[2026-06-08T08:16:40] Launching Arriba 2.4.0
[2026-06-08T08:16:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:16:53] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s41.Aligned.sortedByCoord.out.bam' (total=10299530)
[2026-06-08T08:23:36] Marking multi-mapping alignments (marked=7142287)
[2026-06-08T08:23:41] Detecting strandedness (reverse)
[2026-06-08T08:23:41] Assigning strands to alignments 
[2026-06-08T08:23:43] Annotating alignments 
[2026-06-08T08:24:19] Filtering duplicates (remaining=5446979)
[2026-06-08T08:24:25] 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=4847348)
[2026-06-08T08:24:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4847348)
[2026-06-08T08:24:29] Filtering viral contigs with expression lower than the top 5 (remaining=4847348)
[2026-06-08T08:24:34] Filtering viral contigs with less than 5% coverage (remaining=4847348)
[2026-06-08T08:24:36] Estimating fragment length (mate gap mean=-82.646, mate gap stddev=31.1471, read length mean=129.152)
[2026-06-08T08:24:36] Filtering read-through fragments with a distance <=10000bp (remaining=4624268)
[2026-06-08T08:24:38] Filtering inconsistently clipped mates (remaining=4540903)
[2026-06-08T08:24:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4169177)
[2026-06-08T08:24:44] Filtering fragments with small insert size (remaining=4168326)
[2026-06-08T08:24:46] Filtering alignments with long gaps (remaining=4168326)
[2026-06-08T08:24:48] Filtering fragments with both mates in the same gene (remaining=4166835)
[2026-06-08T08:24:50] Filtering fusions arising from hairpin structures (remaining=3910714)
[2026-06-08T08:24:53] Filtering reads with a mismatch p-value <=0.01 (remaining=1626476)
[2026-06-08T08:25:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=805457)
[2026-06-08T08:25:12] Finding fusions and counting supporting reads (total=672040)
[2026-06-08T08:25:27] Merging adjacent fusion breakpoints (remaining=667533)
[2026-06-08T08:25:28] Filtering multi-mapping fusions by alignment score and read support (remaining=369947)
[2026-06-08T08:26:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:26:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=367021)
[2026-06-08T08:26:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=227882)
[2026-06-08T08:26:09] Filtering fusions with <2 supporting reads (remaining=22627)
[2026-06-08T08:26:10] Filtering fusions with an e-value >=0.3 (remaining=6689)
[2026-06-08T08:26:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6725)
[2026-06-08T08:26:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6494)
[2026-06-08T08:26:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6516)
[2026-06-08T08:26:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4435)
[2026-06-08T08:26:21] Searching for fusions with spliced split reads (remaining=4531)
[2026-06-08T08:26:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=2963)
[2026-06-08T08:26:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2933)
[2026-06-08T08:26:27] Searching for fusions with >=4 spliced events (remaining=3442)
[2026-06-08T08:26:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1320)
[2026-06-08T08:26:42] Filtering fusions with anchors <=23nt (remaining=958)
[2026-06-08T08:26:43] Filtering end-to-end fusions with low support (remaining=934)
[2026-06-08T08:26:43] Filtering fusions with no coverage around the breakpoints (remaining=923)
[2026-06-08T08:26:44] Indexing gene sequences 
[2026-06-08T08:26:48] Filtering genes with >=30% identity (remaining=267)
[2026-06-08T08:26:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=68)
[2026-06-08T08:26:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=68)
[2026-06-08T08:26:53] Searching for additional isoforms (remaining=93)
[2026-06-08T08:26:54] Assigning confidence scores to events 
[2026-06-08T08:26:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:26:58] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s41.arriba.fusions.tsv' 
[2026-06-08T08:26:59] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s41.arriba.fusions.discarded.tsv'
[2026-06-08T08:27:24] Freeing resources
[2026-06-08T08:27:42] Done (elapsed time=00:11:02, CPU time=00:11:01, peak memory=15.1gb)