Done.
-parsing GTF file: /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.16EHMmev4K/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.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.16EHMmev4K/fi_workdir/659_bNS-T1-TRNA-1_A23MVY2LT4_2.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.16EHMmev4K/fi_workdir/659_bNS-T1-TRNA-1_A23MVY2LT4_2.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam 659_bNS-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam
* Running CMD: samtools index 659_bNS-T1-TRNA-1_A23MVY2LT4_2.star.sortedByCoord.out.bam
11:23:04 : INFO : Done.
-parsing GTF file: /tmp/nxf.16EHMmev4K/fi_workdir/659_bNS-T1-TRNA-1_A23MVY2LT4_2.gtf
-parsing /tmp/nxf.16EHMmev4K/fi_workdir/659_bNS-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam
[10000]
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[520000] -done parsing /tmp/nxf.16EHMmev4K/fi_workdir/659_bNS-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num genes matched < 2' => 21,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 86,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 3,
'excessive soft clipping' => 3637,
'exons hit < 2' => 2,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 10,
'per_id < 96' => 1904,
'low complexity anchor region' => 1,
' ** passed ** ' => 10919,
'seq-similar region overlap' => 14,
'small anchor length' => 51,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 2
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.16EHMmev4K/fi_workdir/659_bNS-T1-TRNA-1_A23MVY2LT4_2.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[172000] -fusion SPANNING read extraction for scaff: EML4--ALK
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[28000] -fusion SPANNING read extraction for scaff: IGFL1P2--HIF3A
[1000] -fusion SPANNING read extraction for scaff: KLRC4--KLRK1
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[26000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC1
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[26000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHAC2
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[21000] -fusion SPANNING read extraction for scaff: PCDHA6--PCDHA13
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[15000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[17000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[13000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[52000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
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[19000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 1838,
'seq similar region alignment' => 19098
};
EM: Starting log likelihood: -2666.777490
EM: Round [1] log likelihood: -2666.439711
EM: Round [2] log likelihood: -2666.439360
EM: Round [3] log likelihood: -2666.439360
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.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam into /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords
CMD: touch /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords > /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords > /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.16EHMmev4K/fi_workdir/659_bNS-T1-TRNA-1_A23MVY2LT4_2.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.16EHMmev4K/fi_workdir/659_bNS-T1-TRNA-1_A23MVY2LT4_2.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.16EHMmev4K/fi_workdir/659_bNS-T1-TRNA-1_A23MVY2LT4_2.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -2487.678474
EM: Round [1] log likelihood: -2487.664636
EM: Round [2] log likelihood: -2487.664609
EM: Stopping iterations at round 2 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2_1.fastp.fastq.gz: 295237877
Warning - not locating file: /tmp/nxf.16EHMmev4K/659_bNS-T1-TRNA-1_A23MVY2LT4_2.gmap_trinity_GG.fusions.gff3.bed
WARNING, no entry stored in dbm for [ENSG00000280136.2]
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 [ENSG00000242193.11]
ls: cannot access 'IGV_inputs': No such file or directory