Done.
-parsing GTF file: /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.gtf
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.zOdQUXYTnh/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.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1_1.fastp.fastq.gz /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.zOdQUXYTnh/fi_workdir/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.zOdQUXYTnh/fi_workdir/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
* Running CMD: mv Aligned.sortedByCoord.out.bam FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.star.sortedByCoord.out.bam
10:32:40 : INFO : Done.
-parsing GTF file: /tmp/nxf.zOdQUXYTnh/fi_workdir/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.gtf
-parsing /tmp/nxf.zOdQUXYTnh/fi_workdir/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.star.cSorted.dupsMarked.bam
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[2860000] -done parsing /tmp/nxf.zOdQUXYTnh/fi_workdir/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 9,
'per_id < 96' => 9417,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 20,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 252,
'excessive soft clipping' => 24915,
'num genes matched < 2' => 49,
'small anchor length' => 38,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 15,
' ** passed ** ' => 17421,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 4,
'low complexity anchor region' => 53
};
-writing fusion junction support info.
-outputting the spanning read info: /tmp/nxf.zOdQUXYTnh/fi_workdir/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[31000] -fusion SPANNING read extraction for scaff: AC015911.9--SLFN12L
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[76000] -fusion SPANNING read extraction for scaff: CCDC6--RET
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[1269000] -fusion SPANNING read extraction for scaff: CD74--ROS1
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[7000] -fusion SPANNING read extraction for scaff: EGFR--SEPTIN14
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[90000] -fusion SPANNING read extraction for scaff: EML4--ALK
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[108000] -fusion SPANNING read extraction for scaff: ETV6--NTRK3
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[220000] -fusion SPANNING read extraction for scaff: FGFR3--TACC3
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[15000] -fusion SPANNING read extraction for scaff: FGFR3--BAIAP2L1
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[127000] -fusion SPANNING read extraction for scaff: KIF5B--RET
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[148000] -fusion SPANNING read extraction for scaff: LMNA--NTRK1
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[103000] -fusion SPANNING read extraction for scaff: NCOA4--RET
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[63000] -fusion SPANNING read extraction for scaff: TFG--NTRK1
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[24000] -fusion SPANNING read extraction for scaff: TLK2--FAM157A
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[21000] -fusion SPANNING read extraction for scaff: TMPRSS2--ERG
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[13000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
-filtered reads reasons: $VAR1 = {
'lacks exon overlap' => 13111,
'seq similar region alignment' => 51211
};
EM: Starting log likelihood: -24819.222227
EM: Round [1] log likelihood: -24806.781852
EM: Round [2] log likelihood: -24806.716995
EM: Round [3] log likelihood: -24806.716679
EM: Round [4] log likelihood: -24806.716677
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.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.consolidated.bam into /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.consolidated.bam.read_coords > /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.consolidated.bam.frag_coords > /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.consolidated.bam.frag_coords.coord_sorted
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.zOdQUXYTnh/fi_workdir/FFPE_V4_0002_RNA_0001_B23MVV7LT4_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.zOdQUXYTnh/fi_workdir/FFPE_V4_0002_RNA_0001_B23MVV7LT4_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.zOdQUXYTnh/fi_workdir/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.post_blast_and_promiscuity_filter
-done, see /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
EM: Starting log likelihood: -24439.976013
EM: Round [1] log likelihood: -24436.795616
EM: Round [2] log likelihood: -24436.769632
EM: Round [3] log likelihood: -24436.769489
EM: Round [4] log likelihood: -24436.769489
EM: Stopping iterations at round 4 due to insufficient improvement in likelihood.
-total frags in /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1_1.fastp.fastq.gz: 199455448
Warning - not locating file: /tmp/nxf.zOdQUXYTnh/FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.gmap_trinity_GG.fusions.gff3.bed
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 [ENSG00000286030.2]
WARNING, no entry stored in dbm for [ENSG00000236438.7]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
ls: cannot access 'IGV_inputs': No such file or directory