[2026-06-08T07:42:40] Launching Arriba 2.4.0
[2026-06-08T07:42:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:42:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:42:55] Reading chimeric alignments from 'dna_s771.Aligned.sortedByCoord.out.bam' (total=3634615)
[2026-06-08T07:46:18] Marking multi-mapping alignments (marked=1972266)
[2026-06-08T07:46:20] Detecting strandedness (no)
[2026-06-08T07:46:21] Annotating alignments 
[2026-06-08T07:46:42] Filtering duplicates (remaining=2881869)
[2026-06-08T07:46:46] 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=2821813)
[2026-06-08T07:46:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2821813)
[2026-06-08T07:46:48] Filtering viral contigs with expression lower than the top 5 (remaining=2821813)
[2026-06-08T07:46:50] Filtering viral contigs with less than 5% coverage (remaining=2821813)
[2026-06-08T07:46:51] Estimating fragment length (mate gap mean=-44.5147, mate gap stddev=69.5149, read length mean=147.692)
[2026-06-08T07:46:51] Filtering read-through fragments with a distance <=10000bp (remaining=2388337)
[2026-06-08T07:46:52] Filtering inconsistently clipped mates (remaining=2362209)
[2026-06-08T07:46:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2121800)
[2026-06-08T07:46:56] Filtering fragments with small insert size (remaining=2121475)
[2026-06-08T07:46:56] Filtering alignments with long gaps (remaining=2121475)
[2026-06-08T07:46:57] Filtering fragments with both mates in the same gene (remaining=2119438)
[2026-06-08T07:46:58] Filtering fusions arising from hairpin structures (remaining=1958485)
[2026-06-08T07:47:00] Filtering reads with a mismatch p-value <=0.01 (remaining=1330425)
[2026-06-08T07:47:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=809042)
[2026-06-08T07:47:14] Finding fusions and counting supporting reads (total=786424)
[2026-06-08T07:47:24] Merging adjacent fusion breakpoints (remaining=782141)
[2026-06-08T07:47:26] Filtering multi-mapping fusions by alignment score and read support (remaining=454625)
[2026-06-08T07:47:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:47:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=447809)
[2026-06-08T07:47:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=446262)
[2026-06-08T07:47:50] Filtering fusions with <2 supporting reads (remaining=31327)
[2026-06-08T07:47:51] Filtering fusions with an e-value >=0.3 (remaining=23814)
[2026-06-08T07:47:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=23922)
[2026-06-08T07:47:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=22042)
[2026-06-08T07:47:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=22043)
[2026-06-08T07:47:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9673)
[2026-06-08T07:47:58] Searching for fusions with spliced split reads (remaining=9673)
[2026-06-08T07:48:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=1560)
[2026-06-08T07:48:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1543)
[2026-06-08T07:48:06] Searching for fusions with >=4 spliced events (remaining=1543)
[2026-06-08T07:48:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1077)
[2026-06-08T07:48:25] Filtering fusions with anchors <=23nt (remaining=948)
[2026-06-08T07:48:26] Filtering end-to-end fusions with low support (remaining=842)
[2026-06-08T07:48:26] Filtering fusions with no coverage around the breakpoints (remaining=733)
[2026-06-08T07:48:27] Indexing gene sequences 
[2026-06-08T07:48:39] Filtering genes with >=30% identity (remaining=347)
[2026-06-08T07:48:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=70)
[2026-06-08T07:48:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=70)
[2026-06-08T07:48:44] Searching for additional isoforms (remaining=70)
[2026-06-08T07:48:45] Assigning confidence scores to events 
[2026-06-08T07:48:49] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:48:49] Writing fusions to file 'dna_s771.arriba.fusions.tsv' 
[2026-06-08T07:48:50] Writing discarded fusions to file 'dna_s771.arriba.fusions.discarded.tsv'
[2026-06-08T07:49:11] Freeing resources
[2026-06-08T07:49:27] Done (elapsed time=00:06:47, CPU time=00:06:46, peak memory=8.17gb)