[2026-06-08T08:20:40] Launching Arriba 2.4.0
[2026-06-08T08:20:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:56] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s11.Aligned.sortedByCoord.out.bam' (total=11760307)
[2026-06-08T08:27:58] Marking multi-mapping alignments (marked=8300427)
[2026-06-08T08:28:03] Detecting strandedness (reverse)
[2026-06-08T08:28:03] Assigning strands to alignments 
[2026-06-08T08:28:05] Annotating alignments 
[2026-06-08T08:28:40] Filtering duplicates (remaining=6259138)
[2026-06-08T08:28:47] 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=5499996)
[2026-06-08T08:28:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5499996)
[2026-06-08T08:28:51] Filtering viral contigs with expression lower than the top 5 (remaining=5499996)
[2026-06-08T08:28:55] Filtering viral contigs with less than 5% coverage (remaining=5499996)
[2026-06-08T08:28:58] Estimating fragment length (mate gap mean=-86.0406, mate gap stddev=29.8472, read length mean=130.932)
[2026-06-08T08:28:58] Filtering read-through fragments with a distance <=10000bp (remaining=5247731)
[2026-06-08T08:29:00] Filtering inconsistently clipped mates (remaining=5145200)
[2026-06-08T08:29:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4627219)
[2026-06-08T08:29:07] Filtering fragments with small insert size (remaining=4626260)
[2026-06-08T08:29:09] Filtering alignments with long gaps (remaining=4626260)
[2026-06-08T08:29:11] Filtering fragments with both mates in the same gene (remaining=4624538)
[2026-06-08T08:29:13] Filtering fusions arising from hairpin structures (remaining=4253544)
[2026-06-08T08:29:16] Filtering reads with a mismatch p-value <=0.01 (remaining=1762460)
[2026-06-08T08:29:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=982273)
[2026-06-08T08:29:37] Finding fusions and counting supporting reads (total=853550)
[2026-06-08T08:29:52] Merging adjacent fusion breakpoints (remaining=846704)
[2026-06-08T08:29:53] Filtering multi-mapping fusions by alignment score and read support (remaining=447414)
[2026-06-08T08:30:25] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:30:31] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=444126)
[2026-06-08T08:30:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=296537)
[2026-06-08T08:30:33] Filtering fusions with <2 supporting reads (remaining=23666)
[2026-06-08T08:30:33] Filtering fusions with an e-value >=0.3 (remaining=5921)
[2026-06-08T08:30:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5953)
[2026-06-08T08:30:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5642)
[2026-06-08T08:30:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5655)
[2026-06-08T08:30:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4625)
[2026-06-08T08:30:45] Searching for fusions with spliced split reads (remaining=4712)
[2026-06-08T08:30:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=2963)
[2026-06-08T08:30:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2925)
[2026-06-08T08:30:52] Searching for fusions with >=4 spliced events (remaining=3497)
[2026-06-08T08:30:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1299)
[2026-06-08T08:31:07] Filtering fusions with anchors <=23nt (remaining=958)
[2026-06-08T08:31:08] Filtering end-to-end fusions with low support (remaining=927)
[2026-06-08T08:31:08] Filtering fusions with no coverage around the breakpoints (remaining=915)
[2026-06-08T08:31:09] Indexing gene sequences 
[2026-06-08T08:31:13] Filtering genes with >=30% identity (remaining=253)
[2026-06-08T08:31:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=87)
[2026-06-08T08:31:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=78)
[2026-06-08T08:31:18] Searching for additional isoforms (remaining=108)
[2026-06-08T08:31:20] Assigning confidence scores to events 
[2026-06-08T08:31:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:31:23] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s11.arriba.fusions.tsv' 
[2026-06-08T08:31:24] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s11.arriba.fusions.discarded.tsv'
[2026-06-08T08:31:50] Freeing resources
[2026-06-08T08:32:09] Done (elapsed time=00:11:29, CPU time=00:11:27, peak memory=17gb)