Done.
-parsing GTF file: /tmp/nxf.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.TJ8Wutuk08/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.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz /tmp/nxf.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.TJ8Wutuk08/fi_workdir/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.TJ8Wutuk08/fi_workdir/1173_F0Y_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_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.star.sortedByCoord.out.bam
11:15:03 : INFO : Done.
-parsing GTF file: /tmp/nxf.TJ8Wutuk08/fi_workdir/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.gtf
-parsing /tmp/nxf.TJ8Wutuk08/fi_workdir/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam

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[1660000]   -done parsing /tmp/nxf.TJ8Wutuk08/fi_workdir/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 14,
          'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
          'low complexity anchor region' => 33,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 58,
          'per_id < 96' => 7351,
          'seq-similar region overlap' => 15,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 378,
          ' ** passed ** ' => 14186,
          'excessive soft clipping' => 14187,
          'small anchor length' => 54,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 6,
          'exons hit < 2' => 10
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.TJ8Wutuk08/fi_workdir/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

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[184000]   -fusion SPANNING read extraction for scaff: CHD6--DHX35

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[170000]   -fusion SPANNING read extraction for scaff: CHD6--LINC01734

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[98000]   -fusion SPANNING read extraction for scaff: FSIP1--AC013652.1

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[16000]   -fusion SPANNING read extraction for scaff: INPP5A--AL596223.1

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[167000]   -fusion SPANNING read extraction for scaff: ITCH--PHF20

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[3000]   -fusion SPANNING read extraction for scaff: LINC02802--AC245060.4

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[223000]   
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[225000]   
[226000]   
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[230000]   
[231000]   -fusion SPANNING read extraction for scaff: MINK1--CLCN7

[1000]   
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[100000]   
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[102000]   
[103000]   -fusion SPANNING read extraction for scaff: PAN3--POLR1D

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[29000]   
[30000]   
[31000]   
[32000]   
[33000]   
[34000]   
[35000]   -fusion SPANNING read extraction for scaff: PCDHB14--PCDHB15

[1000]   
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[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   
[14000]   
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[17000]   
[18000]   
[19000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6

[1000]   
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[6000]   
[7000]   
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[15000]   
[16000]   
[17000]   
[18000]   
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[20000]   
[21000]   
[22000]   
[23000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10

[1000]   
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[8000]   
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[30000]   
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[50000]   
[51000]   
[52000]   
[53000]   
[54000]   
[55000]   
[56000]   
[57000]   
[58000]   
[59000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8

[1000]   
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[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4

[1000]   
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[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
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[11000]   
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[13000]   
[14000]   
[15000]   
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[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11

[1000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5

[1000]   
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[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7

[1000]   
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[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
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[30000]   
[31000]   
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[33000]   
[34000]   
[35000]   
[36000]   
[37000]   
[38000]   
[39000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3

[1000]   
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[6000]   
[7000]   
[8000]   
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[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9

[1000]   
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[4000]   
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[6000]   
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[8000]   
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[25000]   
[26000]   
[27000]   
[28000]   
[29000]   
[30000]   
[31000]   -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12

[1000]   
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[47000]   
[48000]   
[49000]   
[50000]   
[51000]   
[52000]   
[53000]   -fusion SPANNING read extraction for scaff: PHF20--MYLK2

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[82000]   
[83000]   
[84000]   
[85000]   
[86000]   
[87000]   
[88000]   
[89000]   
[90000]   
[91000]   -fusion SPANNING read extraction for scaff: PTMS--MTRNR2L12

[1000]   
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[163000]   
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[165000]   
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[167000]   
[168000]   
[169000]   -fusion SPANNING read extraction for scaff: SCX--MROH1

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[20000]   
[21000]   -fusion SPANNING read extraction for scaff: SEMA6A--RNU1-23P

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[6000]   
[7000]   
[8000]   
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[20000]   
[21000]   -fusion SPANNING read extraction for scaff: SEMA6A--AL158090.1

[1000]   
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[6000]   
[7000]   
[8000]   -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1

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[8000]   
[9000]   
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[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   -fusion SPANNING read extraction for scaff: TVP23C--CDRT4

[1000]   
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[6000]   
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[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   -fusion SPANNING read extraction for scaff: ZNF419--ZNF772
-filtered reads reasons: $VAR1 = {
          'seq similar region alignment' => 67455,
          'lacks exon overlap' => 50346
        };
EM: Starting log likelihood: -3088.600914
EM: Round [1] log likelihood: -3088.600914
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
-extracting read coordinates from /tmp/nxf.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam into /tmp/nxf.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords

CMD: touch /tmp/nxf.TJ8Wutuk08/1173_F0Y_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.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.read_coords > /tmp/nxf.TJ8Wutuk08/1173_F0Y_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.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.consolidated.bam.frag_coords > /tmp/nxf.TJ8Wutuk08/1173_F0Y_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.TJ8Wutuk08/fi_workdir/1173_F0Y_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.TJ8Wutuk08/fi_workdir/1173_F0Y_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.TJ8Wutuk08/fi_workdir/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2437.693188
EM: Round [1] log likelihood: -2437.693188
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1_1.fastp.fastq.gz: 295160414
Warning - not locating file: /tmp/nxf.TJ8Wutuk08/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_1.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000232527.8]
WARNING, no entry stored in dbm for [ENSG00000272779.1]
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 [ENSG00000229261.1]
WARNING, no entry stored in dbm for [ENSG00000229261.1]
WARNING, no entry stored in dbm for [ENSG00000229261.1]
WARNING, no entry stored in dbm for [ENSG00000229261.1]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
WARNING, no entry stored in dbm for [ENSG00000259345.7]
ls: cannot access 'IGV_inputs': No such file or directory