[2026-06-08T08:17:27] Launching Arriba 2.4.0
[2026-06-08T08:17:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:41] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_05_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=10354290)
[2026-06-08T08:22:28] Marking multi-mapping alignments (marked=6808247)
[2026-06-08T08:22:31] Detecting strandedness (reverse)
[2026-06-08T08:22:31] Assigning strands to alignments 
[2026-06-08T08:22:33] Annotating alignments 
[2026-06-08T08:23:07] Filtering duplicates (remaining=2785660)
[2026-06-08T08:23:12] 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=2657585)
[2026-06-08T08:23:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2657585)
[2026-06-08T08:23:16] Filtering viral contigs with expression lower than the top 5 (remaining=2657585)
[2026-06-08T08:23:20] Filtering viral contigs with less than 5% coverage (remaining=2657585)
[2026-06-08T08:23:22] Estimating fragment length (mate gap mean=-86.0434, mate gap stddev=26.582, read length mean=124.407)
[2026-06-08T08:23:22] Filtering read-through fragments with a distance <=10000bp (remaining=2530531)
[2026-06-08T08:23:24] Filtering inconsistently clipped mates (remaining=2488746)
[2026-06-08T08:23:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2396418)
[2026-06-08T08:23:29] Filtering fragments with small insert size (remaining=2395897)
[2026-06-08T08:23:31] Filtering alignments with long gaps (remaining=2395897)
[2026-06-08T08:23:33] Filtering fragments with both mates in the same gene (remaining=2395347)
[2026-06-08T08:23:35] Filtering fusions arising from hairpin structures (remaining=2316614)
[2026-06-08T08:23:37] Filtering reads with a mismatch p-value <=0.01 (remaining=993124)
[2026-06-08T08:23:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=331681)
[2026-06-08T08:23:50] Finding fusions and counting supporting reads (total=296158)
[2026-06-08T08:24:04] Merging adjacent fusion breakpoints (remaining=293222)
[2026-06-08T08:24:04] Filtering multi-mapping fusions by alignment score and read support (remaining=146427)
[2026-06-08T08:24:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:24:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=145819)
[2026-06-08T08:24:42] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=89216)
[2026-06-08T08:24:42] Filtering fusions with <2 supporting reads (remaining=8105)
[2026-06-08T08:24:43] Filtering fusions with an e-value >=0.3 (remaining=1813)
[2026-06-08T08:24:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1830)
[2026-06-08T08:24:46] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1784)
[2026-06-08T08:24:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1784)
[2026-06-08T08:24:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1782)
[2026-06-08T08:24:50] Searching for fusions with spliced split reads (remaining=1864)
[2026-06-08T08:24:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=1352)
[2026-06-08T08:24:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1334)
[2026-06-08T08:24:55] Searching for fusions with >=4 spliced events (remaining=1505)
[2026-06-08T08:24:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=574)
[2026-06-08T08:25:07] Filtering fusions with anchors <=23nt (remaining=525)
[2026-06-08T08:25:08] Filtering end-to-end fusions with low support (remaining=509)
[2026-06-08T08:25:08] Filtering fusions with no coverage around the breakpoints (remaining=495)
[2026-06-08T08:25:08] Indexing gene sequences 
[2026-06-08T08:25:11] Filtering genes with >=30% identity (remaining=148)
[2026-06-08T08:25:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=48)
[2026-06-08T08:25:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=42)
[2026-06-08T08:25:14] Searching for additional isoforms (remaining=46)
[2026-06-08T08:25:15] Assigning confidence scores to events 
[2026-06-08T08:25:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:25:16] Writing fusions to file 'BVT_FFPE_TRNA_utn_05_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:25:17] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_05_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:25:32] Freeing resources
[2026-06-08T08:25:48] Done (elapsed time=00:08:21, CPU time=00:08:20, peak memory=14.5gb)