[2026-05-28T21:31:50] Launching Arriba 2.4.0
[2026-05-28T21:31:50] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:32:05] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:32:10] Reading chimeric alignments from 'SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=11045432)
[2026-05-28T21:41:45] Marking multi-mapping alignments (marked=7217361)
[2026-05-28T21:41:50] Detecting strandedness (reverse)
[2026-05-28T21:41:50] Assigning strands to alignments 
[2026-05-28T21:41:52] Annotating alignments 
[2026-05-28T21:42:28] Filtering duplicates (remaining=8298695)
[2026-05-28T21:42:37] 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=7661725)
[2026-05-28T21:42:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7661725)
[2026-05-28T21:42:42] Filtering viral contigs with expression lower than the top 5 (remaining=7661725)
[2026-05-28T21:42:47] Filtering viral contigs with less than 5% coverage (remaining=7661725)
[2026-05-28T21:42:49] Estimating fragment length (mate gap mean=-85.9677, mate gap stddev=30.0323, read length mean=132.521)
[2026-05-28T21:42:49] Filtering read-through fragments with a distance <=10000bp (remaining=7235126)
[2026-05-28T21:42:51] Filtering inconsistently clipped mates (remaining=7127260)
[2026-05-28T21:42:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6897223)
[2026-05-28T21:42:59] Filtering fragments with small insert size (remaining=6896122)
[2026-05-28T21:43:01] Filtering alignments with long gaps (remaining=6896121)
[2026-05-28T21:43:03] Filtering fragments with both mates in the same gene (remaining=6894756)
[2026-05-28T21:43:06] Filtering fusions arising from hairpin structures (remaining=6510484)
[2026-05-28T21:43:08] Filtering reads with a mismatch p-value <=0.01 (remaining=3268854)
[2026-05-28T21:43:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=1558330)
[2026-05-28T21:43:38] Finding fusions and counting supporting reads (total=1218827)
[2026-05-28T21:43:58] Merging adjacent fusion breakpoints (remaining=1210172)
[2026-05-28T21:44:00] Filtering multi-mapping fusions by alignment score and read support (remaining=753754)
[2026-05-28T21:44:35] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:44:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=751250)
[2026-05-28T21:44:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=506158)
[2026-05-28T21:44:48] Filtering fusions with <2 supporting reads (remaining=40305)
[2026-05-28T21:44:49] Filtering fusions with an e-value >=0.3 (remaining=8955)
[2026-05-28T21:44:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9000)
[2026-05-28T21:44:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8853)
[2026-05-28T21:44:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8854)
[2026-05-28T21:44:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6517)
[2026-05-28T21:45:03] Searching for fusions with spliced split reads (remaining=6551)
[2026-05-28T21:45:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=3960)
[2026-05-28T21:45:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3938)
[2026-05-28T21:45:12] Searching for fusions with >=4 spliced events (remaining=4996)
[2026-05-28T21:45:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2253)
[2026-05-28T21:45:31] Filtering fusions with anchors <=23nt (remaining=1771)
[2026-05-28T21:45:32] Filtering end-to-end fusions with low support (remaining=1733)
[2026-05-28T21:45:33] Filtering fusions with no coverage around the breakpoints (remaining=1716)
[2026-05-28T21:45:34] Indexing gene sequences 
[2026-05-28T21:45:41] Filtering genes with >=30% identity (remaining=630)
[2026-05-28T21:45:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=368)
[2026-05-28T21:45:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=203)
[2026-05-28T21:45:58] Searching for additional isoforms (remaining=404)
[2026-05-28T21:46:00] Assigning confidence scores to events 
[2026-05-28T21:46:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:46:04] Writing fusions to file 'SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-05-28T21:46:09] Writing discarded fusions to file 'SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-05-28T21:46:52] Freeing resources
[2026-05-28T21:47:14] Done (elapsed time=00:15:24, CPU time=00:15:24, peak memory=16.1gb)