[2026-06-08T09:10:45] Launching Arriba 2.4.0
[2026-06-08T09:10:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:10:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:10:57] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_06_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=11718605)
[2026-06-08T09:18:04] Marking multi-mapping alignments (marked=7321806)
[2026-06-08T09:18:09] Detecting strandedness (reverse)
[2026-06-08T09:18:09] Assigning strands to alignments 
[2026-06-08T09:18:12] Annotating alignments 
[2026-06-08T09:18:51] Filtering duplicates (remaining=5739469)
[2026-06-08T09:18:58] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=5560469)
[2026-06-08T09:19:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5560469)
[2026-06-08T09:19:02] Filtering viral contigs with expression lower than the top 5 (remaining=5560469)
[2026-06-08T09:19:07] Filtering viral contigs with less than 5% coverage (remaining=5560469)
[2026-06-08T09:19:10] Estimating fragment length (mate gap mean=-87.8989, mate gap stddev=28.3445, read length mean=134.448)
[2026-06-08T09:19:10] Filtering read-through fragments with a distance <=10000bp (remaining=5261060)
[2026-06-08T09:19:13] Filtering inconsistently clipped mates (remaining=5181802)
[2026-06-08T09:19:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5038707)
[2026-06-08T09:19:20] Filtering fragments with small insert size (remaining=5038053)
[2026-06-08T09:19:22] Filtering alignments with long gaps (remaining=5038053)
[2026-06-08T09:19:24] Filtering fragments with both mates in the same gene (remaining=5037181)
[2026-06-08T09:19:26] Filtering fusions arising from hairpin structures (remaining=4797937)
[2026-06-08T09:19:29] Filtering reads with a mismatch p-value <=0.01 (remaining=2404529)
[2026-06-08T09:19:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=812131)
[2026-06-08T09:19:53] Finding fusions and counting supporting reads (total=633027)
[2026-06-08T09:20:09] Merging adjacent fusion breakpoints (remaining=627422)
[2026-06-08T09:20:11] Filtering multi-mapping fusions by alignment score and read support (remaining=374797)
[2026-06-08T09:20:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:20:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=372602)
[2026-06-08T09:20:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=203668)
[2026-06-08T09:20:53] Filtering fusions with <2 supporting reads (remaining=28276)
[2026-06-08T09:20:54] Filtering fusions with an e-value >=0.3 (remaining=8699)
[2026-06-08T09:20:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8734)
[2026-06-08T09:20:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8661)
[2026-06-08T09:20:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8661)
[2026-06-08T09:21:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5803)
[2026-06-08T09:21:05] Searching for fusions with spliced split reads (remaining=5905)
[2026-06-08T09:21:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=3663)
[2026-06-08T09:21:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3622)
[2026-06-08T09:21:12] Searching for fusions with >=4 spliced events (remaining=4347)
[2026-06-08T09:21:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1652)
[2026-06-08T09:21:26] Filtering fusions with anchors <=23nt (remaining=1415)
[2026-06-08T09:21:26] Filtering end-to-end fusions with low support (remaining=1374)
[2026-06-08T09:21:27] Filtering fusions with no coverage around the breakpoints (remaining=1331)
[2026-06-08T09:21:27] Indexing gene sequences 
[2026-06-08T09:21:32] Filtering genes with >=30% identity (remaining=370)
[2026-06-08T09:21:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=139)
[2026-06-08T09:21:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=128)
[2026-06-08T09:21:37] Searching for additional isoforms (remaining=155)
[2026-06-08T09:21:38] Assigning confidence scores to events 
[2026-06-08T09:21:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:21:41] Writing fusions to file 'BVT_FFPE_TRNA_bst_06_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T09:21:42] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_06_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T09:22:07] Freeing resources
[2026-06-08T09:22:27] Done (elapsed time=00:11:42, CPU time=00:11:41, peak memory=16gb)