[2026-06-08T08:43:38] Launching Arriba 2.4.0
[2026-06-08T08:43:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:54] Reading chimeric alignments from 'BVT_FFPE_TRNA_kid_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=11992036)
[2026-06-08T08:50:05] Marking multi-mapping alignments (marked=8093630)
[2026-06-08T08:50:10] Detecting strandedness (reverse)
[2026-06-08T08:50:10] Assigning strands to alignments 
[2026-06-08T08:50:12] Annotating alignments 
[2026-06-08T08:50:46] Filtering duplicates (remaining=4181039)
[2026-06-08T08:50:51] 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=3833607)
[2026-06-08T08:50:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3833607)
[2026-06-08T08:50:55] Filtering viral contigs with expression lower than the top 5 (remaining=3833607)
[2026-06-08T08:51:00] Filtering viral contigs with less than 5% coverage (remaining=3833607)
[2026-06-08T08:51:02] Estimating fragment length (mate gap mean=-82.5111, mate gap stddev=27.0659, read length mean=117.115)
[2026-06-08T08:51:02] Filtering read-through fragments with a distance <=10000bp (remaining=3670880)
[2026-06-08T08:51:04] Filtering inconsistently clipped mates (remaining=3609361)
[2026-06-08T08:51:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3504461)
[2026-06-08T08:51:09] Filtering fragments with small insert size (remaining=3503592)
[2026-06-08T08:51:12] Filtering alignments with long gaps (remaining=3503592)
[2026-06-08T08:51:14] Filtering fragments with both mates in the same gene (remaining=3502613)
[2026-06-08T08:51:16] Filtering fusions arising from hairpin structures (remaining=3373434)
[2026-06-08T08:51:18] Filtering reads with a mismatch p-value <=0.01 (remaining=1376523)
[2026-06-08T08:51:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=405568)
[2026-06-08T08:51:33] Finding fusions and counting supporting reads (total=343046)
[2026-06-08T08:51:47] Merging adjacent fusion breakpoints (remaining=340005)
[2026-06-08T08:51:48] Filtering multi-mapping fusions by alignment score and read support (remaining=196055)
[2026-06-08T08:52:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=195312)
[2026-06-08T08:52:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=124282)
[2026-06-08T08:52:24] Filtering fusions with <2 supporting reads (remaining=10709)
[2026-06-08T08:52:24] Filtering fusions with an e-value >=0.3 (remaining=2425)
[2026-06-08T08:52:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2455)
[2026-06-08T08:52:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2414)
[2026-06-08T08:52:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2414)
[2026-06-08T08:52:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2402)
[2026-06-08T08:52:33] Searching for fusions with spliced split reads (remaining=2435)
[2026-06-08T08:52:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=1797)
[2026-06-08T08:52:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1779)
[2026-06-08T08:52:39] Searching for fusions with >=4 spliced events (remaining=2009)
[2026-06-08T08:52:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=842)
[2026-06-08T08:52:52] Filtering fusions with anchors <=23nt (remaining=657)
[2026-06-08T08:52:52] Filtering end-to-end fusions with low support (remaining=640)
[2026-06-08T08:52:53] Filtering fusions with no coverage around the breakpoints (remaining=624)
[2026-06-08T08:52:53] Indexing gene sequences 
[2026-06-08T08:52:56] Filtering genes with >=30% identity (remaining=225)
[2026-06-08T08:52:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=90)
[2026-06-08T08:52:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=86)
[2026-06-08T08:53:00] Searching for additional isoforms (remaining=98)
[2026-06-08T08:53:01] Assigning confidence scores to events 
[2026-06-08T08:53:03] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:03] Writing fusions to file 'BVT_FFPE_TRNA_kid_01_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:04] Writing discarded fusions to file 'BVT_FFPE_TRNA_kid_01_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:53:21] Freeing resources
[2026-06-08T08:53:38] Done (elapsed time=00:10:00, CPU time=00:09:59, peak memory=16.1gb)