[2026-06-08T08:14:26] Launching Arriba 2.4.0
[2026-06-08T08:14:26] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:14:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:14:45] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_07_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=10519948)
[2026-06-08T08:20:18] Marking multi-mapping alignments (marked=6943788)
[2026-06-08T08:20:22] Detecting strandedness (reverse)
[2026-06-08T08:20:22] Assigning strands to alignments 
[2026-06-08T08:20:24] Annotating alignments 
[2026-06-08T08:20:57] Filtering duplicates (remaining=3669400)
[2026-06-08T08:21:03] 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=3475828)
[2026-06-08T08:21:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3475828)
[2026-06-08T08:21:07] Filtering viral contigs with expression lower than the top 5 (remaining=3475828)
[2026-06-08T08:21:11] Filtering viral contigs with less than 5% coverage (remaining=3475828)
[2026-06-08T08:21:13] Estimating fragment length (mate gap mean=-85.0364, mate gap stddev=26.8158, read length mean=120.673)
[2026-06-08T08:21:13] Filtering read-through fragments with a distance <=10000bp (remaining=3240548)
[2026-06-08T08:21:15] Filtering inconsistently clipped mates (remaining=3179000)
[2026-06-08T08:21:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3065591)
[2026-06-08T08:21:20] Filtering fragments with small insert size (remaining=3064850)
[2026-06-08T08:21:22] Filtering alignments with long gaps (remaining=3064850)
[2026-06-08T08:21:24] Filtering fragments with both mates in the same gene (remaining=3064259)
[2026-06-08T08:21:26] Filtering fusions arising from hairpin structures (remaining=2924242)
[2026-06-08T08:21:28] Filtering reads with a mismatch p-value <=0.01 (remaining=1241164)
[2026-06-08T08:21:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=459760)
[2026-06-08T08:21:43] Finding fusions and counting supporting reads (total=418405)
[2026-06-08T08:21:58] Merging adjacent fusion breakpoints (remaining=413125)
[2026-06-08T08:21:59] Filtering multi-mapping fusions by alignment score and read support (remaining=225195)
[2026-06-08T08:22:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:22:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=224370)
[2026-06-08T08:22:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=126809)
[2026-06-08T08:22:38] Filtering fusions with <2 supporting reads (remaining=12646)
[2026-06-08T08:22:38] Filtering fusions with an e-value >=0.3 (remaining=3059)
[2026-06-08T08:22:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3096)
[2026-06-08T08:22:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3012)
[2026-06-08T08:22:42] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3012)
[2026-06-08T08:22:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2991)
[2026-06-08T08:22:48] Searching for fusions with spliced split reads (remaining=3032)
[2026-06-08T08:22:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=2171)
[2026-06-08T08:22:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2146)
[2026-06-08T08:22:53] Searching for fusions with >=4 spliced events (remaining=2399)
[2026-06-08T08:22:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=981)
[2026-06-08T08:23:11] Filtering fusions with anchors <=23nt (remaining=808)
[2026-06-08T08:23:11] Filtering end-to-end fusions with low support (remaining=784)
[2026-06-08T08:23:12] Filtering fusions with no coverage around the breakpoints (remaining=762)
[2026-06-08T08:23:12] Indexing gene sequences 
[2026-06-08T08:23:16] Filtering genes with >=30% identity (remaining=257)
[2026-06-08T08:23:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=75)
[2026-06-08T08:23:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=71)
[2026-06-08T08:23:19] Searching for additional isoforms (remaining=77)
[2026-06-08T08:23:20] Assigning confidence scores to events 
[2026-06-08T08:23:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:23:23] Writing fusions to file 'BVT_FFPE_TRNA_utn_07_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:23:23] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_07_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:23:46] Freeing resources
[2026-06-08T08:24:04] Done (elapsed time=00:09:38, CPU time=00:09:37, peak memory=14.9gb)