[2026-06-08T08:50:44] Launching Arriba 2.4.0
[2026-06-08T08:50:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:50:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:00] Reading chimeric alignments from 'BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=12882300)
[2026-06-08T08:58:06] Marking multi-mapping alignments (marked=8155903)
[2026-06-08T08:58:12] Detecting strandedness (reverse)
[2026-06-08T08:58:12] Assigning strands to alignments 
[2026-06-08T08:58:14] Annotating alignments 
[2026-06-08T08:59:00] Filtering duplicates (remaining=6178077)
[2026-06-08T08:59:09] 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=5951467)
[2026-06-08T08:59:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5951467)
[2026-06-08T08:59:14] Filtering viral contigs with expression lower than the top 5 (remaining=5951467)
[2026-06-08T08:59:21] Filtering viral contigs with less than 5% coverage (remaining=5951467)
[2026-06-08T08:59:24] Estimating fragment length (mate gap mean=-86.9776, mate gap stddev=26.342, read length mean=126.757)
[2026-06-08T08:59:24] Filtering read-through fragments with a distance <=10000bp (remaining=5500050)
[2026-06-08T08:59:27] Filtering inconsistently clipped mates (remaining=5414584)
[2026-06-08T08:59:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5278535)
[2026-06-08T08:59:35] Filtering fragments with small insert size (remaining=5277639)
[2026-06-08T08:59:38] Filtering alignments with long gaps (remaining=5277638)
[2026-06-08T08:59:41] Filtering fragments with both mates in the same gene (remaining=5276669)
[2026-06-08T08:59:44] Filtering fusions arising from hairpin structures (remaining=5043566)
[2026-06-08T08:59:47] Filtering reads with a mismatch p-value <=0.01 (remaining=2429619)
[2026-06-08T09:00:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=1003744)
[2026-06-08T09:00:13] Finding fusions and counting supporting reads (total=806501)
[2026-06-08T09:00:34] Merging adjacent fusion breakpoints (remaining=795610)
[2026-06-08T09:00:36] Filtering multi-mapping fusions by alignment score and read support (remaining=455665)
[2026-06-08T09:01:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:01:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=454399)
[2026-06-08T09:01:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=263769)
[2026-06-08T09:01:30] Filtering fusions with <2 supporting reads (remaining=30491)
[2026-06-08T09:01:30] Filtering fusions with an e-value >=0.3 (remaining=6710)
[2026-06-08T09:01:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6772)
[2026-06-08T09:01:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6666)
[2026-06-08T09:01:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6683)
[2026-06-08T09:01:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6521)
[2026-06-08T09:01:46] Searching for fusions with spliced split reads (remaining=6603)
[2026-06-08T09:01:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=4174)
[2026-06-08T09:01:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4150)
[2026-06-08T09:01:54] Searching for fusions with >=4 spliced events (remaining=5205)
[2026-06-08T09:01:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2377)
[2026-06-08T09:02:09] Filtering fusions with anchors <=23nt (remaining=2072)
[2026-06-08T09:02:09] Filtering end-to-end fusions with low support (remaining=2025)
[2026-06-08T09:02:10] Filtering fusions with no coverage around the breakpoints (remaining=1965)
[2026-06-08T09:02:11] Indexing gene sequences 
[2026-06-08T09:02:17] Filtering genes with >=30% identity (remaining=512)
[2026-06-08T09:02:20] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=104)
[2026-06-08T09:02:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=89)
[2026-06-08T09:02:23] Searching for additional isoforms (remaining=141)
[2026-06-08T09:02:25] Assigning confidence scores to events 
[2026-06-08T09:02:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:02:28] Writing fusions to file 'BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:02:29] Writing discarded fusions to file 'BVT_FFPE_TRNA_bld_02_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:00] Freeing resources
[2026-06-08T09:03:23] Done (elapsed time=00:12:39, CPU time=00:12:38, peak memory=17.4gb)