[2026-05-28T21:26:53] Launching Arriba 2.4.0
[2026-05-28T21:26:53] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:27:07] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:27:11] Reading chimeric alignments from 'RT4_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=12174411)
[2026-05-28T21:35:31] Marking multi-mapping alignments (marked=8243150)
[2026-05-28T21:35:36] Detecting strandedness (reverse)
[2026-05-28T21:35:36] Assigning strands to alignments 
[2026-05-28T21:35:38] Annotating alignments 
[2026-05-28T21:36:17] Filtering duplicates (remaining=8411430)
[2026-05-28T21:36:25] 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=7801417)
[2026-05-28T21:36:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7801417)
[2026-05-28T21:36:29] Filtering viral contigs with expression lower than the top 5 (remaining=7801417)
[2026-05-28T21:36:35] Filtering viral contigs with less than 5% coverage (remaining=7801417)
[2026-05-28T21:36:37] Estimating fragment length (mate gap mean=-86.0219, mate gap stddev=29.5657, read length mean=129.61)
[2026-05-28T21:36:37] Filtering read-through fragments with a distance <=10000bp (remaining=7443913)
[2026-05-28T21:36:39] Filtering inconsistently clipped mates (remaining=7307464)
[2026-05-28T21:36:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7003931)
[2026-05-28T21:36:47] Filtering fragments with small insert size (remaining=7002552)
[2026-05-28T21:36:49] Filtering alignments with long gaps (remaining=7002552)
[2026-05-28T21:36:51] Filtering fragments with both mates in the same gene (remaining=7000963)
[2026-05-28T21:36:54] Filtering fusions arising from hairpin structures (remaining=6511158)
[2026-05-28T21:36:56] Filtering reads with a mismatch p-value <=0.01 (remaining=3067361)
[2026-05-28T21:37:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=1248101)
[2026-05-28T21:37:28] Finding fusions and counting supporting reads (total=992132)
[2026-05-28T21:37:48] Merging adjacent fusion breakpoints (remaining=984901)
[2026-05-28T21:37:50] Filtering multi-mapping fusions by alignment score and read support (remaining=597697)
[2026-05-28T21:38:27] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:38:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=594784)
[2026-05-28T21:38:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=369943)
[2026-05-28T21:38:38] Filtering fusions with <2 supporting reads (remaining=35096)
[2026-05-28T21:38:39] Filtering fusions with an e-value >=0.3 (remaining=8166)
[2026-05-28T21:38:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8215)
[2026-05-28T21:38:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8016)
[2026-05-28T21:38:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8062)
[2026-05-28T21:38:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6340)
[2026-05-28T21:38:53] Searching for fusions with spliced split reads (remaining=6355)
[2026-05-28T21:38:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=4054)
[2026-05-28T21:39:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4025)
[2026-05-28T21:39:02] Searching for fusions with >=4 spliced events (remaining=5134)
[2026-05-28T21:39:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2219)
[2026-05-28T21:39:21] Filtering fusions with anchors <=23nt (remaining=1760)
[2026-05-28T21:39:22] Filtering end-to-end fusions with low support (remaining=1726)
[2026-05-28T21:39:23] Filtering fusions with no coverage around the breakpoints (remaining=1713)
[2026-05-28T21:39:23] Indexing gene sequences 
[2026-05-28T21:39:30] Filtering genes with >=30% identity (remaining=437)
[2026-05-28T21:39:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=189)
[2026-05-28T21:39:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=126)
[2026-05-28T21:39:38] Searching for additional isoforms (remaining=211)
[2026-05-28T21:39:40] Assigning confidence scores to events 
[2026-05-28T21:39:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:39:45] Writing fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T21:39:47] Writing discarded fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T21:40:25] Freeing resources
[2026-05-28T21:40:45] Done (elapsed time=00:13:52, CPU time=00:13:51, peak memory=17.1gb)