[2026-06-08T07:23:44] Launching Arriba 2.4.0
[2026-06-08T07:23:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:24:01] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:24:07] Reading chimeric alignments from 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=633052)
[2026-06-08T07:24:16] Marking multi-mapping alignments (marked=566908)
[2026-06-08T07:24:16] Detecting strandedness (no)
[2026-06-08T07:24:16] Annotating alignments 
[2026-06-08T07:24:19] Filtering duplicates (remaining=319568)
[2026-06-08T07:24:19] 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=268346)
[2026-06-08T07:24:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=268346)
[2026-06-08T07:24:20] Filtering viral contigs with expression lower than the top 5 (remaining=268346)
[2026-06-08T07:24:20] Filtering viral contigs with less than 5% coverage (remaining=268346)
[2026-06-08T07:24:20] Estimating fragment length (mate gap mean=-26.2183, mate gap stddev=16.7193, read length mean=59.4773)
[2026-06-08T07:24:20] Filtering read-through fragments with a distance <=10000bp (remaining=266884)
[2026-06-08T07:24:20] Filtering inconsistently clipped mates (remaining=259107)
[2026-06-08T07:24:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=241475)
[2026-06-08T07:24:21] Filtering fragments with small insert size (remaining=241164)
[2026-06-08T07:24:21] Filtering alignments with long gaps (remaining=241164)
[2026-06-08T07:24:21] Filtering fragments with both mates in the same gene (remaining=240527)
[2026-06-08T07:24:21] Filtering fusions arising from hairpin structures (remaining=231155)
[2026-06-08T07:24:21] Filtering reads with a mismatch p-value <=0.01 (remaining=17731)
[2026-06-08T07:24:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=7129)
[2026-06-08T07:24:22] Finding fusions and counting supporting reads (total=7689)
[2026-06-08T07:24:22] Merging adjacent fusion breakpoints (remaining=7666)
[2026-06-08T07:24:22] Filtering multi-mapping fusions by alignment score and read support (remaining=3066)
[2026-06-08T07:24:24] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:24:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=2999)
[2026-06-08T07:24:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=2728)
[2026-06-08T07:24:25] Filtering fusions with <2 supporting reads (remaining=42)
[2026-06-08T07:24:25] Filtering fusions with an e-value >=0.3 (remaining=35)
[2026-06-08T07:24:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=35)
[2026-06-08T07:24:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10)
[2026-06-08T07:24:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10)
[2026-06-08T07:24:25] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9)
[2026-06-08T07:24:25] Searching for fusions with spliced split reads (remaining=9)
[2026-06-08T07:24:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=9)
[2026-06-08T07:24:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=9)
[2026-06-08T07:24:25] Searching for fusions with >=4 spliced events (remaining=9)
[2026-06-08T07:24:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4)
[2026-06-08T07:24:45] Filtering fusions with anchors <=23nt (remaining=0)
[2026-06-08T07:24:45] Filtering end-to-end fusions with low support (remaining=0)
[2026-06-08T07:24:45] Filtering fusions with no coverage around the breakpoints (remaining=0)
[2026-06-08T07:24:45] Indexing gene sequences 
[2026-06-08T07:24:45] Filtering genes with >=30% identity (remaining=0)
[2026-06-08T07:24:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-08T07:24:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:24:45] Searching for additional isoforms (remaining=0)
[2026-06-08T07:24:45] Assigning confidence scores to events 
[2026-06-08T07:24:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:24:46] Writing fusions to file 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:24:46] Writing discarded fusions to file 'OvarianN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:24:47] Freeing resources
[2026-06-08T07:24:49] Done (elapsed time=00:01:05, CPU time=00:01:04, peak memory=4.72gb)