[2026-06-08T07:28:23] Launching Arriba 2.4.0
[2026-06-08T07:28:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:28:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:28:45] Reading chimeric alignments from 'OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1604839)
[2026-06-08T07:29:19] Marking multi-mapping alignments (marked=1345742)
[2026-06-08T07:29:19] Detecting strandedness (no)
[2026-06-08T07:29:19] Annotating alignments 
[2026-06-08T07:29:26] Filtering duplicates (remaining=466539)
[2026-06-08T07:29:26] 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=398634)
[2026-06-08T07:29:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=398634)
[2026-06-08T07:29:27] Filtering viral contigs with expression lower than the top 5 (remaining=398634)
[2026-06-08T07:29:27] Filtering viral contigs with less than 5% coverage (remaining=398634)
[2026-06-08T07:29:28] Estimating fragment length (mate gap mean=-46.0194, mate gap stddev=26.9193, read length mean=82.0015)
[2026-06-08T07:29:28] Filtering read-through fragments with a distance <=10000bp (remaining=393983)
[2026-06-08T07:29:28] Filtering inconsistently clipped mates (remaining=375697)
[2026-06-08T07:29:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=336162)
[2026-06-08T07:29:29] Filtering fragments with small insert size (remaining=335429)
[2026-06-08T07:29:29] Filtering alignments with long gaps (remaining=335429)
[2026-06-08T07:29:30] Filtering fragments with both mates in the same gene (remaining=334874)
[2026-06-08T07:29:30] Filtering fusions arising from hairpin structures (remaining=313164)
[2026-06-08T07:29:30] Filtering reads with a mismatch p-value <=0.01 (remaining=51630)
[2026-06-08T07:29:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=23316)
[2026-06-08T07:29:32] Finding fusions and counting supporting reads (total=25367)
[2026-06-08T07:29:33] Merging adjacent fusion breakpoints (remaining=25320)
[2026-06-08T07:29:34] Filtering multi-mapping fusions by alignment score and read support (remaining=9259)
[2026-06-08T07:29:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:29:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=9075)
[2026-06-08T07:29:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=8062)
[2026-06-08T07:29:38] Filtering fusions with <2 supporting reads (remaining=83)
[2026-06-08T07:29:38] Filtering fusions with an e-value >=0.3 (remaining=38)
[2026-06-08T07:29:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=38)
[2026-06-08T07:29:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=21)
[2026-06-08T07:29:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=21)
[2026-06-08T07:29:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=18)
[2026-06-08T07:29:39] Searching for fusions with spliced split reads (remaining=18)
[2026-06-08T07:29:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=18)
[2026-06-08T07:29:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=18)
[2026-06-08T07:29:40] Searching for fusions with >=4 spliced events (remaining=18)
[2026-06-08T07:29:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8)
[2026-06-08T07:29:58] Filtering fusions with anchors <=23nt (remaining=3)
[2026-06-08T07:29:58] Filtering end-to-end fusions with low support (remaining=3)
[2026-06-08T07:29:58] Filtering fusions with no coverage around the breakpoints (remaining=0)
[2026-06-08T07:29:58] Indexing gene sequences 
[2026-06-08T07:29:58] Filtering genes with >=30% identity (remaining=0)
[2026-06-08T07:29:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-08T07:29:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:29:59] Searching for additional isoforms (remaining=0)
[2026-06-08T07:29:59] Assigning confidence scores to events 
[2026-06-08T07:29:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:29:59] Writing fusions to file 'OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:29:59] Writing discarded fusions to file 'OvarianNP_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:30:02] Freeing resources
[2026-06-08T07:30:05] Done (elapsed time=00:01:42, CPU time=00:01:42, peak memory=5.7gb)