[2026-06-08T07:26:22] Launching Arriba 2.4.0
[2026-06-08T07:26:22] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:26:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:26:41] Reading chimeric alignments from 'OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1820174)
[2026-06-08T07:27:15] Marking multi-mapping alignments (marked=1527312)
[2026-06-08T07:27:16] Detecting strandedness (reverse)
[2026-06-08T07:27:16] Assigning strands to alignments 
[2026-06-08T07:27:16] Annotating alignments 
[2026-06-08T07:27:23] Filtering duplicates (remaining=529496)
[2026-06-08T07:27:24] 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)
[2026-06-08T07:27:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=439147)
[2026-06-08T07:27:25] Filtering viral contigs with expression lower than the top 5 (remaining=439147)
[2026-06-08T07:27:25] Filtering viral contigs with less than 5% coverage (remaining=439147)
[2026-06-08T07:27:26] Estimating fragment length (mate gap mean=-47.2421, mate gap stddev=26.9896, read length mean=83.0025)
[2026-06-08T07:27:26] Filtering read-through fragments with a distance <=10000bp (remaining=433671)
[2026-06-08T07:27:27] Filtering inconsistently clipped mates (remaining=414666)
[2026-06-08T07:27:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=372087)
[2026-06-08T07:27:27] Filtering fragments with small insert size (remaining=371322)
[2026-06-08T07:27:28] Filtering alignments with long gaps (remaining=371322)
[2026-06-08T07:27:28] Filtering fragments with both mates in the same gene (remaining=370904)
[2026-06-08T07:27:28] Filtering fusions arising from hairpin structures (remaining=347734)
[2026-06-08T07:27:29] Filtering reads with a mismatch p-value <=0.01 (remaining=55521)
[2026-06-08T07:27:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=24639)
[2026-06-08T07:27:30] Finding fusions and counting supporting reads (total=26061)
[2026-06-08T07:27:33] Merging adjacent fusion breakpoints (remaining=25981)
[2026-06-08T07:27:33] Filtering multi-mapping fusions by alignment score and read support (remaining=9756)
[2026-06-08T07:27:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:27:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=9538)
[2026-06-08T07:27:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=8463)
[2026-06-08T07:27:40] Filtering fusions with <2 supporting reads (remaining=118)
[2026-06-08T07:27:40] Filtering fusions with an e-value >=0.3 (remaining=56)
[2026-06-08T07:27:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=56)
[2026-06-08T07:27:41] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=34)
[2026-06-08T07:27:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=34)
[2026-06-08T07:27:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=28)
[2026-06-08T07:27:41] Searching for fusions with spliced split reads (remaining=28)
[2026-06-08T07:27:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=24)
[2026-06-08T07:27:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=23)
[2026-06-08T07:27:42] Searching for fusions with >=4 spliced events (remaining=23)
[2026-06-08T07:27:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9)
[2026-06-08T07:27:57] Filtering fusions with anchors <=23nt (remaining=7)
[2026-06-08T07:27:57] Filtering end-to-end fusions with low support (remaining=7)
[2026-06-08T07:27:57] Filtering fusions with no coverage around the breakpoints (remaining=6)
[2026-06-08T07:27:57] Indexing gene sequences 
[2026-06-08T07:27:58] Filtering genes with >=30% identity (remaining=4)
[2026-06-08T07:27:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-06-08T07:27:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-06-08T07:27:58] Searching for additional isoforms (remaining=1)
[2026-06-08T07:27:58] Assigning confidence scores to events 
[2026-06-08T07:27:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:27:59] Writing fusions to file 'OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:27:59] Writing discarded fusions to file 'OvarianNP_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:28:02] Freeing resources
[2026-06-08T07:28:06] Done (elapsed time=00:01:44, CPU time=00:01:43, peak memory=5.94gb)