[2026-06-08T08:29:07] Launching Arriba 2.4.0
[2026-06-08T08:29:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:29:16] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:29:20] Reading chimeric alignments from 'RT4_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=12174411)
[2026-06-08T08:36:29] Marking multi-mapping alignments (marked=8243150)
[2026-06-08T08:36:34] Detecting strandedness (reverse)
[2026-06-08T08:36:34] Assigning strands to alignments 
[2026-06-08T08:36:37] Annotating alignments 
[2026-06-08T08:37:21] Filtering duplicates (remaining=8411430)
[2026-06-08T08:37:33] 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)
[2026-06-08T08:37:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7801417)
[2026-06-08T08:37:39] Filtering viral contigs with expression lower than the top 5 (remaining=7801417)
[2026-06-08T08:37:45] Filtering viral contigs with less than 5% coverage (remaining=7801417)
[2026-06-08T08:37:48] Estimating fragment length (mate gap mean=-86.0219, mate gap stddev=29.5657, read length mean=129.61)
[2026-06-08T08:37:48] Filtering read-through fragments with a distance <=10000bp (remaining=7443913)
[2026-06-08T08:37:52] Filtering inconsistently clipped mates (remaining=7307464)
[2026-06-08T08:37:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7003931)
[2026-06-08T08:38:03] Filtering fragments with small insert size (remaining=7002552)
[2026-06-08T08:38:07] Filtering alignments with long gaps (remaining=7002552)
[2026-06-08T08:38:10] Filtering fragments with both mates in the same gene (remaining=7000963)
[2026-06-08T08:38:15] Filtering fusions arising from hairpin structures (remaining=6511158)
[2026-06-08T08:38:20] Filtering reads with a mismatch p-value <=0.01 (remaining=3067361)
[2026-06-08T08:38:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=1248101)
[2026-06-08T08:38:53] Finding fusions and counting supporting reads (total=992132)
[2026-06-08T08:39:17] Merging adjacent fusion breakpoints (remaining=984901)
[2026-06-08T08:39:19] Filtering multi-mapping fusions by alignment score and read support (remaining=597697)
[2026-06-08T08:40:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=594784)
[2026-06-08T08:40:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=369943)
[2026-06-08T08:40:16] Filtering fusions with <2 supporting reads (remaining=35096)
[2026-06-08T08:40:17] Filtering fusions with an e-value >=0.3 (remaining=8166)
[2026-06-08T08:40:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8215)
[2026-06-08T08:40:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8016)
[2026-06-08T08:40:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8062)
[2026-06-08T08:40:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6340)
[2026-06-08T08:40:34] Searching for fusions with spliced split reads (remaining=6355)
[2026-06-08T08:40:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=4054)
[2026-06-08T08:40:45] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4025)
[2026-06-08T08:40:46] Searching for fusions with >=4 spliced events (remaining=5134)
[2026-06-08T08:40:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2219)
[2026-06-08T08:41:05] Filtering fusions with anchors <=23nt (remaining=1760)
[2026-06-08T08:41:07] Filtering end-to-end fusions with low support (remaining=1726)
[2026-06-08T08:41:08] Filtering fusions with no coverage around the breakpoints (remaining=1713)
[2026-06-08T08:41:09] Indexing gene sequences 
[2026-06-08T08:41:15] Filtering genes with >=30% identity (remaining=437)
[2026-06-08T08:41:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=189)
[2026-06-08T08:41:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=126)
[2026-06-08T08:41:25] Searching for additional isoforms (remaining=211)
[2026-06-08T08:41:27] Assigning confidence scores to events 
[2026-06-08T08:41:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:33] Writing fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:41:35] Writing discarded fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:24] Freeing resources
[2026-06-08T08:42:53] Done (elapsed time=00:13:46, CPU time=00:13:44, peak memory=17.1gb)