Done.
-parsing GTF file: /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.fWxZrjsLy2/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.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1_1.fastp.fastq.gz /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.fWxZrjsLy2/fi_workdir/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.fWxZrjsLy2/fi_workdir/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.star.sortedByCoord.out.bam
09:18:21 : INFO : Done.
-parsing GTF file: /tmp/nxf.fWxZrjsLy2/fi_workdir/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.gtf
-parsing /tmp/nxf.fWxZrjsLy2/fi_workdir/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam
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[4390000] -done parsing /tmp/nxf.fWxZrjsLy2/fi_workdir/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'excessive soft clipping' => 42260,
'num_hits: 6 != num_counted_on_fusion_contigs 2 ' => 8,
' ** passed ** ' => 122126,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 375,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 8,
'num genes matched < 2' => 212,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 8,
'per_id < 96' => 26593,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 85,
'exons hit < 2' => 21,
'small anchor length' => 275
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.fWxZrjsLy2/fi_workdir/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[3952000] -fusion SPANNING read extraction for scaff: FGFR3--TACC3
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[93000] -fusion SPANNING read extraction for scaff: PEDS1--RNU6-639P
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[93000] -fusion SPANNING read extraction for scaff: PEDS1--LINC01728
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[79000] -fusion SPANNING read extraction for scaff: PPME1--TCF7L2
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[58000] -fusion SPANNING read extraction for scaff: PTBP3--HSDL2
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[39000] -fusion SPANNING read extraction for scaff: RBMS1--AFF3
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[50000] -fusion SPANNING read extraction for scaff: RPN2--PTPRT
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[18000] -fusion SPANNING read extraction for scaff: USP12--MTIF3
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[5000] -fusion SPANNING read extraction for scaff: USP12--RNU6-63P
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 11610
};
EM: Starting log likelihood: -13605.040787
EM: Round [1] log likelihood: -13605.040787
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.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.consolidated.bam into /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.consolidated.bam.read_coords > /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.consolidated.bam.frag_coords > /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.fWxZrjsLy2/fi_workdir/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_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.fWxZrjsLy2/fi_workdir/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_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.fWxZrjsLy2/fi_workdir/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -12549.214573
EM: Round [1] log likelihood: -12549.214573
EM: Stopping iterations at round 1 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1_1.fastp.fastq.gz: 159122119
Warning - not locating file: /tmp/nxf.fWxZrjsLy2/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.gmap_trinity_GG.fusions.gff3.bed
ls: cannot access 'IGV_inputs': No such file or directory