[2026-05-28T22:20:39] Launching Arriba 2.4.0
[2026-05-28T22:20:39] Loading assembly from 'ref_genome.fa' 
[2026-05-28T22:20:52] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T22:20:56] Reading chimeric alignments from 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=92580598)
[2026-05-28T22:39:11] Marking multi-mapping alignments (marked=86112847)
[2026-05-28T22:39:43] Detecting strandedness (no)
[2026-05-28T22:39:43] Annotating alignments 
[2026-05-28T22:45:48] Filtering duplicates (remaining=8301886)
[2026-05-28T22:46:35] 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)
[2026-05-28T22:46:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4670077)
[2026-05-28T22:47:02] Filtering viral contigs with expression lower than the top 5 (remaining=4670077)
[2026-05-28T22:47:29] Filtering viral contigs with less than 5% coverage (remaining=4670077)
[2026-05-28T22:47:43] Estimating fragment length (mate gap mean=-58.5561, mate gap stddev=28.8176, read length mean=99.0777)
[2026-05-28T22:47:43] Filtering read-through fragments with a distance <=10000bp (remaining=4581856)
[2026-05-28T22:47:56] Filtering inconsistently clipped mates (remaining=4479429)
[2026-05-28T22:48:10] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4078509)
[2026-05-28T22:48:25] Filtering fragments with small insert size (remaining=4073652)
[2026-05-28T22:48:39] Filtering alignments with long gaps (remaining=4073652)
[2026-05-28T22:48:52] Filtering fragments with both mates in the same gene (remaining=4071371)
[2026-05-28T22:49:06] Filtering fusions arising from hairpin structures (remaining=3891042)
[2026-05-28T22:49:19] Filtering reads with a mismatch p-value <=0.01 (remaining=531802)
[2026-05-28T22:49:37] Filtering reads with low entropy (k-mer content >=60%) (remaining=206504)
[2026-05-28T22:50:10] Finding fusions and counting supporting reads (total=139796)
[2026-05-28T22:51:29] Merging adjacent fusion breakpoints (remaining=134847)
[2026-05-28T22:51:31] Filtering multi-mapping fusions by alignment score and read support (remaining=52942)
[2026-05-28T22:54:08] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T22:54:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=49959)
[2026-05-28T22:54:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=40324)
[2026-05-28T22:54:22] Filtering fusions with <2 supporting reads (remaining=3602)
[2026-05-28T22:54:23] Filtering fusions with an e-value >=0.3 (remaining=481)
[2026-05-28T22:54:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=495)
[2026-05-28T22:54:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=349)
[2026-05-28T22:54:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=349)
[2026-05-28T22:54:42] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=349)
[2026-05-28T22:55:04] Searching for fusions with spliced split reads (remaining=365)
[2026-05-28T22:55:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=290)
[2026-05-28T22:55:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=284)
[2026-05-28T22:55:28] Searching for fusions with >=4 spliced events (remaining=300)
[2026-05-28T22:55:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=129)
[2026-05-28T22:55:49] Filtering fusions with anchors <=23nt (remaining=94)
[2026-05-28T22:55:50] Filtering end-to-end fusions with low support (remaining=89)
[2026-05-28T22:55:51] Filtering fusions with no coverage around the breakpoints (remaining=88)
[2026-05-28T22:55:51] Indexing gene sequences 
[2026-05-28T22:55:53] Filtering genes with >=30% identity (remaining=46)
[2026-05-28T22:55:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=18)
[2026-05-28T22:55:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=7)
[2026-05-28T22:55:57] Searching for additional isoforms (remaining=7)
[2026-05-28T22:55:59] Assigning confidence scores to events 
[2026-05-28T22:56:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T22:56:03] Writing fusions to file 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T22:56:03] Writing discarded fusions to file 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T22:56:33] Freeing resources
[2026-05-28T22:58:36] Done (elapsed time=00:37:57, CPU time=00:37:57, peak memory=103gb)