Done.
-parsing GTF file: /tmp/nxf.tfHYSsibyR/rna_s1221_S42.gtf
* Running CMD: /usr/local/bin/STAR  --runThreadN 8  --genomeDir /tmp/nxf.tfHYSsibyR/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.tfHYSsibyR/rna_s1221_S42_1.fastp.fastq.gz /tmp/nxf.tfHYSsibyR/rna_s1221_S42_2.fastp.fastq.gz  --genomeFastaFiles /tmp/nxf.tfHYSsibyR/fi_workdir/rna_s1221_S42.fa  --outSAMfilter KeepAllAddedReferences  --sjdbGTFfile /tmp/nxf.tfHYSsibyR/fi_workdir/rna_s1221_S42.gtf  --alignSJstitchMismatchNmax 5 -1 5 5  --scoreGapNoncan -6  --readFilesCommand 'gunzip -c' 
* Running CMD: mv Aligned.sortedByCoord.out.bam rna_s1221_S42.star.sortedByCoord.out.bam
* Running CMD: samtools index rna_s1221_S42.star.sortedByCoord.out.bam
00:27:36 : INFO : Done.
-parsing GTF file: /tmp/nxf.tfHYSsibyR/fi_workdir/rna_s1221_S42.gtf
-parsing /tmp/nxf.tfHYSsibyR/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam

[10000]   
[20000]   
[30000]   
[40000]   
[50000]   -done parsing /tmp/nxf.tfHYSsibyR/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.  Extracting junction info.
junction read elimination tally: $VAR1 = {
          ' ** passed ** ' => 351,
          'num_hits: 1 != num_counted_on_fusion_contigs 2 ' => 32,
          'excessive soft clipping' => 503,
          'low complexity anchor region' => 4,
          'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 1,
          'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 6,
          'per_id < 96' => 142,
          'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 2
        };
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.tfHYSsibyR/fi_workdir/rna_s1221_S42.star.cSorted.dupsMarked.bam.fusion_spanning_info.
 - counting read alignments among fusion contigs.

[1000]   -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L

[1000]   
[2000]   
[3000]   
[4000]   
[5000]   
[6000]   
[7000]   
[8000]   
[9000]   
[10000]   
[11000]   
[12000]   
[13000]   
[14000]   
[15000]   
[16000]   
[17000]   
[18000]   
[19000]   
[20000]   
[21000]   
[22000]   
[23000]   
[24000]   
[25000]   
[26000]   
[27000]   
[28000]   
[29000]   -fusion SPANNING read extraction for scaff: CD74--ROS1
-fusion SPANNING read extraction for scaff: EGFR--SEPTIN14

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: ETV6--NTRK3

[1000]   
[2000]   
[3000]   
[4000]   -fusion SPANNING read extraction for scaff: FGFR3--TACC3
-fusion SPANNING read extraction for scaff: FGFR3--BAIAP2L1

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: KIF5B--RET

[1000]   
[2000]   
[3000]   
[4000]   -fusion SPANNING read extraction for scaff: LMNA--NTRK1

[1000]   
[2000]   
[3000]   -fusion SPANNING read extraction for scaff: NCOA4--RET
-fusion SPANNING read extraction for scaff: PAX8--PPARG

[1000]   
[2000]   -fusion SPANNING read extraction for scaff: SLC45A3--BRAF
-filtered reads reasons: $VAR1 = {
          'lacks exon overlap' => 317,
          'seq similar region alignment' => 549
        };
EM: Starting log likelihood: -478.690299
EM: Round [1] log likelihood: -478.690299
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-extracting read coordinates from /tmp/nxf.tfHYSsibyR/rna_s1221_S42.consolidated.bam into /tmp/nxf.tfHYSsibyR/rna_s1221_S42.consolidated.bam.read_coords

CMD: touch /tmp/nxf.tfHYSsibyR/rna_s1221_S42.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.tfHYSsibyR/rna_s1221_S42.consolidated.bam.read_coords > /tmp/nxf.tfHYSsibyR/rna_s1221_S42.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.tfHYSsibyR/rna_s1221_S42.consolidated.bam.frag_coords > /tmp/nxf.tfHYSsibyR/rna_s1221_S42.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.tfHYSsibyR/fi_workdir/rna_s1221_S42.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.tfHYSsibyR/fi_workdir/rna_s1221_S42.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.tfHYSsibyR/fi_workdir/rna_s1221_S42.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.tfHYSsibyR/rna_s1221_S42.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.tfHYSsibyR/rna_s1221_S42.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -478.690299
EM: Round [1] log likelihood: -478.690299
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.tfHYSsibyR/rna_s1221_S42_1.fastp.fastq.gz: 9932006
Warning - not locating file: /tmp/nxf.tfHYSsibyR/rna_s1221_S42.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000286030.2]
ls: cannot access 'IGV_inputs': No such file or directory