
EM: Round [155] log likelihood: -1196.141714
EM: Round [156] log likelihood: -1196.141528
EM: Round [157] log likelihood: -1196.141347
EM: Round [158] log likelihood: -1196.141171
EM: Round [159] log likelihood: -1196.141000
EM: Round [160] log likelihood: -1196.140834
EM: Round [161] log likelihood: -1196.140673
EM: Round [162] log likelihood: -1196.140517
EM: Round [163] log likelihood: -1196.140366
EM: Round [164] log likelihood: -1196.140219
EM: Round [165] log likelihood: -1196.140076
EM: Round [166] log likelihood: -1196.139938
EM: Round [167] log likelihood: -1196.139804
EM: Round [168] log likelihood: -1196.139673
EM: Round [169] log likelihood: -1196.139547
EM: Round [170] log likelihood: -1196.139424
EM: Round [171] log likelihood: -1196.139305
EM: Round [172] log likelihood: -1196.139189
EM: Round [173] log likelihood: -1196.139077
EM: Round [174] log likelihood: -1196.138968
EM: Round [175] log likelihood: -1196.138862
EM: Round [176] log likelihood: -1196.138759
EM: Round [177] log likelihood: -1196.138660
EM: Stopping iterations at round 177 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.aLTRApY6Xv/fi_workdir/tih_rna_sample_00626_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.aLTRApY6Xv/fi_workdir/tih_rna_sample_00626_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.aLTRApY6Xv/fi_workdir/tih_rna_sample_00626_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1133.931723
EM: Round [1] log likelihood: -1133.931723
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1_1.fastp.fastq.gz: 296380313
Warning - not locating file: /tmp/nxf.aLTRApY6Xv/tih_rna_sample_00626_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
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]
WARNING, no entry stored in dbm for [ENSG00000231203.1]
WARNING, no entry stored in dbm for [ENSG00000231203.1]
ls: cannot access 'IGV_inputs': No such file or directory