[2026-06-08T08:38:45] Launching Arriba 2.4.0
[2026-06-08T08:38:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:38:58] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_09_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=14075967)
[2026-06-08T08:45:55] Marking multi-mapping alignments (marked=9393781)
[2026-06-08T08:46:01] Detecting strandedness (reverse)
[2026-06-08T08:46:01] Assigning strands to alignments 
[2026-06-08T08:46:03] Annotating alignments 
[2026-06-08T08:46:50] Filtering duplicates (remaining=7111984)
[2026-06-08T08:46:59] 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=6691622)
[2026-06-08T08:47:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6691622)
[2026-06-08T08:47:05] Filtering viral contigs with expression lower than the top 5 (remaining=6691622)
[2026-06-08T08:47:11] Filtering viral contigs with less than 5% coverage (remaining=6691622)
[2026-06-08T08:47:14] Estimating fragment length (mate gap mean=-85.2521, mate gap stddev=27.2692, read length mean=123.165)
[2026-06-08T08:47:14] Filtering read-through fragments with a distance <=10000bp (remaining=6225812)
[2026-06-08T08:47:17] Filtering inconsistently clipped mates (remaining=6094032)
[2026-06-08T08:47:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5954724)
[2026-06-08T08:47:25] Filtering fragments with small insert size (remaining=5953254)
[2026-06-08T08:47:28] Filtering alignments with long gaps (remaining=5953253)
[2026-06-08T08:47:31] Filtering fragments with both mates in the same gene (remaining=5952258)
[2026-06-08T08:47:34] Filtering fusions arising from hairpin structures (remaining=5586346)
[2026-06-08T08:47:38] Filtering reads with a mismatch p-value <=0.01 (remaining=2615006)
[2026-06-08T08:47:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=1067871)
[2026-06-08T08:48:05] Finding fusions and counting supporting reads (total=855497)
[2026-06-08T08:48:26] Merging adjacent fusion breakpoints (remaining=841961)
[2026-06-08T08:48:28] Filtering multi-mapping fusions by alignment score and read support (remaining=487101)
[2026-06-08T08:49:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:49:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=485912)
[2026-06-08T08:49:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=278210)
[2026-06-08T08:49:23] Filtering fusions with <2 supporting reads (remaining=30265)
[2026-06-08T08:49:24] Filtering fusions with an e-value >=0.3 (remaining=6261)
[2026-06-08T08:49:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6321)
[2026-06-08T08:49:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6152)
[2026-06-08T08:49:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6152)
[2026-06-08T08:49:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6052)
[2026-06-08T08:49:38] Searching for fusions with spliced split reads (remaining=6147)
[2026-06-08T08:49:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=4041)
[2026-06-08T08:49:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4023)
[2026-06-08T08:49:47] Searching for fusions with >=4 spliced events (remaining=5005)
[2026-06-08T08:49:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2342)
[2026-06-08T08:50:03] Filtering fusions with anchors <=23nt (remaining=1929)
[2026-06-08T08:50:04] Filtering end-to-end fusions with low support (remaining=1884)
[2026-06-08T08:50:05] Filtering fusions with no coverage around the breakpoints (remaining=1861)
[2026-06-08T08:50:06] Indexing gene sequences 
[2026-06-08T08:50:12] Filtering genes with >=30% identity (remaining=645)
[2026-06-08T08:50:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=268)
[2026-06-08T08:50:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=194)
[2026-06-08T08:50:21] Searching for additional isoforms (remaining=260)
[2026-06-08T08:50:22] Assigning confidence scores to events 
[2026-06-08T08:50:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:50:26] Writing fusions to file 'BVT_FFPE_TRNA_stm_09_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:50:29] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_09_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:02] Freeing resources
[2026-06-08T08:51:24] Done (elapsed time=00:12:39, CPU time=00:12:38, peak memory=18.7gb)