[2026-05-28T21:39:38] Launching Arriba 2.4.0
[2026-05-28T21:39:38] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:39:55] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:40:02] Reading chimeric alignments from 'OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=26950811)
[2026-05-28T21:52:00] Marking multi-mapping alignments (marked=21612941)
[2026-05-28T21:52:12] Detecting strandedness (no)
[2026-05-28T21:52:12] Annotating alignments 
[2026-05-28T21:54:35] Filtering duplicates (remaining=5442267)
[2026-05-28T21:54:52] 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=4088522)
[2026-05-28T21:54:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4088522)
[2026-05-28T21:55:04] Filtering viral contigs with expression lower than the top 5 (remaining=4088522)
[2026-05-28T21:55:16] Filtering viral contigs with less than 5% coverage (remaining=4088522)
[2026-05-28T21:55:22] Estimating fragment length (mate gap mean=-72.1998, mate gap stddev=29.8277, read length mean=105.097)
[2026-05-28T21:55:22] Filtering read-through fragments with a distance <=10000bp (remaining=3987101)
[2026-05-28T21:55:27] Filtering inconsistently clipped mates (remaining=3870541)
[2026-05-28T21:55:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3559863)
[2026-05-28T21:55:39] Filtering fragments with small insert size (remaining=3556735)
[2026-05-28T21:55:44] Filtering alignments with long gaps (remaining=3556735)
[2026-05-28T21:55:49] Filtering fragments with both mates in the same gene (remaining=3555006)
[2026-05-28T21:55:54] Filtering fusions arising from hairpin structures (remaining=3347474)
[2026-05-28T21:55:59] Filtering reads with a mismatch p-value <=0.01 (remaining=899082)
[2026-05-28T21:56:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=319410)
[2026-05-28T21:56:23] Finding fusions and counting supporting reads (total=266561)
[2026-05-28T21:56:52] Merging adjacent fusion breakpoints (remaining=262201)
[2026-05-28T21:56:53] Filtering multi-mapping fusions by alignment score and read support (remaining=121400)
[2026-05-28T21:58:01] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:58:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=119581)
[2026-05-28T21:58:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=86260)
[2026-05-28T21:58:09] Filtering fusions with <2 supporting reads (remaining=5052)
[2026-05-28T21:58:10] Filtering fusions with an e-value >=0.3 (remaining=1078)
[2026-05-28T21:58:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1090)
[2026-05-28T21:58:16] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=946)
[2026-05-28T21:58:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=946)
[2026-05-28T21:58:17] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=946)
[2026-05-28T21:58:25] Searching for fusions with spliced split reads (remaining=1026)
[2026-05-28T21:58:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=757)
[2026-05-28T21:58:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=742)
[2026-05-28T21:58:35] Searching for fusions with >=4 spliced events (remaining=789)
[2026-05-28T21:58:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=296)
[2026-05-28T21:58:52] Filtering fusions with anchors <=23nt (remaining=228)
[2026-05-28T21:58:53] Filtering end-to-end fusions with low support (remaining=212)
[2026-05-28T21:58:53] Filtering fusions with no coverage around the breakpoints (remaining=208)
[2026-05-28T21:58:54] Indexing gene sequences 
[2026-05-28T21:58:56] Filtering genes with >=30% identity (remaining=62)
[2026-05-28T21:58:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=20)
[2026-05-28T21:58:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=16)
[2026-05-28T21:58:59] Searching for additional isoforms (remaining=18)
[2026-05-28T21:59:00] Assigning confidence scores to events 
[2026-05-28T21:59:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:59:04] Writing fusions to file 'OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:59:04] Writing discarded fusions to file 'OvarianN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:59:39] Freeing resources
[2026-05-28T22:00:41] Done (elapsed time=00:21:03, CPU time=00:21:03, peak memory=31.5gb)