[2026-05-28T20:16:12] Launching Arriba 2.4.0
[2026-05-28T20:16:12] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:16:26] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:16:30] Reading chimeric alignments from 'OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=3825711)
[2026-05-28T20:17:55] Marking multi-mapping alignments (marked=3095272)
[2026-05-28T20:17:57] Detecting strandedness (reverse)
[2026-05-28T20:17:57] Assigning strands to alignments 
[2026-05-28T20:17:57] Annotating alignments 
[2026-05-28T20:18:11] Filtering duplicates (remaining=1046405)
[2026-05-28T20:18:13] 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=881939)
[2026-05-28T20:18:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=881939)
[2026-05-28T20:18:14] Filtering viral contigs with expression lower than the top 5 (remaining=881939)
[2026-05-28T20:18:15] Filtering viral contigs with less than 5% coverage (remaining=881939)
[2026-05-28T20:18:16] Estimating fragment length (mate gap mean=-55.0804, mate gap stddev=28.1824, read length mean=92.3185)
[2026-05-28T20:18:16] Filtering read-through fragments with a distance <=10000bp (remaining=870028)
[2026-05-28T20:18:17] Filtering inconsistently clipped mates (remaining=836468)
[2026-05-28T20:18:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=729708)
[2026-05-28T20:18:19] Filtering fragments with small insert size (remaining=728742)
[2026-05-28T20:18:19] Filtering alignments with long gaps (remaining=728742)
[2026-05-28T20:18:20] Filtering fragments with both mates in the same gene (remaining=728038)
[2026-05-28T20:18:21] Filtering fusions arising from hairpin structures (remaining=686175)
[2026-05-28T20:18:21] Filtering reads with a mismatch p-value <=0.01 (remaining=139845)
[2026-05-28T20:18:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=59173)
[2026-05-28T20:18:25] Finding fusions and counting supporting reads (total=62081)
[2026-05-28T20:18:29] Merging adjacent fusion breakpoints (remaining=61865)
[2026-05-28T20:18:29] Filtering multi-mapping fusions by alignment score and read support (remaining=22968)
[2026-05-28T20:18:40] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:18:41] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=22467)
[2026-05-28T20:18:41] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=20063)
[2026-05-28T20:18:42] Filtering fusions with <2 supporting reads (remaining=322)
[2026-05-28T20:18:42] Filtering fusions with an e-value >=0.3 (remaining=104)
[2026-05-28T20:18:42] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=105)
[2026-05-28T20:18:43] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=68)
[2026-05-28T20:18:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=68)
[2026-05-28T20:18:43] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=63)
[2026-05-28T20:18:44] Searching for fusions with spliced split reads (remaining=69)
[2026-05-28T20:18:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=57)
[2026-05-28T20:18:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=56)
[2026-05-28T20:18:46] Searching for fusions with >=4 spliced events (remaining=56)
[2026-05-28T20:18:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=19)
[2026-05-28T20:19:05] Filtering fusions with anchors <=23nt (remaining=14)
[2026-05-28T20:19:05] Filtering end-to-end fusions with low support (remaining=12)
[2026-05-28T20:19:05] Filtering fusions with no coverage around the breakpoints (remaining=9)
[2026-05-28T20:19:05] Indexing gene sequences 
[2026-05-28T20:19:05] Filtering genes with >=30% identity (remaining=3)
[2026-05-28T20:19:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:19:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:19:06] Searching for additional isoforms (remaining=0)
[2026-05-28T20:19:06] Assigning confidence scores to events 
[2026-05-28T20:19:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:19:07] Writing fusions to file 'OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:19:07] Writing discarded fusions to file 'OvarianNP_FFPE_L05_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:19:13] Freeing resources
[2026-05-28T20:19:21] Done (elapsed time=00:03:09, CPU time=00:03:08, peak memory=7.97gb)