Done.
-parsing GTF file: /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.wvwbwTPvCC/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.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.wvwbwTPvCC/fi_workdir/tih_rna_sample_00714_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.wvwbwTPvCC/fi_workdir/tih_rna_sample_00714_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00714_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00714_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:28:00 : INFO : Done.
-parsing GTF file: /tmp/nxf.wvwbwTPvCC/fi_workdir/tih_rna_sample_00714_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.wvwbwTPvCC/fi_workdir/tih_rna_sample_00714_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[440000]   -done parsing /tmp/nxf.wvwbwTPvCC/fi_workdir/tih_rna_sample_00714_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 39,
          'excessive soft clipping' => 2662,
          'low complexity anchor region' => 2,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 12,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 21,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 16,
          'per_id < 96' => 1073,
          'small anchor length' => 2,
          'exons hit < 2' => 2,
          ' ** passed ** ' => 1548,
          'num genes matched < 2' => 136
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.wvwbwTPvCC/fi_workdir/tih_rna_sample_00714_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[68000]   -fusion SPANNING read extraction for scaff: DNAJC10--PDE1A

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[44000]   -fusion SPANNING read extraction for scaff: NCAPG2--AC019084.1

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[12000]   -fusion SPANNING read extraction for scaff: PMS2P6--CCDC146

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[64000]   -fusion SPANNING read extraction for scaff: ST3GAL4--DCPS

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[120000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[29000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[28000]   -fusion SPANNING read extraction for scaff: TLK2--LINC01347

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

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[27000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

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[22000]   -fusion SPANNING read extraction for scaff: UBE2F--RAMP1
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 2253
        };
EM: Starting log likelihood: -1993.893658
EM: Round [1] log likelihood: -1988.002635
EM: Round [2] log likelihood: -1985.543806
EM: Round [3] log likelihood: -1984.096699
EM: Round [4] log likelihood: -1983.184627
EM: Round [5] log likelihood: -1982.578919
EM: Round [6] log likelihood: -1982.160154
EM: Round [7] log likelihood: -1981.861995
EM: Round [8] log likelihood: -1981.645442
EM: Round [9] log likelihood: -1981.486239
EM: Round [10] log likelihood: -1981.368468
EM: Round [11] log likelihood: -1981.281177
EM: Round [12] log likelihood: -1981.216541
EM: Round [13] log likelihood: -1981.168818
EM: Round [14] log likelihood: -1981.133726
EM: Round [15] log likelihood: -1981.108041
EM: Round [16] log likelihood: -1981.089333
EM: Round [17] log likelihood: -1981.075774
EM: Round [18] log likelihood: -1981.065992
EM: Round [19] log likelihood: -1981.058966
EM: Round [20] log likelihood: -1981.053939
EM: Round [21] log likelihood: -1981.050356
EM: Round [22] log likelihood: -1981.047810
EM: Round [23] log likelihood: -1981.046006
EM: Round [24] log likelihood: -1981.044731
EM: Round [25] log likelihood: -1981.043831
EM: Round [26] log likelihood: -1981.043198
EM: Round [27] log likelihood: -1981.042753
EM: Round [28] log likelihood: -1981.042441
EM: Round [29] log likelihood: -1981.042222
EM: Round [30] log likelihood: -1981.042068
EM: Round [31] log likelihood: -1981.041961
EM: Round [32] log likelihood: -1981.041886
EM: Stopping iterations at round 32 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.wvwbwTPvCC/fi_workdir/tih_rna_sample_00714_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.wvwbwTPvCC/fi_workdir/tih_rna_sample_00714_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.wvwbwTPvCC/fi_workdir/tih_rna_sample_00714_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1921.635186
EM: Round [1] log likelihood: -1921.534865
EM: Round [2] log likelihood: -1921.534795
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1_1.fastp.fastq.gz: 295902418
Warning - not locating file: /tmp/nxf.wvwbwTPvCC/tih_rna_sample_00714_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000174384.9]
WARNING, no entry stored in dbm for [ENSG00000259692.6]
ls: cannot access 'IGV_inputs': No such file or directory