Done.
-parsing GTF file: /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.4kgCUh1jCq/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.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.4kgCUh1jCq/fi_workdir/tih_rna_sample_00754_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.4kgCUh1jCq/fi_workdir/tih_rna_sample_00754_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00754_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00754_B23MVV7LT4_1.star.sortedByCoord.out.bam
10:29:32 : INFO : Done.
-parsing GTF file: /tmp/nxf.4kgCUh1jCq/fi_workdir/tih_rna_sample_00754_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.4kgCUh1jCq/fi_workdir/tih_rna_sample_00754_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[1730000]   -done parsing /tmp/nxf.4kgCUh1jCq/fi_workdir/tih_rna_sample_00754_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          ' ** passed ** ' => 5283,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 48,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 24,
          'excessive soft clipping' => 10164,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 21,
          'low complexity anchor region' => 41,
          'num genes matched < 2' => 35,
          'seq-similar region overlap' => 48,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'small anchor length' => 33,
          'num_hits: 5 != num_counted_on_fusion_contigs 3 ' => 3,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 9,
          'per_id < 96' => 5821,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 200
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.4kgCUh1jCq/fi_workdir/tih_rna_sample_00754_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[16000]   -fusion SPANNING read extraction for scaff: ARNTL--BTBD10

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[16000]   -fusion SPANNING read extraction for scaff: CAP2--RCAN2

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[29000]   -fusion SPANNING read extraction for scaff: CDC73--RO60

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[57000]   
[58000]   -fusion SPANNING read extraction for scaff: CROCCP3--DAB2

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[100000]   -fusion SPANNING read extraction for scaff: CTNNA1--UBE2D2

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[20000]   -fusion SPANNING read extraction for scaff: DOC2B--DHX40

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[48000]   -fusion SPANNING read extraction for scaff: DTNB--BTN2A1

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[47000]   -fusion SPANNING read extraction for scaff: DYRK1A--LINC01111

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[10000]   -fusion SPANNING read extraction for scaff: FHOD3--AC137761.1

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[10000]   -fusion SPANNING read extraction for scaff: FHOD3--LINC01691

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[10000]   -fusion SPANNING read extraction for scaff: FHOD3--AC242852.1

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[13000]   -fusion SPANNING read extraction for scaff: GCLC--MIR99AHG

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[21000]   -fusion SPANNING read extraction for scaff: GDA--CD24P4

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[27000]   -fusion SPANNING read extraction for scaff: GMPR--JARID2

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[48000]   -fusion SPANNING read extraction for scaff: KCTD3--AL450990.1

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[8000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[14000]   -fusion SPANNING read extraction for scaff: NDUFV3--BMP5

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[49000]   -fusion SPANNING read extraction for scaff: NEBL--PLXDC2

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[16000]   -fusion SPANNING read extraction for scaff: NFKBIL1--AL157371.2

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[86000]   -fusion SPANNING read extraction for scaff: NUP153--AL009177.1

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[40000]   -fusion SPANNING read extraction for scaff: PAPLN--CLVS1

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[22000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA8

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[18000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB6

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[27000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC3

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[9000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC5

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA10

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[8000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGC4

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[20000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA12

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[21000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA11

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[20000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGA9

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[16000]   -fusion SPANNING read extraction for scaff: PCDHGA4--PCDHGB7

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[69000]   -fusion SPANNING read extraction for scaff: PLEKHM1--SLC5A10

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[28000]   
[29000]   -fusion SPANNING read extraction for scaff: POFUT2--EYS

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[233000]   
[234000]   -fusion SPANNING read extraction for scaff: PTPRF--ASCC1

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[107000]   -fusion SPANNING read extraction for scaff: QKI--AL137005.1

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[28000]   
[29000]   -fusion SPANNING read extraction for scaff: RO60--CDC73

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[34000]   
[35000]   -fusion SPANNING read extraction for scaff: RRP1B--SLC22A23

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[21000]   -fusion SPANNING read extraction for scaff: RRP1B--AL033523.1

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[33000]   -fusion SPANNING read extraction for scaff: SLFN11--SLFN12

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[80000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[39000]   -fusion SPANNING read extraction for scaff: TLK2--FAM157A

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[6000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[14000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[42000]   -fusion SPANNING read extraction for scaff: UPF2--GPR158

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[21000]   -fusion SPANNING read extraction for scaff: VTI1A--ZDHHC3

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[42000]   -fusion SPANNING read extraction for scaff: WRNIP1--CHODL

