[2026-06-08T07:40:37] Launching Arriba 2.4.0
[2026-06-08T07:40:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:40:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:41:00] Reading chimeric alignments from 'dna_s762.Aligned.sortedByCoord.out.bam' (total=3903404)
[2026-06-08T07:45:43] Marking multi-mapping alignments (marked=2125235)
[2026-06-08T07:45:45] Detecting strandedness (no)
[2026-06-08T07:45:45] Annotating alignments 
[2026-06-08T07:46:03] Filtering duplicates (remaining=3151223)
[2026-06-08T07:46:07] 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=3059436)
[2026-06-08T07:46:08] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3059436)
[2026-06-08T07:46:09] Filtering viral contigs with expression lower than the top 5 (remaining=3059436)
[2026-06-08T07:46:11] Filtering viral contigs with less than 5% coverage (remaining=3059436)
[2026-06-08T07:46:12] Estimating fragment length (mate gap mean=-31.5896, mate gap stddev=83.2087, read length mean=148.234)
[2026-06-08T07:46:12] Filtering read-through fragments with a distance <=10000bp (remaining=2587230)
[2026-06-08T07:46:13] Filtering inconsistently clipped mates (remaining=2564141)
[2026-06-08T07:46:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2332433)
[2026-06-08T07:46:15] Filtering fragments with small insert size (remaining=2332085)
[2026-06-08T07:46:16] Filtering alignments with long gaps (remaining=2332085)
[2026-06-08T07:46:17] Filtering fragments with both mates in the same gene (remaining=2330322)
[2026-06-08T07:46:18] Filtering fusions arising from hairpin structures (remaining=2174421)
[2026-06-08T07:46:19] Filtering reads with a mismatch p-value <=0.01 (remaining=1503506)
[2026-06-08T07:46:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=819515)
[2026-06-08T07:46:34] Finding fusions and counting supporting reads (total=800409)
[2026-06-08T07:46:44] Merging adjacent fusion breakpoints (remaining=796441)
[2026-06-08T07:46:45] Filtering multi-mapping fusions by alignment score and read support (remaining=464096)
[2026-06-08T07:47:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:47:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=456155)
[2026-06-08T07:47:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=453864)
[2026-06-08T07:47:07] Filtering fusions with <2 supporting reads (remaining=32248)
[2026-06-08T07:47:07] Filtering fusions with an e-value >=0.3 (remaining=24865)
[2026-06-08T07:47:08] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=24959)
[2026-06-08T07:47:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=22644)
[2026-06-08T07:47:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=22644)
[2026-06-08T07:47:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10431)
[2026-06-08T07:47:13] Searching for fusions with spliced split reads (remaining=10431)
[2026-06-08T07:47:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=1436)
[2026-06-08T07:47:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1417)
[2026-06-08T07:47:18] Searching for fusions with >=4 spliced events (remaining=1417)
[2026-06-08T07:47:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=971)
[2026-06-08T07:47:42] Filtering fusions with anchors <=23nt (remaining=869)
[2026-06-08T07:47:42] Filtering end-to-end fusions with low support (remaining=773)
[2026-06-08T07:47:42] Filtering fusions with no coverage around the breakpoints (remaining=647)
[2026-06-08T07:47:43] Indexing gene sequences 
[2026-06-08T07:47:53] Filtering genes with >=30% identity (remaining=293)
[2026-06-08T07:47:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=65)
[2026-06-08T07:47:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=65)
[2026-06-08T07:47:57] Searching for additional isoforms (remaining=65)
[2026-06-08T07:47:58] Assigning confidence scores to events 
[2026-06-08T07:48:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:48:01] Writing fusions to file 'dna_s762.arriba.fusions.tsv' 
[2026-06-08T07:48:01] Writing discarded fusions to file 'dna_s762.arriba.fusions.discarded.tsv'
[2026-06-08T07:48:25] Freeing resources
[2026-06-08T07:48:37] Done (elapsed time=00:08:00, CPU time=00:07:58, peak memory=8.45gb)