[2026-05-28T20:11:16] Launching Arriba 2.4.0
[2026-05-28T20:11:16] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:11:31] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:11:37] Reading chimeric alignments from 'OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1820174)
[2026-05-28T20:12:10] Marking multi-mapping alignments (marked=1527312)
[2026-05-28T20:12:11] Detecting strandedness (reverse)
[2026-05-28T20:12:11] Assigning strands to alignments 
[2026-05-28T20:12:11] Annotating alignments 
[2026-05-28T20:12:18] Filtering duplicates (remaining=529496)
[2026-05-28T20:12:18] 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=439147)
[2026-05-28T20:12:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=439147)
[2026-05-28T20:12:19] Filtering viral contigs with expression lower than the top 5 (remaining=439147)
[2026-05-28T20:12:19] Filtering viral contigs with less than 5% coverage (remaining=439147)
[2026-05-28T20:12:20] Estimating fragment length (mate gap mean=-47.2421, mate gap stddev=26.9896, read length mean=83.0025)
[2026-05-28T20:12:20] Filtering read-through fragments with a distance <=10000bp (remaining=433671)
[2026-05-28T20:12:21] Filtering inconsistently clipped mates (remaining=414666)
[2026-05-28T20:12:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=372087)
[2026-05-28T20:12:22] Filtering fragments with small insert size (remaining=371322)
[2026-05-28T20:12:22] Filtering alignments with long gaps (remaining=371322)
[2026-05-28T20:12:22] Filtering fragments with both mates in the same gene (remaining=370904)
[2026-05-28T20:12:22] Filtering fusions arising from hairpin structures (remaining=347734)
[2026-05-28T20:12:23] Filtering reads with a mismatch p-value <=0.01 (remaining=55521)
[2026-05-28T20:12:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=24639)
[2026-05-28T20:12:25] Finding fusions and counting supporting reads (total=26061)
[2026-05-28T20:12:27] Merging adjacent fusion breakpoints (remaining=25981)
[2026-05-28T20:12:27] Filtering multi-mapping fusions by alignment score and read support (remaining=9756)
[2026-05-28T20:12:32] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:12:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=9538)
[2026-05-28T20:12:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=8463)
[2026-05-28T20:12:33] Filtering fusions with <2 supporting reads (remaining=118)
[2026-05-28T20:12:33] Filtering fusions with an e-value >=0.3 (remaining=56)
[2026-05-28T20:12:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=56)
[2026-05-28T20:12:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=34)
[2026-05-28T20:12:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=34)
[2026-05-28T20:12:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=28)
[2026-05-28T20:12:34] Searching for fusions with spliced split reads (remaining=28)
[2026-05-28T20:12:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=24)
[2026-05-28T20:12:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=23)
[2026-05-28T20:12:35] Searching for fusions with >=4 spliced events (remaining=23)
[2026-05-28T20:12:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9)
[2026-05-28T20:12:52] Filtering fusions with anchors <=23nt (remaining=7)
[2026-05-28T20:12:52] Filtering end-to-end fusions with low support (remaining=7)
[2026-05-28T20:12:52] Filtering fusions with no coverage around the breakpoints (remaining=6)
[2026-05-28T20:12:53] Indexing gene sequences 
[2026-05-28T20:12:53] Filtering genes with >=30% identity (remaining=4)
[2026-05-28T20:12:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-05-28T20:12:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-05-28T20:12:53] Searching for additional isoforms (remaining=1)
[2026-05-28T20:12:53] Assigning confidence scores to events 
[2026-05-28T20:12:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:12:54] Writing fusions to file 'OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:12:54] Writing discarded fusions to file 'OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:12:58] Freeing resources
[2026-05-28T20:13:02] Done (elapsed time=00:01:46, CPU time=00:01:46, peak memory=5.95gb)