[2026-06-08T08:08:33] Launching Arriba 2.4.0
[2026-06-08T08:08:33] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:08:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:08:52] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s35.Aligned.sortedByCoord.out.bam' (total=10275231)
[2026-06-08T08:15:10] Marking multi-mapping alignments (marked=7436626)
[2026-06-08T08:15:14] Detecting strandedness (reverse)
[2026-06-08T08:15:14] Assigning strands to alignments 
[2026-06-08T08:15:16] Annotating alignments 
[2026-06-08T08:15:48] Filtering duplicates (remaining=4894234)
[2026-06-08T08:15:54] 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=4242255)
[2026-06-08T08:15:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4242255)
[2026-06-08T08:15:58] Filtering viral contigs with expression lower than the top 5 (remaining=4242255)
[2026-06-08T08:16:02] Filtering viral contigs with less than 5% coverage (remaining=4242255)
[2026-06-08T08:16:04] Estimating fragment length (mate gap mean=-83.6458, mate gap stddev=31.9954, read length mean=128.269)
[2026-06-08T08:16:04] Filtering read-through fragments with a distance <=10000bp (remaining=4072554)
[2026-06-08T08:16:06] Filtering inconsistently clipped mates (remaining=3998710)
[2026-06-08T08:16:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3565569)
[2026-06-08T08:16:11] Filtering fragments with small insert size (remaining=3564596)
[2026-06-08T08:16:13] Filtering alignments with long gaps (remaining=3564596)
[2026-06-08T08:16:15] Filtering fragments with both mates in the same gene (remaining=3563132)
[2026-06-08T08:16:17] Filtering fusions arising from hairpin structures (remaining=3338073)
[2026-06-08T08:16:18] Filtering reads with a mismatch p-value <=0.01 (remaining=1270153)
[2026-06-08T08:16:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=641268)
[2026-06-08T08:16:34] Finding fusions and counting supporting reads (total=564084)
[2026-06-08T08:16:47] Merging adjacent fusion breakpoints (remaining=560511)
[2026-06-08T08:16:49] Filtering multi-mapping fusions by alignment score and read support (remaining=279196)
[2026-06-08T08:17:17] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:17:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=276667)
[2026-06-08T08:17:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=186948)
[2026-06-08T08:17:23] Filtering fusions with <2 supporting reads (remaining=14253)
[2026-06-08T08:17:23] Filtering fusions with an e-value >=0.3 (remaining=3776)
[2026-06-08T08:17:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3801)
[2026-06-08T08:17:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3550)
[2026-06-08T08:17:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3552)
[2026-06-08T08:17:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3093)
[2026-06-08T08:17:32] Searching for fusions with spliced split reads (remaining=3147)
[2026-06-08T08:17:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=2048)
[2026-06-08T08:17:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2015)
[2026-06-08T08:17:38] Searching for fusions with >=4 spliced events (remaining=2260)
[2026-06-08T08:17:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=763)
[2026-06-08T08:17:52] Filtering fusions with anchors <=23nt (remaining=555)
[2026-06-08T08:17:53] Filtering end-to-end fusions with low support (remaining=534)
[2026-06-08T08:17:54] Filtering fusions with no coverage around the breakpoints (remaining=519)
[2026-06-08T08:17:54] Indexing gene sequences 
[2026-06-08T08:17:57] Filtering genes with >=30% identity (remaining=161)
[2026-06-08T08:17:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=63)
[2026-06-08T08:17:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=60)
[2026-06-08T08:18:00] Searching for additional isoforms (remaining=74)
[2026-06-08T08:18:01] Assigning confidence scores to events 
[2026-06-08T08:18:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:18:04] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s35.arriba.fusions.tsv' 
[2026-06-08T08:18:05] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s35.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:25] Freeing resources
[2026-06-08T08:18:41] Done (elapsed time=00:10:08, CPU time=00:10:07, peak memory=15.2gb)