[2026-06-08T08:17:23] Launching Arriba 2.4.0
[2026-06-08T08:17:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:38] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_04_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=8926242)
[2026-06-08T08:21:44] Marking multi-mapping alignments (marked=5828213)
[2026-06-08T08:21:48] Detecting strandedness (reverse)
[2026-06-08T08:21:48] Assigning strands to alignments 
[2026-06-08T08:21:49] Annotating alignments 
[2026-06-08T08:22:17] Filtering duplicates (remaining=2440793)
[2026-06-08T08:22:21] 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=2301900)
[2026-06-08T08:22:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2301900)
[2026-06-08T08:22:24] Filtering viral contigs with expression lower than the top 5 (remaining=2301900)
[2026-06-08T08:22:27] Filtering viral contigs with less than 5% coverage (remaining=2301900)
[2026-06-08T08:22:29] Estimating fragment length (mate gap mean=-84.7187, mate gap stddev=27.0086, read length mean=123.365)
[2026-06-08T08:22:29] Filtering read-through fragments with a distance <=10000bp (remaining=2198735)
[2026-06-08T08:22:31] Filtering inconsistently clipped mates (remaining=2160844)
[2026-06-08T08:22:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2084467)
[2026-06-08T08:22:34] Filtering fragments with small insert size (remaining=2083956)
[2026-06-08T08:22:36] Filtering alignments with long gaps (remaining=2083956)
[2026-06-08T08:22:37] Filtering fragments with both mates in the same gene (remaining=2083510)
[2026-06-08T08:22:39] Filtering fusions arising from hairpin structures (remaining=2016495)
[2026-06-08T08:22:41] Filtering reads with a mismatch p-value <=0.01 (remaining=852850)
[2026-06-08T08:22:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=237762)
[2026-06-08T08:22:51] Finding fusions and counting supporting reads (total=221453)
[2026-06-08T08:23:02] Merging adjacent fusion breakpoints (remaining=219927)
[2026-06-08T08:23:02] Filtering multi-mapping fusions by alignment score and read support (remaining=117419)
[2026-06-08T08:23:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:23:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=116904)
[2026-06-08T08:23:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=68930)
[2026-06-08T08:23:32] Filtering fusions with <2 supporting reads (remaining=5132)
[2026-06-08T08:23:33] Filtering fusions with an e-value >=0.3 (remaining=1221)
[2026-06-08T08:23:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1234)
[2026-06-08T08:23:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1198)
[2026-06-08T08:23:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1198)
[2026-06-08T08:23:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1166)
[2026-06-08T08:23:39] Searching for fusions with spliced split reads (remaining=1267)
[2026-06-08T08:23:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=952)
[2026-06-08T08:23:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=944)
[2026-06-08T08:23:44] Searching for fusions with >=4 spliced events (remaining=1014)
[2026-06-08T08:23:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=357)
[2026-06-08T08:23:55] Filtering fusions with anchors <=23nt (remaining=308)
[2026-06-08T08:23:55] Filtering end-to-end fusions with low support (remaining=303)
[2026-06-08T08:23:56] Filtering fusions with no coverage around the breakpoints (remaining=296)
[2026-06-08T08:23:56] Indexing gene sequences 
[2026-06-08T08:23:58] Filtering genes with >=30% identity (remaining=120)
[2026-06-08T08:23:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=44)
[2026-06-08T08:23:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=36)
[2026-06-08T08:23:59] Searching for additional isoforms (remaining=42)
[2026-06-08T08:24:00] Assigning confidence scores to events 
[2026-06-08T08:24:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:24:01] Writing fusions to file 'BVT_FFPE_TRNA_stm_04_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:24:02] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_04_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:24:13] Freeing resources
[2026-06-08T08:24:26] Done (elapsed time=00:07:03, CPU time=00:07:01, peak memory=12.9gb)