Done.
-parsing GTF file: /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.BKn2tIT8Qn/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.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.BKn2tIT8Qn/fi_workdir/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.BKn2tIT8Qn/fi_workdir/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam 1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
11:54:07 : INFO : Done.
-parsing GTF file: /tmp/nxf.BKn2tIT8Qn/fi_workdir/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.BKn2tIT8Qn/fi_workdir/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam

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[1160000]   -done parsing /tmp/nxf.BKn2tIT8Qn/fi_workdir/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 14,
          'exons hit < 2' => 12,
          'excessive soft clipping' => 8163,
          'num genes matched < 2' => 40,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 144,
          'num_hits: 5 != num_counted_on_fusion_contigs 4 ' => 4,
          'small anchor length' => 3,
          'per_id < 96' => 4597,
          'num_hits: 5 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 9,
          'low complexity anchor region' => 8,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 458,
          ' ** passed ** ' => 4272
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.BKn2tIT8Qn/fi_workdir/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[68000]   
[69000]   -fusion SPANNING read extraction for scaff: ABHD2--TTC23

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[13000]   
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[20000]   
[21000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: AC092807.3--DDAH1

[1000]   
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[7000]   
[8000]   -fusion SPANNING read extraction for scaff: AC097520.2--GRID2

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[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: AL139042.1--CNR1

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[39000]   
[40000]   -fusion SPANNING read extraction for scaff: CCDC198--NPIPB10P

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[204000]   
[205000]   -fusion SPANNING read extraction for scaff: CELSR1--CERK

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[54000]   
[55000]   
[56000]   -fusion SPANNING read extraction for scaff: CTTNBP2NL--WNT2B

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[106000]   
[107000]   -fusion SPANNING read extraction for scaff: DCBLD2--AC138776.1

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[83000]   
[84000]   -fusion SPANNING read extraction for scaff: DLC1--MSR1

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[53000]   
[54000]   -fusion SPANNING read extraction for scaff: ETNK1--AC084816.1

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[12000]   -fusion SPANNING read extraction for scaff: FBXO25--AC240565.1

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[20000]   
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[24000]   
[25000]   -fusion SPANNING read extraction for scaff: GOLGA6L10--GOLGA2P6

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: GTF2A1L--STON1-GTF2A1L

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[6000]   
[7000]   -fusion SPANNING read extraction for scaff: MTAP--CDKN2B-AS1

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[3000]   
[4000]   -fusion SPANNING read extraction for scaff: PLGRKT--AL162384.1

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[11000]   -fusion SPANNING read extraction for scaff: PLGRKT--IL33

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[69000]   
[70000]   -fusion SPANNING read extraction for scaff: PTPN2--NPIPB10P

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[19000]   -fusion SPANNING read extraction for scaff: RAB38--AP000676.5

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[163000]   -fusion SPANNING read extraction for scaff: STX16--NPEPL1

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[71000]   -fusion SPANNING read extraction for scaff: TLK2--AC240565.1

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[42000]   -fusion SPANNING read extraction for scaff: TPTE--AL356585.3

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[23000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 5695
        };
EM: Starting log likelihood: -7417.056071
EM: Round [1] log likelihood: -7416.932824
EM: Round [2] log likelihood: -7416.929139
EM: Round [3] log likelihood: -7416.929000
EM: Round [4] log likelihood: -7416.928994
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.BKn2tIT8Qn/fi_workdir/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_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.BKn2tIT8Qn/fi_workdir/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_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.BKn2tIT8Qn/fi_workdir/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -7179.652185
EM: Round [1] log likelihood: -7179.543196
EM: Round [2] log likelihood: -7179.539512
EM: Round [3] log likelihood: -7179.539373
EM: Round [4] log likelihood: -7179.539367
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 294980563
Warning - not locating file: /tmp/nxf.BKn2tIT8Qn/1173_LQD_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000228739.1]
WARNING, no entry stored in dbm for [ENSG00000228739.1]
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 [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 [ENSG00000240498.9]
WARNING, no entry stored in dbm for [ENSG00000240498.9]
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000279231.1]
WARNING, no entry stored in dbm for [ENSG00000234426.3]
WARNING, no entry stored in dbm for [ENSG00000234426.3]
WARNING, no entry stored in dbm for [ENSG00000234426.3]
WARNING, no entry stored in dbm for [ENSG00000234426.3]
WARNING, no entry stored in dbm for [ENSG00000241621.1]
WARNING, no entry stored in dbm for [ENSG00000287392.1]
WARNING, no entry stored in dbm for [ENSG00000287392.1]
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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 [ENSG00000285835.1]
WARNING, no entry stored in dbm for [ENSG00000285835.1]
WARNING, no entry stored in dbm for [ENSG00000285835.1]
WARNING, no entry stored in dbm for [ENSG00000285835.1]
WARNING, no entry stored in dbm for [ENSG00000256995.8]
WARNING, no entry stored in dbm for [ENSG00000256995.8]
WARNING, no entry stored in dbm for [ENSG00000256995.8]
WARNING, no entry stored in dbm for [ENSG00000256995.8]
WARNING, no entry stored in dbm for [ENSG00000256995.8]
WARNING, no entry stored in dbm for [ENSG00000256995.8]
WARNING, no entry stored in dbm for [ENSG00000068781.21]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000196796.5]
WARNING, no entry stored in dbm for [ENSG00000286406.1]
WARNING, no entry stored in dbm for [ENSG00000286406.1]
ls: cannot access 'IGV_inputs': No such file or directory