Done.
-parsing GTF file: /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.Lo5klXAqwY/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.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.Lo5klXAqwY/fi_workdir/tih_rna_sample_00602_B23MVV7LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.Lo5klXAqwY/fi_workdir/tih_rna_sample_00602_B23MVV7LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam tih_rna_sample_00602_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index tih_rna_sample_00602_B23MVV7LT4_1.star.sortedByCoord.out.bam
11:54:47 : INFO : Done.
-parsing GTF file: /tmp/nxf.Lo5klXAqwY/fi_workdir/tih_rna_sample_00602_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.Lo5klXAqwY/fi_workdir/tih_rna_sample_00602_B23MVV7LT4_1.star.cSorted.dupsMarked.bam

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[840000]   -done parsing /tmp/nxf.Lo5klXAqwY/fi_workdir/tih_rna_sample_00602_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 12,
          'num genes matched < 2' => 10,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 117,
          'excessive soft clipping' => 4099,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 38,
          'seq-similar region overlap' => 36,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 6,
          'per_id < 96' => 2236,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 3,
          'exons hit < 2' => 3,
          ' ** passed ** ' => 2520
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.Lo5klXAqwY/fi_workdir/tih_rna_sample_00602_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[12000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

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[5000]   -fusion SPANNING read extraction for scaff: AP001347.1--ANKRD20A11P

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[267000]   
[268000]   -fusion SPANNING read extraction for scaff: DNM2--SMARCA4

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[17000]   -fusion SPANNING read extraction for scaff: EFL1--GOLGA6L11P

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[9000]   -fusion SPANNING read extraction for scaff: KLRC4--KLRK1

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[67000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[32000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[31000]   -fusion SPANNING read extraction for scaff: TLK2--LINC01347

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[5000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[23000]   -fusion SPANNING read extraction for scaff: TMED7--TICAM2

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

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[341000]   -fusion SPANNING read extraction for scaff: UBA1--ZFX
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 45,
          'lacks exon overlap' => 6361
        };
EM: Starting log likelihood: -4158.452451
EM: Round [1] log likelihood: -4150.990326
EM: Round [2] log likelihood: -4148.242731
EM: Round [3] log likelihood: -4146.370323
EM: Round [4] log likelihood: -4145.048958
EM: Round [5] log likelihood: -4144.101419
EM: Round [6] log likelihood: -4143.414488
EM: Round [7] log likelihood: -4142.912652
EM: Round [8] log likelihood: -4142.544021
EM: Round [9] log likelihood: -4142.272163
EM: Round [10] log likelihood: -4142.071093
EM: Round [11] log likelihood: -4141.922064
EM: Round [12] log likelihood: -4141.811434
EM: Round [13] log likelihood: -4141.729214
EM: Round [14] log likelihood: -4141.668057
EM: Round [15] log likelihood: -4141.622538
EM: Round [16] log likelihood: -4141.588642
EM: Round [17] log likelihood: -4141.563393
EM: Round [18] log likelihood: -4141.544580
EM: Round [19] log likelihood: -4141.530560
EM: Round [20] log likelihood: -4141.520109
EM: Round [21] log likelihood: -4141.512320
EM: Round [22] log likelihood: -4141.506512
EM: Round [23] log likelihood: -4141.502183
EM: Round [24] log likelihood: -4141.498955
EM: Round [25] log likelihood: -4141.496548
EM: Round [26] log likelihood: -4141.494753
EM: Round [27] log likelihood: -4141.493415
EM: Round [28] log likelihood: -4141.492418
EM: Round [29] log likelihood: -4141.491674
EM: Round [30] log likelihood: -4141.491119
EM: Round [31] log likelihood: -4141.490705
EM: Round [32] log likelihood: -4141.490397
EM: Round [33] log likelihood: -4141.490167
EM: Round [34] log likelihood: -4141.489995
EM: Round [35] log likelihood: -4141.489868
EM: Round [36] log likelihood: -4141.489772
EM: Stopping iterations at round 36 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.Lo5klXAqwY/fi_workdir/tih_rna_sample_00602_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.Lo5klXAqwY/fi_workdir/tih_rna_sample_00602_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.Lo5klXAqwY/fi_workdir/tih_rna_sample_00602_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -3939.111885
EM: Round [1] log likelihood: -3938.672559
EM: Round [2] log likelihood: -3938.670766
EM: Round [3] log likelihood: -3938.670758
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1_1.fastp.fastq.gz: 295763628
Warning - not locating file: /tmp/nxf.Lo5klXAqwY/tih_rna_sample_00602_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000224905.7]
WARNING, no entry stored in dbm for [ENSG00000215559.8]
WARNING, no entry stored in dbm for [ENSG00000223698.3]
ls: cannot access 'IGV_inputs': No such file or directory