Done.
-parsing GTF file: /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.v4W9t1d1P2/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.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.v4W9t1d1P2/fi_workdir/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.v4W9t1d1P2/fi_workdir/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bQZ-T1-TRNA-1_A23MVY2LT4_1.star.sortedByCoord.out.bam
11:57:01 : INFO : Done.
-parsing GTF file: /tmp/nxf.v4W9t1d1P2/fi_workdir/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gtf
-parsing /tmp/nxf.v4W9t1d1P2/fi_workdir/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam

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[370000]   -done parsing /tmp/nxf.v4W9t1d1P2/fi_workdir/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 270,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 44,
          ' ** passed ** ' => 1601,
          'excessive soft clipping' => 2839,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 17,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 27,
          'per_id < 96' => 1691,
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 14
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.v4W9t1d1P2/fi_workdir/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[102000]   -fusion SPANNING read extraction for scaff: AGAP3--BRAF
-fusion SPANNING read extraction for scaff: GUCY1B2--NKAIN2

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[32000]   -fusion SPANNING read extraction for scaff: SMARCD3--MGAM

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[201000]   -fusion SPANNING read extraction for scaff: SYNE2--MTHFD1

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[17000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[22000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 3539
        };
EM: Starting log likelihood: -1412.711445
EM: Round [1] log likelihood: -1410.566673
EM: Round [2] log likelihood: -1410.565392
EM: Round [3] log likelihood: -1410.565392
EM: Stopping iterations at round 3 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam into /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords > /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.frag_coords > /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.v4W9t1d1P2/fi_workdir/659_bQZ-T1-TRNA-1_A23MVY2LT4_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.v4W9t1d1P2/fi_workdir/659_bQZ-T1-TRNA-1_A23MVY2LT4_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.v4W9t1d1P2/fi_workdir/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -1381.078766
EM: Round [1] log likelihood: -1380.704178
EM: Round [2] log likelihood: -1380.704161
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1_1.fastp.fastq.gz: 270100702
Warning - not locating file: /tmp/nxf.v4W9t1d1P2/659_bQZ-T1-TRNA-1_A23MVY2LT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000123201.14]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
ls: cannot access 'IGV_inputs': No such file or directory