[2026-05-28T21:16:42] Launching Arriba 2.4.0
[2026-05-28T21:16:42] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:16:55] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:16:59] Reading chimeric alignments from 'OvarianND_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=9728901)
[2026-05-28T21:25:57] Marking multi-mapping alignments (marked=6327535)
[2026-05-28T21:26:02] Detecting strandedness (reverse)
[2026-05-28T21:26:02] Assigning strands to alignments 
[2026-05-28T21:26:04] Annotating alignments 
[2026-05-28T21:26:50] Filtering duplicates (remaining=5604680)
[2026-05-28T21:27:00] 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=5384697)
[2026-05-28T21:27:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5384697)
[2026-05-28T21:27:05] Filtering viral contigs with expression lower than the top 5 (remaining=5384697)
[2026-05-28T21:27:10] Filtering viral contigs with less than 5% coverage (remaining=5384697)
[2026-05-28T21:27:12] Estimating fragment length (mate gap mean=-81.4575, mate gap stddev=28.7293, read length mean=122.813)
[2026-05-28T21:27:12] Filtering read-through fragments with a distance <=10000bp (remaining=5141527)
[2026-05-28T21:27:15] Filtering inconsistently clipped mates (remaining=5053196)
[2026-05-28T21:27:17] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4788273)
[2026-05-28T21:27:21] Filtering fragments with small insert size (remaining=4787371)
[2026-05-28T21:27:24] Filtering alignments with long gaps (remaining=4787370)
[2026-05-28T21:27:26] Filtering fragments with both mates in the same gene (remaining=4786000)
[2026-05-28T21:27:29] Filtering fusions arising from hairpin structures (remaining=4575743)
[2026-05-28T21:27:31] Filtering reads with a mismatch p-value <=0.01 (remaining=2172034)
[2026-05-28T21:27:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=916980)
[2026-05-28T21:27:57] Finding fusions and counting supporting reads (total=597055)
[2026-05-28T21:28:21] Merging adjacent fusion breakpoints (remaining=592551)
[2026-05-28T21:28:23] Filtering multi-mapping fusions by alignment score and read support (remaining=341588)
[2026-05-28T21:29:09] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:29:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=339806)
[2026-05-28T21:29:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=206760)
[2026-05-28T21:29:22] Filtering fusions with <2 supporting reads (remaining=30255)
[2026-05-28T21:29:23] Filtering fusions with an e-value >=0.3 (remaining=7661)
[2026-05-28T21:29:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7709)
[2026-05-28T21:29:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7588)
[2026-05-28T21:29:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7588)
[2026-05-28T21:29:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7288)
[2026-05-28T21:29:36] Searching for fusions with spliced split reads (remaining=7387)
[2026-05-28T21:29:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=4584)
[2026-05-28T21:29:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4540)
[2026-05-28T21:29:45] Searching for fusions with >=4 spliced events (remaining=5143)
[2026-05-28T21:29:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1463)
[2026-05-28T21:30:11] Filtering fusions with anchors <=23nt (remaining=1220)
[2026-05-28T21:30:12] Filtering end-to-end fusions with low support (remaining=1182)
[2026-05-28T21:30:13] Filtering fusions with no coverage around the breakpoints (remaining=1165)
[2026-05-28T21:30:14] Indexing gene sequences 
[2026-05-28T21:30:27] Filtering genes with >=30% identity (remaining=344)
[2026-05-28T21:30:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=150)
[2026-05-28T21:30:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=141)
[2026-05-28T21:30:40] Searching for additional isoforms (remaining=190)
[2026-05-28T21:30:42] Assigning confidence scores to events 
[2026-05-28T21:30:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:30:48] Writing fusions to file 'OvarianND_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:30:51] Writing discarded fusions to file 'OvarianND_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:31:41] Freeing resources
[2026-05-28T21:32:15] Done (elapsed time=00:15:33, CPU time=00:15:32, peak memory=14.2gb)