[2026-06-08T08:36:07] Launching Arriba 2.4.0
[2026-06-08T08:36:07] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:21] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:25] Reading chimeric alignments from 'FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11798558)
[2026-06-08T08:44:02] Marking multi-mapping alignments (marked=7562703)
[2026-06-08T08:44:06] Detecting strandedness (reverse)
[2026-06-08T08:44:06] Assigning strands to alignments 
[2026-06-08T08:44:08] Annotating alignments 
[2026-06-08T08:44:42] Filtering duplicates (remaining=6912390)
[2026-06-08T08:44:49] 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=6619635)
[2026-06-08T08:44:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6619635)
[2026-06-08T08:44:54] Filtering viral contigs with expression lower than the top 5 (remaining=6619635)
[2026-06-08T08:45:00] Filtering viral contigs with less than 5% coverage (remaining=6619635)
[2026-06-08T08:45:02] Estimating fragment length (mate gap mean=-87.4565, mate gap stddev=31.357, read length mean=136.779)
[2026-06-08T08:45:02] Filtering read-through fragments with a distance <=10000bp (remaining=6380855)
[2026-06-08T08:45:05] Filtering inconsistently clipped mates (remaining=6300254)
[2026-06-08T08:45:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6132101)
[2026-06-08T08:45:12] Filtering fragments with small insert size (remaining=6131582)
[2026-06-08T08:45:14] Filtering alignments with long gaps (remaining=6131582)
[2026-06-08T08:45:16] Filtering fragments with both mates in the same gene (remaining=6130723)
[2026-06-08T08:45:19] Filtering fusions arising from hairpin structures (remaining=5851685)
[2026-06-08T08:45:22] Filtering reads with a mismatch p-value <=0.01 (remaining=2808010)
[2026-06-08T08:45:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=867324)
[2026-06-08T08:45:48] Finding fusions and counting supporting reads (total=609110)
[2026-06-08T08:46:06] Merging adjacent fusion breakpoints (remaining=603447)
[2026-06-08T08:46:08] Filtering multi-mapping fusions by alignment score and read support (remaining=382168)
[2026-06-08T08:46:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=380019)
[2026-06-08T08:46:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=217155)
[2026-06-08T08:46:54] Filtering fusions with <2 supporting reads (remaining=31744)
[2026-06-08T08:46:54] Filtering fusions with an e-value >=0.3 (remaining=10104)
[2026-06-08T08:46:55] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10149)
[2026-06-08T08:46:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10066)
[2026-06-08T08:47:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10091)
[2026-06-08T08:47:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7793)
[2026-06-08T08:47:06] Searching for fusions with spliced split reads (remaining=7915)
[2026-06-08T08:47:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=4263)
[2026-06-08T08:47:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4225)
[2026-06-08T08:47:14] Searching for fusions with >=4 spliced events (remaining=5136)
[2026-06-08T08:47:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2032)
[2026-06-08T08:47:36] Filtering fusions with anchors <=23nt (remaining=1545)
[2026-06-08T08:47:37] Filtering end-to-end fusions with low support (remaining=1492)
[2026-06-08T08:47:38] Filtering fusions with no coverage around the breakpoints (remaining=1444)
[2026-06-08T08:47:38] Indexing gene sequences 
[2026-06-08T08:47:45] Filtering genes with >=30% identity (remaining=361)
[2026-06-08T08:47:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=124)
[2026-06-08T08:47:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=120)
[2026-06-08T08:47:52] Searching for additional isoforms (remaining=152)
[2026-06-08T08:47:54] Assigning confidence scores to events 
[2026-06-08T08:47:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:57] Writing fusions to file 'FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:47:59] Writing discarded fusions to file 'FFPE_V4_0002_RNA_0001_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:30] Freeing resources
[2026-06-08T08:48:52] Done (elapsed time=00:12:45, CPU time=00:12:43, peak memory=16.1gb)