[2026-06-08T08:57:40] Launching Arriba 2.4.0
[2026-06-08T08:57:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:57:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:57:53] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_05_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=12340788)
[2026-06-08T09:05:28] Marking multi-mapping alignments (marked=7672070)
[2026-06-08T09:05:34] Detecting strandedness (reverse)
[2026-06-08T09:05:34] Assigning strands to alignments 
[2026-06-08T09:05:36] Annotating alignments 
[2026-06-08T09:06:20] Filtering duplicates (remaining=3848223)
[2026-06-08T09:06:27] 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=3702687)
[2026-06-08T09:06:29] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3702687)
[2026-06-08T09:06:32] Filtering viral contigs with expression lower than the top 5 (remaining=3702687)
[2026-06-08T09:06:37] Filtering viral contigs with less than 5% coverage (remaining=3702687)
[2026-06-08T09:06:40] Estimating fragment length (mate gap mean=-89.083, mate gap stddev=26.855, read length mean=129.524)
[2026-06-08T09:06:40] Filtering read-through fragments with a distance <=10000bp (remaining=3492554)
[2026-06-08T09:06:43] Filtering inconsistently clipped mates (remaining=3430723)
[2026-06-08T09:06:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3327669)
[2026-06-08T09:06:50] Filtering fragments with small insert size (remaining=3326946)
[2026-06-08T09:06:53] Filtering alignments with long gaps (remaining=3326946)
[2026-06-08T09:06:55] Filtering fragments with both mates in the same gene (remaining=3326366)
[2026-06-08T09:06:58] Filtering fusions arising from hairpin structures (remaining=3191127)
[2026-06-08T09:07:01] Filtering reads with a mismatch p-value <=0.01 (remaining=1402759)
[2026-06-08T09:07:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=436159)
[2026-06-08T09:07:20] Finding fusions and counting supporting reads (total=380861)
[2026-06-08T09:07:38] Merging adjacent fusion breakpoints (remaining=377634)
[2026-06-08T09:07:39] Filtering multi-mapping fusions by alignment score and read support (remaining=227112)
[2026-06-08T09:08:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:08:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=226257)
[2026-06-08T09:08:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=124543)
[2026-06-08T09:08:28] Filtering fusions with <2 supporting reads (remaining=11915)
[2026-06-08T09:08:28] Filtering fusions with an e-value >=0.3 (remaining=2449)
[2026-06-08T09:08:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2480)
[2026-06-08T09:08:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2441)
[2026-06-08T09:08:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2441)
[2026-06-08T09:08:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2401)
[2026-06-08T09:08:39] Searching for fusions with spliced split reads (remaining=2460)
[2026-06-08T09:08:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=1819)
[2026-06-08T09:08:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1809)
[2026-06-08T09:08:46] Searching for fusions with >=4 spliced events (remaining=2084)
[2026-06-08T09:08:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=859)
[2026-06-08T09:08:59] Filtering fusions with anchors <=23nt (remaining=748)
[2026-06-08T09:08:59] Filtering end-to-end fusions with low support (remaining=734)
[2026-06-08T09:09:00] Filtering fusions with no coverage around the breakpoints (remaining=717)
[2026-06-08T09:09:00] Indexing gene sequences 
[2026-06-08T09:09:04] Filtering genes with >=30% identity (remaining=295)
[2026-06-08T09:09:06] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=151)
[2026-06-08T09:09:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=126)
[2026-06-08T09:09:09] Searching for additional isoforms (remaining=147)
[2026-06-08T09:09:10] Assigning confidence scores to events 
[2026-06-08T09:09:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:09:12] Writing fusions to file 'BVT_FFPE_TRNA_stm_05_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T09:09:13] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_05_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T09:09:34] Freeing resources
[2026-06-08T09:09:55] Done (elapsed time=00:12:15, CPU time=00:12:13, peak memory=16.5gb)