[2026-06-08T08:35:38] Launching Arriba 2.4.0
[2026-06-08T08:35:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:51] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=12873956)
[2026-06-08T08:42:17] Marking multi-mapping alignments (marked=8295375)
[2026-06-08T08:42:23] Detecting strandedness (reverse)
[2026-06-08T08:42:23] Assigning strands to alignments 
[2026-06-08T08:42:25] Annotating alignments 
[2026-06-08T08:43:09] Filtering duplicates (remaining=5925950)
[2026-06-08T08:43:16] 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=5627422)
[2026-06-08T08:43:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5627422)
[2026-06-08T08:43:21] Filtering viral contigs with expression lower than the top 5 (remaining=5627422)
[2026-06-08T08:43:27] Filtering viral contigs with less than 5% coverage (remaining=5627422)
[2026-06-08T08:43:30] Estimating fragment length (mate gap mean=-83.7418, mate gap stddev=26.8062, read length mean=120.862)
[2026-06-08T08:43:30] Filtering read-through fragments with a distance <=10000bp (remaining=5210909)
[2026-06-08T08:43:32] Filtering inconsistently clipped mates (remaining=5107502)
[2026-06-08T08:43:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4975166)
[2026-06-08T08:43:39] Filtering fragments with small insert size (remaining=4974028)
[2026-06-08T08:43:42] Filtering alignments with long gaps (remaining=4974028)
[2026-06-08T08:43:44] Filtering fragments with both mates in the same gene (remaining=4973075)
[2026-06-08T08:43:47] Filtering fusions arising from hairpin structures (remaining=4709087)
[2026-06-08T08:43:50] Filtering reads with a mismatch p-value <=0.01 (remaining=2131280)
[2026-06-08T08:44:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=862317)
[2026-06-08T08:44:13] Finding fusions and counting supporting reads (total=731830)
[2026-06-08T08:44:32] Merging adjacent fusion breakpoints (remaining=721430)
[2026-06-08T08:44:34] Filtering multi-mapping fusions by alignment score and read support (remaining=409321)
[2026-06-08T08:45:14] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=408084)
[2026-06-08T08:45:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=246676)
[2026-06-08T08:45:23] Filtering fusions with <2 supporting reads (remaining=22667)
[2026-06-08T08:45:23] Filtering fusions with an e-value >=0.3 (remaining=4618)
[2026-06-08T08:45:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4675)
[2026-06-08T08:45:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4563)
[2026-06-08T08:45:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4563)
[2026-06-08T08:45:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4503)
[2026-06-08T08:45:36] Searching for fusions with spliced split reads (remaining=4581)
[2026-06-08T08:45:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=2929)
[2026-06-08T08:45:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2913)
[2026-06-08T08:45:44] Searching for fusions with >=4 spliced events (remaining=3607)
[2026-06-08T08:45:45] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1838)
[2026-06-08T08:45:58] Filtering fusions with anchors <=23nt (remaining=1610)
[2026-06-08T08:45:59] Filtering end-to-end fusions with low support (remaining=1573)
[2026-06-08T08:46:00] Filtering fusions with no coverage around the breakpoints (remaining=1542)
[2026-06-08T08:46:00] Indexing gene sequences 
[2026-06-08T08:46:05] Filtering genes with >=30% identity (remaining=455)
[2026-06-08T08:46:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=136)
[2026-06-08T08:46:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=125)
[2026-06-08T08:46:11] Searching for additional isoforms (remaining=146)
[2026-06-08T08:46:12] Assigning confidence scores to events 
[2026-06-08T08:46:15] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:16] Writing fusions to file 'BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:46:17] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:47] Freeing resources
[2026-06-08T08:47:08] Done (elapsed time=00:11:30, CPU time=00:11:28, peak memory=17.3gb)