[2026-06-08T08:48:44] Launching Arriba 2.4.0
[2026-06-08T08:48:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:02] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_09_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=13438315)
[2026-06-08T08:56:40] Marking multi-mapping alignments (marked=8776803)
[2026-06-08T08:56:46] Detecting strandedness (reverse)
[2026-06-08T08:56:46] Assigning strands to alignments 
[2026-06-08T08:56:49] Annotating alignments 
[2026-06-08T08:57:36] Filtering duplicates (remaining=5433587)
[2026-06-08T08:57:44] 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=5186253)
[2026-06-08T08:57:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5186253)
[2026-06-08T08:57:50] Filtering viral contigs with expression lower than the top 5 (remaining=5186253)
[2026-06-08T08:57:56] Filtering viral contigs with less than 5% coverage (remaining=5186253)
[2026-06-08T08:57:59] Estimating fragment length (mate gap mean=-87.5052, mate gap stddev=27.2596, read length mean=126.109)
[2026-06-08T08:58:00] Filtering read-through fragments with a distance <=10000bp (remaining=4890582)
[2026-06-08T08:58:02] Filtering inconsistently clipped mates (remaining=4804096)
[2026-06-08T08:58:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4668559)
[2026-06-08T08:58:10] Filtering fragments with small insert size (remaining=4667150)
[2026-06-08T08:58:13] Filtering alignments with long gaps (remaining=4667150)
[2026-06-08T08:58:15] Filtering fragments with both mates in the same gene (remaining=4666404)
[2026-06-08T08:58:18] Filtering fusions arising from hairpin structures (remaining=4470547)
[2026-06-08T08:58:21] Filtering reads with a mismatch p-value <=0.01 (remaining=1978548)
[2026-06-08T08:58:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=665930)
[2026-06-08T08:58:45] Finding fusions and counting supporting reads (total=565255)
[2026-06-08T08:59:06] Merging adjacent fusion breakpoints (remaining=558668)
[2026-06-08T08:59:07] Filtering multi-mapping fusions by alignment score and read support (remaining=326724)
[2026-06-08T08:59:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=325700)
[2026-06-08T09:00:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=183526)
[2026-06-08T09:00:03] Filtering fusions with <2 supporting reads (remaining=19013)
[2026-06-08T09:00:03] Filtering fusions with an e-value >=0.3 (remaining=4097)
[2026-06-08T09:00:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4130)
[2026-06-08T09:00:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4044)
[2026-06-08T09:00:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4044)
[2026-06-08T09:00:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3977)
[2026-06-08T09:00:16] Searching for fusions with spliced split reads (remaining=4055)
[2026-06-08T09:00:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=2786)
[2026-06-08T09:00:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2780)
[2026-06-08T09:00:24] Searching for fusions with >=4 spliced events (remaining=3343)
[2026-06-08T09:00:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1419)
[2026-06-08T09:00:39] Filtering fusions with anchors <=23nt (remaining=1171)
[2026-06-08T09:00:39] Filtering end-to-end fusions with low support (remaining=1148)
[2026-06-08T09:00:40] Filtering fusions with no coverage around the breakpoints (remaining=1117)
[2026-06-08T09:00:41] Indexing gene sequences 
[2026-06-08T09:00:46] Filtering genes with >=30% identity (remaining=404)
[2026-06-08T09:00:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=188)
[2026-06-08T09:00:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=130)
[2026-06-08T09:00:52] Searching for additional isoforms (remaining=175)
[2026-06-08T09:00:53] Assigning confidence scores to events 
[2026-06-08T09:00:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:56] Writing fusions to file 'BVT_FFPE_TRNA_stm_09_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:00:58] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_09_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:27] Freeing resources
[2026-06-08T09:01:51] Done (elapsed time=00:13:07, CPU time=00:13:06, peak memory=17.8gb)