[2026-06-08T08:04:30] Launching Arriba 2.4.0
[2026-06-08T08:04:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:04:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:04:48] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s28.Aligned.sortedByCoord.out.bam' (total=10959263)
[2026-06-08T08:11:37] Marking multi-mapping alignments (marked=8090652)
[2026-06-08T08:11:42] Detecting strandedness (reverse)
[2026-06-08T08:11:42] Assigning strands to alignments 
[2026-06-08T08:11:44] Annotating alignments 
[2026-06-08T08:12:23] Filtering duplicates (remaining=4958254)
[2026-06-08T08:12:29] 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=4273935)
[2026-06-08T08:12:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4273935)
[2026-06-08T08:12:34] Filtering viral contigs with expression lower than the top 5 (remaining=4273935)
[2026-06-08T08:12:39] Filtering viral contigs with less than 5% coverage (remaining=4273935)
[2026-06-08T08:12:41] Estimating fragment length (mate gap mean=-82.8555, mate gap stddev=31.4504, read length mean=125.682)
[2026-06-08T08:12:41] Filtering read-through fragments with a distance <=10000bp (remaining=4100049)
[2026-06-08T08:12:44] Filtering inconsistently clipped mates (remaining=4021064)
[2026-06-08T08:12:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3544610)
[2026-06-08T08:12:51] Filtering fragments with small insert size (remaining=3543600)
[2026-06-08T08:12:53] Filtering alignments with long gaps (remaining=3543599)
[2026-06-08T08:12:55] Filtering fragments with both mates in the same gene (remaining=3541927)
[2026-06-08T08:12:57] Filtering fusions arising from hairpin structures (remaining=3309881)
[2026-06-08T08:13:00] Filtering reads with a mismatch p-value <=0.01 (remaining=1256405)
[2026-06-08T08:13:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=645366)
[2026-06-08T08:13:18] Finding fusions and counting supporting reads (total=571903)
[2026-06-08T08:13:34] Merging adjacent fusion breakpoints (remaining=568146)
[2026-06-08T08:13:35] Filtering multi-mapping fusions by alignment score and read support (remaining=277113)
[2026-06-08T08:14:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:14:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=274589)
[2026-06-08T08:14:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=188607)
[2026-06-08T08:14:16] Filtering fusions with <2 supporting reads (remaining=13696)
[2026-06-08T08:14:16] Filtering fusions with an e-value >=0.3 (remaining=3358)
[2026-06-08T08:14:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3384)
[2026-06-08T08:14:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3088)
[2026-06-08T08:14:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3090)
[2026-06-08T08:14:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2769)
[2026-06-08T08:14:27] Searching for fusions with spliced split reads (remaining=2836)
[2026-06-08T08:14:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=1902)
[2026-06-08T08:14:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1873)
[2026-06-08T08:14:33] Searching for fusions with >=4 spliced events (remaining=2149)
[2026-06-08T08:14:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=703)
[2026-06-08T08:14:52] Filtering fusions with anchors <=23nt (remaining=535)
[2026-06-08T08:14:52] Filtering end-to-end fusions with low support (remaining=512)
[2026-06-08T08:14:53] Filtering fusions with no coverage around the breakpoints (remaining=499)
[2026-06-08T08:14:53] Indexing gene sequences 
[2026-06-08T08:14:56] Filtering genes with >=30% identity (remaining=156)
[2026-06-08T08:14:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=48)
[2026-06-08T08:14:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=46)
[2026-06-08T08:15:00] Searching for additional isoforms (remaining=67)
[2026-06-08T08:15:01] Assigning confidence scores to events 
[2026-06-08T08:15:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:15:04] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s28.arriba.fusions.tsv' 
[2026-06-08T08:15:05] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s28.arriba.fusions.discarded.tsv'
[2026-06-08T08:15:30] Freeing resources
[2026-06-08T08:15:48] Done (elapsed time=00:11:18, CPU time=00:11:17, peak memory=16gb)