[2026-06-08T08:15:35] Launching Arriba 2.4.0
[2026-06-08T08:15:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:49] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s37.Aligned.sortedByCoord.out.bam' (total=11937807)
[2026-06-08T08:22:56] Marking multi-mapping alignments (marked=8664891)
[2026-06-08T08:23:02] Detecting strandedness (reverse)
[2026-06-08T08:23:02] Assigning strands to alignments 
[2026-06-08T08:23:05] Annotating alignments 
[2026-06-08T08:24:02] Filtering duplicates (remaining=5054331)
[2026-06-08T08:24:12] 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=4435388)
[2026-06-08T08:24:15] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4435388)
[2026-06-08T08:24:18] Filtering viral contigs with expression lower than the top 5 (remaining=4435388)
[2026-06-08T08:24:24] Filtering viral contigs with less than 5% coverage (remaining=4435388)
[2026-06-08T08:24:27] Estimating fragment length (mate gap mean=-82.8291, mate gap stddev=30.1895, read length mean=124.848)
[2026-06-08T08:24:27] Filtering read-through fragments with a distance <=10000bp (remaining=4265525)
[2026-06-08T08:24:30] Filtering inconsistently clipped mates (remaining=4182614)
[2026-06-08T08:24:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3613104)
[2026-06-08T08:24:38] Filtering fragments with small insert size (remaining=3612141)
[2026-06-08T08:24:41] Filtering alignments with long gaps (remaining=3612141)
[2026-06-08T08:24:44] Filtering fragments with both mates in the same gene (remaining=3610167)
[2026-06-08T08:24:47] Filtering fusions arising from hairpin structures (remaining=3396651)
[2026-06-08T08:24:50] Filtering reads with a mismatch p-value <=0.01 (remaining=1316062)
[2026-06-08T08:25:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=665540)
[2026-06-08T08:25:23] Finding fusions and counting supporting reads (total=604874)
[2026-06-08T08:25:49] Merging adjacent fusion breakpoints (remaining=601555)
[2026-06-08T08:25:51] Filtering multi-mapping fusions by alignment score and read support (remaining=286732)
[2026-06-08T08:26:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:26:54] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=284311)
[2026-06-08T08:26:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=207957)
[2026-06-08T08:26:57] Filtering fusions with <2 supporting reads (remaining=12552)
[2026-06-08T08:26:58] Filtering fusions with an e-value >=0.3 (remaining=2847)
[2026-06-08T08:26:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2867)
[2026-06-08T08:27:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2497)
[2026-06-08T08:27:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2497)
[2026-06-08T08:27:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2348)
[2026-06-08T08:27:15] Searching for fusions with spliced split reads (remaining=2384)
[2026-06-08T08:27:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=1743)
[2026-06-08T08:27:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1712)
[2026-06-08T08:27:27] Searching for fusions with >=4 spliced events (remaining=1954)
[2026-06-08T08:27:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=639)
[2026-06-08T08:27:47] Filtering fusions with anchors <=23nt (remaining=488)
[2026-06-08T08:27:48] Filtering end-to-end fusions with low support (remaining=462)
[2026-06-08T08:27:48] Filtering fusions with no coverage around the breakpoints (remaining=456)
[2026-06-08T08:27:49] Indexing gene sequences 
[2026-06-08T08:27:55] Filtering genes with >=30% identity (remaining=147)
[2026-06-08T08:27:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=51)
[2026-06-08T08:27:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=50)
[2026-06-08T08:28:01] Searching for additional isoforms (remaining=57)
[2026-06-08T08:28:03] Assigning confidence scores to events 
[2026-06-08T08:28:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:28:08] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s37.arriba.fusions.tsv' 
[2026-06-08T08:28:09] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s37.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:50] Freeing resources
[2026-06-08T08:29:21] Done (elapsed time=00:13:46, CPU time=00:13:43, peak memory=16.8gb)