[2026-06-08T08:53:43] Launching Arriba 2.4.0
[2026-06-08T08:53:43] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:52] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:56] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=12187186)
[2026-06-08T09:00:45] Marking multi-mapping alignments (marked=7825461)
[2026-06-08T09:00:50] Detecting strandedness (reverse)
[2026-06-08T09:00:50] Assigning strands to alignments 
[2026-06-08T09:00:53] Annotating alignments 
[2026-06-08T09:01:36] Filtering duplicates (remaining=6922734)
[2026-06-08T09:01:45] 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=6600637)
[2026-06-08T09:01:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6600637)
[2026-06-08T09:01:51] Filtering viral contigs with expression lower than the top 5 (remaining=6600637)
[2026-06-08T09:01:57] Filtering viral contigs with less than 5% coverage (remaining=6600637)
[2026-06-08T09:02:00] Estimating fragment length (mate gap mean=-88.0445, mate gap stddev=28.0465, read length mean=130.54)
[2026-06-08T09:02:00] Filtering read-through fragments with a distance <=10000bp (remaining=6154664)
[2026-06-08T09:02:03] Filtering inconsistently clipped mates (remaining=6021072)
[2026-06-08T09:02:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5850321)
[2026-06-08T09:02:11] Filtering fragments with small insert size (remaining=5849385)
[2026-06-08T09:02:14] Filtering alignments with long gaps (remaining=5849385)
[2026-06-08T09:02:17] Filtering fragments with both mates in the same gene (remaining=5848461)
[2026-06-08T09:02:20] Filtering fusions arising from hairpin structures (remaining=5470171)
[2026-06-08T09:02:23] Filtering reads with a mismatch p-value <=0.01 (remaining=2712796)
[2026-06-08T09:02:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=1110594)
[2026-06-08T09:02:54] Finding fusions and counting supporting reads (total=873982)
[2026-06-08T09:03:16] Merging adjacent fusion breakpoints (remaining=861979)
[2026-06-08T09:03:18] Filtering multi-mapping fusions by alignment score and read support (remaining=511114)
[2026-06-08T09:04:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=508885)
[2026-06-08T09:04:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=294030)
[2026-06-08T09:04:12] Filtering fusions with <2 supporting reads (remaining=32640)
[2026-06-08T09:04:13] Filtering fusions with an e-value >=0.3 (remaining=7836)
[2026-06-08T09:04:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7912)
[2026-06-08T09:04:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7777)
[2026-06-08T09:04:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7777)
[2026-06-08T09:04:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6853)
[2026-06-08T09:04:27] Searching for fusions with spliced split reads (remaining=6865)
[2026-06-08T09:04:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=4579)
[2026-06-08T09:04:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4498)
[2026-06-08T09:04:36] Searching for fusions with >=4 spliced events (remaining=5669)
[2026-06-08T09:04:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2419)
[2026-06-08T09:04:53] Filtering fusions with anchors <=23nt (remaining=2044)
[2026-06-08T09:04:54] Filtering end-to-end fusions with low support (remaining=1997)
[2026-06-08T09:04:55] Filtering fusions with no coverage around the breakpoints (remaining=1957)
[2026-06-08T09:04:56] Indexing gene sequences 
[2026-06-08T09:05:03] Filtering genes with >=30% identity (remaining=652)
[2026-06-08T09:05:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=374)
[2026-06-08T09:05:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=276)
[2026-06-08T09:05:20] Searching for additional isoforms (remaining=378)
[2026-06-08T09:05:22] Assigning confidence scores to events 
[2026-06-08T09:05:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:26] Writing fusions to file 'BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:29] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_05_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:06] Freeing resources
[2026-06-08T09:06:27] Done (elapsed time=00:12:44, CPU time=00:12:43, peak memory=16.8gb)