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[16000]   -fusion SPANNING read extraction for scaff: ZDHHC3--CDHR3
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 27713,
          'seq similar region alignment' => 39490
        };
EM: Starting log likelihood: -7010.785957
EM: Round [1] log likelihood: -7009.855323
EM: Round [2] log likelihood: -7009.672257
EM: Round [3] log likelihood: -7009.510541
EM: Round [4] log likelihood: -7009.366674
EM: Round [5] log likelihood: -7009.238474
EM: Round [6] log likelihood: -7009.124066
EM: Round [7] log likelihood: -7009.021825
EM: Round [8] log likelihood: -7008.930343
EM: Round [9] log likelihood: -7008.848392
EM: Round [10] log likelihood: -7008.774901
EM: Round [11] log likelihood: -7008.708929
EM: Round [12] log likelihood: -7008.649652
EM: Round [13] log likelihood: -7008.596342
EM: Round [14] log likelihood: -7008.548358
EM: Round [15] log likelihood: -7008.505134
EM: Round [16] log likelihood: -7008.466169
EM: Round [17] log likelihood: -7008.431016
EM: Round [18] log likelihood: -7008.399281
EM: Round [19] log likelihood: -7008.370613
EM: Round [20] log likelihood: -7008.344697
EM: Round [21] log likelihood: -7008.321256
EM: Round [22] log likelihood: -7008.300040
EM: Round [23] log likelihood: -7008.280827
EM: Round [24] log likelihood: -7008.263417
EM: Round [25] log likelihood: -7008.247633
EM: Round [26] log likelihood: -7008.233315
EM: Round [27] log likelihood: -7008.220321
EM: Round [28] log likelihood: -7008.208521
EM: Round [29] log likelihood: -7008.197800
EM: Round [30] log likelihood: -7008.188056
EM: Round [31] log likelihood: -7008.179194
EM: Round [32] log likelihood: -7008.171132
EM: Round [33] log likelihood: -7008.163793
EM: Round [34] log likelihood: -7008.157110
EM: Round [35] log likelihood: -7008.151022
EM: Round [36] log likelihood: -7008.145472
EM: Round [37] log likelihood: -7008.140412
EM: Round [38] log likelihood: -7008.135796
EM: Round [39] log likelihood: -7008.131584
EM: Round [40] log likelihood: -7008.127739
EM: Round [41] log likelihood: -7008.124227
EM: Round [42] log likelihood: -7008.121018
EM: Round [43] log likelihood: -7008.118086
EM: Round [44] log likelihood: -7008.115404
EM: Round [45] log likelihood: -7008.112952
EM: Round [46] log likelihood: -7008.110709
EM: Round [47] log likelihood: -7008.108655
EM: Round [48] log likelihood: -7008.106775
EM: Round [49] log likelihood: -7008.105053
EM: Round [50] log likelihood: -7008.103476
EM: Round [51] log likelihood: -7008.102031
EM: Round [52] log likelihood: -7008.100706
EM: Round [53] log likelihood: -7008.099491
EM: Round [54] log likelihood: -7008.098377
EM: Round [55] log likelihood: -7008.097354
EM: Round [56] log likelihood: -7008.096416
EM: Round [57] log likelihood: -7008.095555
EM: Round [58] log likelihood: -7008.094765
EM: Round [59] log likelihood: -7008.094039
EM: Round [60] log likelihood: -7008.093372
EM: Round [61] log likelihood: -7008.092759
EM: Round [62] log likelihood: -7008.092196
EM: Round [63] log likelihood: -7008.091679
EM: Round [64] log likelihood: -7008.091203
EM: Round [65] log likelihood: -7008.090765
EM: Round [66] log likelihood: -7008.090363
EM: Round [67] log likelihood: -7008.089993
EM: Round [68] log likelihood: -7008.089652
EM: Round [69] log likelihood: -7008.089339
EM: Round [70] log likelihood: -7008.089050
EM: Round [71] log likelihood: -7008.088785
EM: Round [72] log likelihood: -7008.088540
EM: Round [73] log likelihood: -7008.088315
EM: Round [74] log likelihood: -7008.088108
EM: Round [75] log likelihood: -7008.087917
EM: Round [76] log likelihood: -7008.087741
EM: Round [77] log likelihood: -7008.087578
EM: Round [78] log likelihood: -7008.087429
EM: Round [79] log likelihood: -7008.087291
EM: Round [80] log likelihood: -7008.087165
EM: Round [81] log likelihood: -7008.087048
EM: Round [82] log likelihood: -7008.086940
EM: Round [83] log likelihood: -7008.086840
EM: Stopping iterations at round 83 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.4kgCUh1jCq/fi_workdir/tih_rna_sample_00754_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.4kgCUh1jCq/fi_workdir/tih_rna_sample_00754_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.4kgCUh1jCq/fi_workdir/tih_rna_sample_00754_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -6661.392982
EM: Round [1] log likelihood: -6661.075622
EM: Round [2] log likelihood: -6661.075239
EM: Round [3] log likelihood: -6661.075239
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1_1.fastp.fastq.gz: 217976912
Warning - not locating file: /tmp/nxf.4kgCUh1jCq/tih_rna_sample_00754_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000236438.7]
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 [ENSG00000286277.1]
WARNING, no entry stored in dbm for [ENSG00000286277.1]
WARNING, no entry stored in dbm for [ENSG00000254300.1]
WARNING, no entry stored in dbm for [ENSG00000254300.1]
WARNING, no entry stored in dbm for [ENSG00000260158.1]
WARNING, no entry stored in dbm for [ENSG00000185275.6]
WARNING, no entry stored in dbm for [ENSG00000080947.15]
WARNING, no entry stored in dbm for [ENSG00000283573.1]
WARNING, no entry stored in dbm for [ENSG00000215386.13]
WARNING, no entry stored in dbm for [ENSG00000215386.13]
WARNING, no entry stored in dbm for [ENSG00000215386.13]
WARNING, no entry stored in dbm for [ENSG00000215386.13]
WARNING, no entry stored in dbm for [ENSG00000235538.5]
ls: cannot access 'IGV_inputs': No such file or directory