[2026-06-08T09:16:50] Launching Arriba 2.4.0
[2026-06-08T09:16:50] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:16:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:17:00] Reading chimeric alignments from 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=92580598)
[2026-06-08T09:27:31] Marking multi-mapping alignments (marked=86112847)
[2026-06-08T09:27:55] Detecting strandedness (no)
[2026-06-08T09:27:55] Annotating alignments 
[2026-06-08T09:32:43] Filtering duplicates (remaining=8301886)
[2026-06-08T09:33:23] 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=4670077)
[2026-06-08T09:33:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4670077)
[2026-06-08T09:33:54] Filtering viral contigs with expression lower than the top 5 (remaining=4670077)
[2026-06-08T09:34:25] Filtering viral contigs with less than 5% coverage (remaining=4670077)
[2026-06-08T09:34:41] Estimating fragment length (mate gap mean=-58.5561, mate gap stddev=28.8176, read length mean=99.0777)
[2026-06-08T09:34:41] Filtering read-through fragments with a distance <=10000bp (remaining=4581856)
[2026-06-08T09:34:56] Filtering inconsistently clipped mates (remaining=4479429)
[2026-06-08T09:35:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4078509)
[2026-06-08T09:35:28] Filtering fragments with small insert size (remaining=4073652)
[2026-06-08T09:35:43] Filtering alignments with long gaps (remaining=4073652)
[2026-06-08T09:35:59] Filtering fragments with both mates in the same gene (remaining=4071371)
[2026-06-08T09:36:15] Filtering fusions arising from hairpin structures (remaining=3891042)
[2026-06-08T09:36:31] Filtering reads with a mismatch p-value <=0.01 (remaining=531802)
[2026-06-08T09:36:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=206504)
[2026-06-08T09:37:23] Finding fusions and counting supporting reads (total=139796)
[2026-06-08T09:38:19] Merging adjacent fusion breakpoints (remaining=134847)
[2026-06-08T09:38:21] Filtering multi-mapping fusions by alignment score and read support (remaining=52942)
[2026-06-08T09:40:22] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:40:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=49959)
[2026-06-08T09:40:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=40324)
[2026-06-08T09:40:34] Filtering fusions with <2 supporting reads (remaining=3602)
[2026-06-08T09:40:34] Filtering fusions with an e-value >=0.3 (remaining=481)
[2026-06-08T09:40:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=495)
[2026-06-08T09:40:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=349)
[2026-06-08T09:40:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=349)
[2026-06-08T09:40:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=349)
[2026-06-08T09:41:15] Searching for fusions with spliced split reads (remaining=365)
[2026-06-08T09:41:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=290)
[2026-06-08T09:41:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=284)
[2026-06-08T09:41:38] Searching for fusions with >=4 spliced events (remaining=300)
[2026-06-08T09:41:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=129)
[2026-06-08T09:41:49] Filtering fusions with anchors <=23nt (remaining=94)
[2026-06-08T09:41:50] Filtering end-to-end fusions with low support (remaining=89)
[2026-06-08T09:41:50] Filtering fusions with no coverage around the breakpoints (remaining=88)
[2026-06-08T09:41:51] Indexing gene sequences 
[2026-06-08T09:41:52] Filtering genes with >=30% identity (remaining=46)
[2026-06-08T09:41:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=18)
[2026-06-08T09:41:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=7)
[2026-06-08T09:41:56] Searching for additional isoforms (remaining=7)
[2026-06-08T09:41:58] Assigning confidence scores to events 
[2026-06-08T09:42:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:42:00] Writing fusions to file 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:42:01] Writing discarded fusions to file 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:42:21] Freeing resources
[2026-06-08T09:44:11] Done (elapsed time=00:27:21, CPU time=00:27:19, peak memory=103gb)