[2026-05-28T00:04:52] Launching Arriba 2.4.0
[2026-05-28T00:04:52] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:03] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:05:08] Reading chimeric alignments from 'FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3738747)
[2026-05-28T00:07:29] Marking multi-mapping alignments (marked=2494677)
[2026-05-28T00:07:30] Detecting strandedness (reverse)
[2026-05-28T00:07:30] Assigning strands to alignments 
[2026-05-28T00:07:31] Annotating alignments 
[2026-05-28T00:07:44] Filtering duplicates (remaining=2489290)
[2026-05-28T00:07:47] 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=2282461)
[2026-05-28T00:07:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2282461)
[2026-05-28T00:07:48] Filtering viral contigs with expression lower than the top 5 (remaining=2282461)
[2026-05-28T00:07:49] Filtering viral contigs with less than 5% coverage (remaining=2282461)
[2026-05-28T00:07:51] Estimating fragment length (mate gap mean=-87.8471, mate gap stddev=31.8245, read length mean=133.258)
[2026-05-28T00:07:51] Filtering read-through fragments with a distance <=10000bp (remaining=2168724)
[2026-05-28T00:07:51] Filtering inconsistently clipped mates (remaining=2121105)
[2026-05-28T00:07:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2058104)
[2026-05-28T00:07:54] Filtering fragments with small insert size (remaining=2057838)
[2026-05-28T00:07:54] Filtering alignments with long gaps (remaining=2057838)
[2026-05-28T00:07:55] Filtering fragments with both mates in the same gene (remaining=2057447)
[2026-05-28T00:07:56] Filtering fusions arising from hairpin structures (remaining=1889035)
[2026-05-28T00:07:57] Filtering reads with a mismatch p-value <=0.01 (remaining=879620)
[2026-05-28T00:08:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=382783)
[2026-05-28T00:08:06] Finding fusions and counting supporting reads (total=292756)
[2026-05-28T00:08:12] Merging adjacent fusion breakpoints (remaining=289613)
[2026-05-28T00:08:13] Filtering multi-mapping fusions by alignment score and read support (remaining=181322)
[2026-05-28T00:08:25] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=179907)
[2026-05-28T00:08:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=98708)
[2026-05-28T00:08:29] Filtering fusions with <2 supporting reads (remaining=14386)
[2026-05-28T00:08:29] Filtering fusions with an e-value >=0.3 (remaining=5282)
[2026-05-28T00:08:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5322)
[2026-05-28T00:08:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5269)
[2026-05-28T00:08:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5279)
[2026-05-28T00:08:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3904)
[2026-05-28T00:08:33] Searching for fusions with spliced split reads (remaining=3937)
[2026-05-28T00:08:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=2405)
[2026-05-28T00:08:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2376)
[2026-05-28T00:08:36] Searching for fusions with >=4 spliced events (remaining=2612)
[2026-05-28T00:08:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=855)
[2026-05-28T00:08:50] Filtering fusions with anchors <=23nt (remaining=596)
[2026-05-28T00:08:50] Filtering end-to-end fusions with low support (remaining=569)
[2026-05-28T00:08:50] Filtering fusions with no coverage around the breakpoints (remaining=545)
[2026-05-28T00:08:51] Indexing gene sequences 
[2026-05-28T00:08:53] Filtering genes with >=30% identity (remaining=156)
[2026-05-28T00:08:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=58)
[2026-05-28T00:08:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=57)
[2026-05-28T00:08:56] Searching for additional isoforms (remaining=76)
[2026-05-28T00:08:56] Assigning confidence scores to events 
[2026-05-28T00:08:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:57] Writing fusions to file 'FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:08:58] Writing discarded fusions to file 'FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:10] Freeing resources
[2026-05-28T00:09:16] Done (elapsed time=00:04:24, CPU time=00:04:23, peak memory=8.1gb)