[2026-06-08T08:34:40] Launching Arriba 2.4.0
[2026-06-08T08:34:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:34:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:34:52] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_04_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=11620889)
[2026-06-08T08:41:09] Marking multi-mapping alignments (marked=7518963)
[2026-06-08T08:41:13] Detecting strandedness (reverse)
[2026-06-08T08:41:13] Assigning strands to alignments 
[2026-06-08T08:41:16] Annotating alignments 
[2026-06-08T08:41:56] Filtering duplicates (remaining=4997051)
[2026-06-08T08:42:02] 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=4784054)
[2026-06-08T08:42:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4784054)
[2026-06-08T08:42:08] Filtering viral contigs with expression lower than the top 5 (remaining=4784054)
[2026-06-08T08:42:13] Filtering viral contigs with less than 5% coverage (remaining=4784054)
[2026-06-08T08:42:16] Estimating fragment length (mate gap mean=-88.1823, mate gap stddev=27.3225, read length mean=127.473)
[2026-06-08T08:42:16] Filtering read-through fragments with a distance <=10000bp (remaining=4528238)
[2026-06-08T08:42:19] Filtering inconsistently clipped mates (remaining=4419590)
[2026-06-08T08:42:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4261328)
[2026-06-08T08:42:26] Filtering fragments with small insert size (remaining=4260451)
[2026-06-08T08:42:29] Filtering alignments with long gaps (remaining=4260449)
[2026-06-08T08:42:32] Filtering fragments with both mates in the same gene (remaining=4259654)
[2026-06-08T08:42:35] Filtering fusions arising from hairpin structures (remaining=3974220)
[2026-06-08T08:42:37] Filtering reads with a mismatch p-value <=0.01 (remaining=1895623)
[2026-06-08T08:42:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=669245)
[2026-06-08T08:42:59] Finding fusions and counting supporting reads (total=544050)
[2026-06-08T08:43:16] Merging adjacent fusion breakpoints (remaining=538350)
[2026-06-08T08:43:17] Filtering multi-mapping fusions by alignment score and read support (remaining=305300)
[2026-06-08T08:43:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=304124)
[2026-06-08T08:44:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=178785)
[2026-06-08T08:44:01] Filtering fusions with <2 supporting reads (remaining=19748)
[2026-06-08T08:44:01] Filtering fusions with an e-value >=0.3 (remaining=4703)
[2026-06-08T08:44:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4757)
[2026-06-08T08:44:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4666)
[2026-06-08T08:44:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4666)
[2026-06-08T08:44:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4553)
[2026-06-08T08:44:12] Searching for fusions with spliced split reads (remaining=4665)
[2026-06-08T08:44:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=3292)
[2026-06-08T08:44:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3261)
[2026-06-08T08:44:19] Searching for fusions with >=4 spliced events (remaining=3988)
[2026-06-08T08:44:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1718)
[2026-06-08T08:44:33] Filtering fusions with anchors <=23nt (remaining=1519)
[2026-06-08T08:44:33] Filtering end-to-end fusions with low support (remaining=1488)
[2026-06-08T08:44:34] Filtering fusions with no coverage around the breakpoints (remaining=1454)
[2026-06-08T08:44:34] Indexing gene sequences 
[2026-06-08T08:44:41] Filtering genes with >=30% identity (remaining=600)
[2026-06-08T08:44:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=395)
[2026-06-08T08:44:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=270)
[2026-06-08T08:44:56] Searching for additional isoforms (remaining=367)
[2026-06-08T08:44:57] Assigning confidence scores to events 
[2026-06-08T08:44:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:44:59] Writing fusions to file 'BVT_FFPE_TRNA_bst_04_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:02] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_04_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:45:27] Freeing resources
[2026-06-08T08:45:45] Done (elapsed time=00:11:05, CPU time=00:11:04, peak memory=16gb)