[2026-06-08T08:21:35] Launching Arriba 2.4.0
[2026-06-08T08:21:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:21:57] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s44.Aligned.sortedByCoord.out.bam' (total=11756822)
[2026-06-08T08:29:38] Marking multi-mapping alignments (marked=8531263)
[2026-06-08T08:29:43] Detecting strandedness (reverse)
[2026-06-08T08:29:43] Assigning strands to alignments 
[2026-06-08T08:29:46] Annotating alignments 
[2026-06-08T08:30:27] Filtering duplicates (remaining=5410596)
[2026-06-08T08:30:34] 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=4691814)
[2026-06-08T08:30:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4691814)
[2026-06-08T08:30:38] Filtering viral contigs with expression lower than the top 5 (remaining=4691814)
[2026-06-08T08:30:43] Filtering viral contigs with less than 5% coverage (remaining=4691814)
[2026-06-08T08:30:46] Estimating fragment length (mate gap mean=-80.2376, mate gap stddev=31.7513, read length mean=123.194)
[2026-06-08T08:30:46] Filtering read-through fragments with a distance <=10000bp (remaining=4506125)
[2026-06-08T08:30:48] Filtering inconsistently clipped mates (remaining=4422342)
[2026-06-08T08:30:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3887070)
[2026-06-08T08:30:54] Filtering fragments with small insert size (remaining=3885968)
[2026-06-08T08:30:57] Filtering alignments with long gaps (remaining=3885968)
[2026-06-08T08:30:59] Filtering fragments with both mates in the same gene (remaining=3884301)
[2026-06-08T08:31:01] Filtering fusions arising from hairpin structures (remaining=3666308)
[2026-06-08T08:31:03] Filtering reads with a mismatch p-value <=0.01 (remaining=1377206)
[2026-06-08T08:31:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=697663)
[2026-06-08T08:31:22] Finding fusions and counting supporting reads (total=625114)
[2026-06-08T08:31:38] Merging adjacent fusion breakpoints (remaining=621824)
[2026-06-08T08:31:40] Filtering multi-mapping fusions by alignment score and read support (remaining=304896)
[2026-06-08T08:32:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=302176)
[2026-06-08T08:32:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=214874)
[2026-06-08T08:32:20] Filtering fusions with <2 supporting reads (remaining=14491)
[2026-06-08T08:32:21] Filtering fusions with an e-value >=0.3 (remaining=3456)
[2026-06-08T08:32:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3477)
[2026-06-08T08:32:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3146)
[2026-06-08T08:32:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3146)
[2026-06-08T08:32:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2835)
[2026-06-08T08:32:32] Searching for fusions with spliced split reads (remaining=2890)
[2026-06-08T08:32:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=1951)
[2026-06-08T08:32:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1922)
[2026-06-08T08:32:39] Searching for fusions with >=4 spliced events (remaining=2165)
[2026-06-08T08:32:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=714)
[2026-06-08T08:32:56] Filtering fusions with anchors <=23nt (remaining=532)
[2026-06-08T08:32:57] Filtering end-to-end fusions with low support (remaining=512)
[2026-06-08T08:32:57] Filtering fusions with no coverage around the breakpoints (remaining=504)
[2026-06-08T08:32:58] Indexing gene sequences 
[2026-06-08T08:33:02] Filtering genes with >=30% identity (remaining=167)
[2026-06-08T08:33:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=64)
[2026-06-08T08:33:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=60)
[2026-06-08T08:33:05] Searching for additional isoforms (remaining=82)
[2026-06-08T08:33:06] Assigning confidence scores to events 
[2026-06-08T08:33:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:33:10] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s44.arriba.fusions.tsv' 
[2026-06-08T08:33:11] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s44.arriba.fusions.discarded.tsv'
[2026-06-08T08:33:35] Freeing resources
[2026-06-08T08:33:54] Done (elapsed time=00:12:19, CPU time=00:12:18, peak memory=16.7gb)