[2026-05-28T21:16:42] Launching Arriba 2.4.0
[2026-05-28T21:16:42] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:16:56] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:17:01] Reading chimeric alignments from 'OvarianND_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=10065953)
[2026-05-28T21:27:51] Marking multi-mapping alignments (marked=6557980)
[2026-05-28T21:27:57] Detecting strandedness (reverse)
[2026-05-28T21:27:57] Assigning strands to alignments 
[2026-05-28T21:28:00] Annotating alignments 
[2026-05-28T21:29:04] Filtering duplicates (remaining=5245667)
[2026-05-28T21:29:16] 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=5026874)
[2026-05-28T21:29:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5026874)
[2026-05-28T21:29:22] Filtering viral contigs with expression lower than the top 5 (remaining=5026874)
[2026-05-28T21:29:30] Filtering viral contigs with less than 5% coverage (remaining=5026874)
[2026-05-28T21:29:34] Estimating fragment length (mate gap mean=-82.5509, mate gap stddev=27.9392, read length mean=123.191)
[2026-05-28T21:29:34] Filtering read-through fragments with a distance <=10000bp (remaining=4809234)
[2026-05-28T21:29:37] Filtering inconsistently clipped mates (remaining=4728343)
[2026-05-28T21:29:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4507603)
[2026-05-28T21:29:48] Filtering fragments with small insert size (remaining=4506777)
[2026-05-28T21:29:51] Filtering alignments with long gaps (remaining=4506776)
[2026-05-28T21:29:55] Filtering fragments with both mates in the same gene (remaining=4505626)
[2026-05-28T21:29:59] Filtering fusions arising from hairpin structures (remaining=4307320)
[2026-05-28T21:30:03] Filtering reads with a mismatch p-value <=0.01 (remaining=2038716)
[2026-05-28T21:30:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=831289)
[2026-05-28T21:30:39] Finding fusions and counting supporting reads (total=557810)
[2026-05-28T21:31:07] Merging adjacent fusion breakpoints (remaining=553001)
[2026-05-28T21:31:10] Filtering multi-mapping fusions by alignment score and read support (remaining=313512)
[2026-05-28T21:32:11] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:32:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=311872)
[2026-05-28T21:32:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=188025)
[2026-05-28T21:32:25] Filtering fusions with <2 supporting reads (remaining=28795)
[2026-05-28T21:32:26] Filtering fusions with an e-value >=0.3 (remaining=8146)
[2026-05-28T21:32:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8188)
[2026-05-28T21:32:33] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8099)
[2026-05-28T21:32:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8099)
[2026-05-28T21:32:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6632)
[2026-05-28T21:32:44] Searching for fusions with spliced split reads (remaining=6709)
[2026-05-28T21:32:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=4278)
[2026-05-28T21:32:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4236)
[2026-05-28T21:32:56] Searching for fusions with >=4 spliced events (remaining=4771)
[2026-05-28T21:32:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1327)
[2026-05-28T21:33:31] Filtering fusions with anchors <=23nt (remaining=1099)
[2026-05-28T21:33:32] Filtering end-to-end fusions with low support (remaining=1077)
[2026-05-28T21:33:33] Filtering fusions with no coverage around the breakpoints (remaining=1066)
[2026-05-28T21:33:34] Indexing gene sequences 
[2026-05-28T21:33:45] Filtering genes with >=30% identity (remaining=330)
[2026-05-28T21:33:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=143)
[2026-05-28T21:33:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=139)
[2026-05-28T21:33:58] Searching for additional isoforms (remaining=161)
[2026-05-28T21:34:00] Assigning confidence scores to events 
[2026-05-28T21:34:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:34:06] Writing fusions to file 'OvarianND_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:34:08] Writing discarded fusions to file 'OvarianND_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:35:01] Freeing resources
[2026-05-28T21:35:38] Done (elapsed time=00:18:56, CPU time=00:18:54, peak memory=14.4gb)