[2026-06-08T08:43:46] Launching Arriba 2.4.0
[2026-06-08T08:43:46] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:58] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=11976626)
[2026-06-08T08:51:13] Marking multi-mapping alignments (marked=7483574)
[2026-06-08T08:51:18] Detecting strandedness (reverse)
[2026-06-08T08:51:18] Assigning strands to alignments 
[2026-06-08T08:51:21] Annotating alignments 
[2026-06-08T08:52:05] Filtering duplicates (remaining=7346350)
[2026-06-08T08:52:14] 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=7057784)
[2026-06-08T08:52:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7057784)
[2026-06-08T08:52:20] Filtering viral contigs with expression lower than the top 5 (remaining=7057784)
[2026-06-08T08:52:26] Filtering viral contigs with less than 5% coverage (remaining=7057784)
[2026-06-08T08:52:30] Estimating fragment length (mate gap mean=-88.7577, mate gap stddev=27.1499, read length mean=130.126)
[2026-06-08T08:52:30] Filtering read-through fragments with a distance <=10000bp (remaining=6568731)
[2026-06-08T08:52:33] Filtering inconsistently clipped mates (remaining=6425871)
[2026-06-08T08:52:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6262216)
[2026-06-08T08:52:42] Filtering fragments with small insert size (remaining=6260941)
[2026-06-08T08:52:45] Filtering alignments with long gaps (remaining=6260941)
[2026-06-08T08:52:48] Filtering fragments with both mates in the same gene (remaining=6260014)
[2026-06-08T08:52:51] Filtering fusions arising from hairpin structures (remaining=5834263)
[2026-06-08T08:52:55] Filtering reads with a mismatch p-value <=0.01 (remaining=2816530)
[2026-06-08T08:53:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=1142512)
[2026-06-08T08:53:25] Finding fusions and counting supporting reads (total=915966)
[2026-06-08T08:53:48] Merging adjacent fusion breakpoints (remaining=905136)
[2026-06-08T08:53:50] Filtering multi-mapping fusions by alignment score and read support (remaining=552526)
[2026-06-08T08:54:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:44] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=551078)
[2026-06-08T08:54:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=325041)
[2026-06-08T08:54:46] Filtering fusions with <2 supporting reads (remaining=32260)
[2026-06-08T08:54:47] Filtering fusions with an e-value >=0.3 (remaining=6922)
[2026-06-08T08:54:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6997)
[2026-06-08T08:54:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6880)
[2026-06-08T08:54:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6880)
[2026-06-08T08:54:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6543)
[2026-06-08T08:55:02] Searching for fusions with spliced split reads (remaining=6689)
[2026-06-08T08:55:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=4352)
[2026-06-08T08:55:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4311)
[2026-06-08T08:55:12] Searching for fusions with >=4 spliced events (remaining=5494)
[2026-06-08T08:55:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2721)
[2026-06-08T08:55:30] Filtering fusions with anchors <=23nt (remaining=2287)
[2026-06-08T08:55:30] Filtering end-to-end fusions with low support (remaining=2230)
[2026-06-08T08:55:31] Filtering fusions with no coverage around the breakpoints (remaining=2182)
[2026-06-08T08:55:32] Indexing gene sequences 
[2026-06-08T08:55:40] Filtering genes with >=30% identity (remaining=590)
[2026-06-08T08:55:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=246)
[2026-06-08T08:55:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=199)
[2026-06-08T08:55:53] Searching for additional isoforms (remaining=253)
[2026-06-08T08:55:54] Assigning confidence scores to events 
[2026-06-08T08:55:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:59] Writing fusions to file 'BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:56:02] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_02_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:45] Freeing resources
[2026-06-08T08:57:10] Done (elapsed time=00:13:24, CPU time=00:13:23, peak memory=16.6gb)