[2026-06-08T08:13:37] Launching Arriba 2.4.0
[2026-06-08T08:13:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:13:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:13:50] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s29.Aligned.sortedByCoord.out.bam' (total=12094096)
[2026-06-08T08:20:32] Marking multi-mapping alignments (marked=8654903)
[2026-06-08T08:20:36] Detecting strandedness (reverse)
[2026-06-08T08:20:36] Assigning strands to alignments 
[2026-06-08T08:20:39] Annotating alignments 
[2026-06-08T08:21:22] Filtering duplicates (remaining=5370116)
[2026-06-08T08:21:28] 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=4713244)
[2026-06-08T08:21:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4713244)
[2026-06-08T08:21:33] Filtering viral contigs with expression lower than the top 5 (remaining=4713244)
[2026-06-08T08:21:38] Filtering viral contigs with less than 5% coverage (remaining=4713244)
[2026-06-08T08:21:41] Estimating fragment length (mate gap mean=-83.1206, mate gap stddev=30.6778, read length mean=125.726)
[2026-06-08T08:21:41] Filtering read-through fragments with a distance <=10000bp (remaining=4532550)
[2026-06-08T08:21:43] Filtering inconsistently clipped mates (remaining=4443898)
[2026-06-08T08:21:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3833832)
[2026-06-08T08:21:50] Filtering fragments with small insert size (remaining=3832800)
[2026-06-08T08:21:52] Filtering alignments with long gaps (remaining=3832800)
[2026-06-08T08:21:54] Filtering fragments with both mates in the same gene (remaining=3830951)
[2026-06-08T08:21:56] Filtering fusions arising from hairpin structures (remaining=3579371)
[2026-06-08T08:21:59] Filtering reads with a mismatch p-value <=0.01 (remaining=1358559)
[2026-06-08T08:22:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=707330)
[2026-06-08T08:22:17] Finding fusions and counting supporting reads (total=638044)
[2026-06-08T08:22:34] Merging adjacent fusion breakpoints (remaining=633935)
[2026-06-08T08:22:35] Filtering multi-mapping fusions by alignment score and read support (remaining=301651)
[2026-06-08T08:23:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:23:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=299033)
[2026-06-08T08:23:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=215306)
[2026-06-08T08:23:20] Filtering fusions with <2 supporting reads (remaining=13942)
[2026-06-08T08:23:21] Filtering fusions with an e-value >=0.3 (remaining=3184)
[2026-06-08T08:23:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3204)
[2026-06-08T08:23:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2770)
[2026-06-08T08:23:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2771)
[2026-06-08T08:23:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2591)
[2026-06-08T08:23:33] Searching for fusions with spliced split reads (remaining=2638)
[2026-06-08T08:23:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=1891)
[2026-06-08T08:23:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1861)
[2026-06-08T08:23:41] Searching for fusions with >=4 spliced events (remaining=2093)
[2026-06-08T08:23:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=636)
[2026-06-08T08:23:55] Filtering fusions with anchors <=23nt (remaining=476)
[2026-06-08T08:23:55] Filtering end-to-end fusions with low support (remaining=463)
[2026-06-08T08:23:56] Filtering fusions with no coverage around the breakpoints (remaining=458)
[2026-06-08T08:23:57] Indexing gene sequences 
[2026-06-08T08:24:00] Filtering genes with >=30% identity (remaining=149)
[2026-06-08T08:24:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=58)
[2026-06-08T08:24:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=54)
[2026-06-08T08:24:04] Searching for additional isoforms (remaining=66)
[2026-06-08T08:24:05] Assigning confidence scores to events 
[2026-06-08T08:24:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:24:08] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s29.arriba.fusions.tsv' 
[2026-06-08T08:24:09] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s29.arriba.fusions.discarded.tsv'
[2026-06-08T08:24:35] Freeing resources
[2026-06-08T08:24:54] Done (elapsed time=00:11:17, CPU time=00:11:16, peak memory=17.1gb)