[2026-05-28T21:17:44] Launching Arriba 2.4.0
[2026-05-28T21:17:44] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:17:58] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:18:03] Reading chimeric alignments from 'OvarianND_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=11277809)
[2026-05-28T21:27:28] Marking multi-mapping alignments (marked=7497469)
[2026-05-28T21:27:33] Detecting strandedness (reverse)
[2026-05-28T21:27:33] Assigning strands to alignments 
[2026-05-28T21:27:36] Annotating alignments 
[2026-05-28T21:28:31] Filtering duplicates (remaining=5755674)
[2026-05-28T21:28:43] 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=5447508)
[2026-05-28T21:28:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5447508)
[2026-05-28T21:28:48] Filtering viral contigs with expression lower than the top 5 (remaining=5447508)
[2026-05-28T21:28:54] Filtering viral contigs with less than 5% coverage (remaining=5447508)
[2026-05-28T21:28:57] Estimating fragment length (mate gap mean=-82.3912, mate gap stddev=28.9947, read length mean=121.865)
[2026-05-28T21:28:57] Filtering read-through fragments with a distance <=10000bp (remaining=5210203)
[2026-05-28T21:29:00] Filtering inconsistently clipped mates (remaining=5115160)
[2026-05-28T21:29:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4888165)
[2026-05-28T21:29:07] Filtering fragments with small insert size (remaining=4887034)
[2026-05-28T21:29:09] Filtering alignments with long gaps (remaining=4887034)
[2026-05-28T21:29:12] Filtering fragments with both mates in the same gene (remaining=4885755)
[2026-05-28T21:29:15] Filtering fusions arising from hairpin structures (remaining=4635101)
[2026-05-28T21:29:18] Filtering reads with a mismatch p-value <=0.01 (remaining=2055839)
[2026-05-28T21:29:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=857645)
[2026-05-28T21:29:40] Finding fusions and counting supporting reads (total=635689)
[2026-05-28T21:30:02] Merging adjacent fusion breakpoints (remaining=629661)
[2026-05-28T21:30:04] Filtering multi-mapping fusions by alignment score and read support (remaining=358065)
[2026-05-28T21:30:56] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:31:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=356111)
[2026-05-28T21:31:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=213445)
[2026-05-28T21:31:11] Filtering fusions with <2 supporting reads (remaining=28320)
[2026-05-28T21:31:12] Filtering fusions with an e-value >=0.3 (remaining=7878)
[2026-05-28T21:31:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7932)
[2026-05-28T21:31:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7832)
[2026-05-28T21:31:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7832)
[2026-05-28T21:31:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5994)
[2026-05-28T21:31:30] Searching for fusions with spliced split reads (remaining=6092)
[2026-05-28T21:31:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=4077)
[2026-05-28T21:31:43] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4032)
[2026-05-28T21:31:44] Searching for fusions with >=4 spliced events (remaining=4615)
[2026-05-28T21:31:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1400)
[2026-05-28T21:32:17] Filtering fusions with anchors <=23nt (remaining=1142)
[2026-05-28T21:32:17] Filtering end-to-end fusions with low support (remaining=1114)
[2026-05-28T21:32:18] Filtering fusions with no coverage around the breakpoints (remaining=1091)
[2026-05-28T21:32:19] Indexing gene sequences 
[2026-05-28T21:32:33] Filtering genes with >=30% identity (remaining=310)
[2026-05-28T21:32:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=123)
[2026-05-28T21:32:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-05-28T21:32:45] Searching for additional isoforms (remaining=144)
[2026-05-28T21:32:47] Assigning confidence scores to events 
[2026-05-28T21:32:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:32:54] Writing fusions to file 'OvarianND_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:32:57] Writing discarded fusions to file 'OvarianND_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:33:54] Freeing resources
[2026-05-28T21:34:31] Done (elapsed time=00:16:47, CPU time=00:16:46, peak memory=15.8gb)