[2026-06-08T08:53:37] Launching Arriba 2.4.0
[2026-06-08T08:53:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:53] Reading chimeric alignments from 'FFPE_V4_0002_RNA_0006_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam' (total=12490960)
[2026-06-08T09:01:08] Marking multi-mapping alignments (marked=7979843)
[2026-06-08T09:01:13] Detecting strandedness (reverse)
[2026-06-08T09:01:13] Assigning strands to alignments 
[2026-06-08T09:01:15] Annotating alignments 
[2026-06-08T09:01:51] Filtering duplicates (remaining=7159743)
[2026-06-08T09:01:59] 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=6790968)
[2026-06-08T09:02:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6790968)
[2026-06-08T09:02:03] Filtering viral contigs with expression lower than the top 5 (remaining=6790968)
[2026-06-08T09:02:08] Filtering viral contigs with less than 5% coverage (remaining=6790968)
[2026-06-08T09:02:11] Estimating fragment length (mate gap mean=-88.513, mate gap stddev=33.3394, read length mean=139.607)
[2026-06-08T09:02:11] Filtering read-through fragments with a distance <=10000bp (remaining=6516517)
[2026-06-08T09:02:13] Filtering inconsistently clipped mates (remaining=6424997)
[2026-06-08T09:02:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6214320)
[2026-06-08T09:02:19] Filtering fragments with small insert size (remaining=6213577)
[2026-06-08T09:02:22] Filtering alignments with long gaps (remaining=6213577)
[2026-06-08T09:02:24] Filtering fragments with both mates in the same gene (remaining=6212616)
[2026-06-08T09:02:26] Filtering fusions arising from hairpin structures (remaining=5870809)
[2026-06-08T09:02:29] Filtering reads with a mismatch p-value <=0.01 (remaining=3031127)
[2026-06-08T09:02:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=938529)
[2026-06-08T09:02:54] Finding fusions and counting supporting reads (total=700215)
[2026-06-08T09:03:11] Merging adjacent fusion breakpoints (remaining=694103)
[2026-06-08T09:03:12] Filtering multi-mapping fusions by alignment score and read support (remaining=438812)
[2026-06-08T09:03:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:03:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=435642)
[2026-06-08T09:03:52] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=252532)
[2026-06-08T09:03:53] Filtering fusions with <2 supporting reads (remaining=35885)
[2026-06-08T09:03:53] Filtering fusions with an e-value >=0.3 (remaining=13423)
[2026-06-08T09:03:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13463)
[2026-06-08T09:03:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13361)
[2026-06-08T09:03:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13379)
[2026-06-08T09:04:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8885)
[2026-06-08T09:04:05] Searching for fusions with spliced split reads (remaining=8906)
[2026-06-08T09:04:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=4320)
[2026-06-08T09:04:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4271)
[2026-06-08T09:04:13] Searching for fusions with >=4 spliced events (remaining=5269)
[2026-06-08T09:04:14] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2070)
[2026-06-08T09:04:29] Filtering fusions with anchors <=23nt (remaining=1563)
[2026-06-08T09:04:30] Filtering end-to-end fusions with low support (remaining=1499)
[2026-06-08T09:04:31] Filtering fusions with no coverage around the breakpoints (remaining=1443)
[2026-06-08T09:04:31] Indexing gene sequences 
[2026-06-08T09:04:36] Filtering genes with >=30% identity (remaining=365)
[2026-06-08T09:04:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=118)
[2026-06-08T09:04:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=113)
[2026-06-08T09:04:43] Searching for additional isoforms (remaining=153)
[2026-06-08T09:04:44] Assigning confidence scores to events 
[2026-06-08T09:04:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:04:47] Writing fusions to file 'FFPE_V4_0002_RNA_0006_A23MVY2LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:04:48] Writing discarded fusions to file 'FFPE_V4_0002_RNA_0006_A23MVY2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:13] Freeing resources
[2026-06-08T09:05:32] Done (elapsed time=00:11:55, CPU time=00:11:54, peak memory=17gb)