[2026-06-08T08:52:48] Launching Arriba 2.4.0
[2026-06-08T08:52:48] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:52:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:02] Reading chimeric alignments from 'FFPE_V4_0002_RNA_0001_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=13233614)
[2026-06-08T09:00:53] Marking multi-mapping alignments (marked=8604275)
[2026-06-08T09:00:59] Detecting strandedness (reverse)
[2026-06-08T09:00:59] Assigning strands to alignments 
[2026-06-08T09:01:02] Annotating alignments 
[2026-06-08T09:01:48] Filtering duplicates (remaining=6768836)
[2026-06-08T09:01:57] 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=6348819)
[2026-06-08T09:02:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6348819)
[2026-06-08T09:02:03] Filtering viral contigs with expression lower than the top 5 (remaining=6348819)
[2026-06-08T09:02:10] Filtering viral contigs with less than 5% coverage (remaining=6348819)
[2026-06-08T09:02:13] Estimating fragment length (mate gap mean=-85.5224, mate gap stddev=34.0503, read length mean=135.936)
[2026-06-08T09:02:13] Filtering read-through fragments with a distance <=10000bp (remaining=6105251)
[2026-06-08T09:02:16] Filtering inconsistently clipped mates (remaining=6011493)
[2026-06-08T09:02:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5782176)
[2026-06-08T09:02:24] Filtering fragments with small insert size (remaining=5781449)
[2026-06-08T09:02:27] Filtering alignments with long gaps (remaining=5781449)
[2026-06-08T09:02:30] Filtering fragments with both mates in the same gene (remaining=5780559)
[2026-06-08T09:02:33] Filtering fusions arising from hairpin structures (remaining=5443170)
[2026-06-08T09:02:37] Filtering reads with a mismatch p-value <=0.01 (remaining=2844776)
[2026-06-08T09:02:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=858857)
[2026-06-08T09:03:06] Finding fusions and counting supporting reads (total=629926)
[2026-06-08T09:03:27] Merging adjacent fusion breakpoints (remaining=623641)
[2026-06-08T09:03:29] Filtering multi-mapping fusions by alignment score and read support (remaining=381479)
[2026-06-08T09:04:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=378521)
[2026-06-08T09:04:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=223686)
[2026-06-08T09:04:22] Filtering fusions with <2 supporting reads (remaining=32677)
[2026-06-08T09:04:23] Filtering fusions with an e-value >=0.3 (remaining=12275)
[2026-06-08T09:04:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12319)
[2026-06-08T09:04:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12191)
[2026-06-08T09:04:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12211)
[2026-06-08T09:04:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8191)
[2026-06-08T09:04:36] Searching for fusions with spliced split reads (remaining=8340)
[2026-06-08T09:04:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=4285)
[2026-06-08T09:04:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4233)
[2026-06-08T09:04:45] Searching for fusions with >=4 spliced events (remaining=5040)
[2026-06-08T09:04:47] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1912)
[2026-06-08T09:05:03] Filtering fusions with anchors <=23nt (remaining=1412)
[2026-06-08T09:05:03] Filtering end-to-end fusions with low support (remaining=1362)
[2026-06-08T09:05:04] Filtering fusions with no coverage around the breakpoints (remaining=1294)
[2026-06-08T09:05:05] Indexing gene sequences 
[2026-06-08T09:05:11] Filtering genes with >=30% identity (remaining=367)
[2026-06-08T09:05:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=103)
[2026-06-08T09:05:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=97)
[2026-06-08T09:05:17] Searching for additional isoforms (remaining=131)
[2026-06-08T09:05:19] Assigning confidence scores to events 
[2026-06-08T09:05:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:22] Writing fusions to file 'FFPE_V4_0002_RNA_0001_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:24] Writing discarded fusions to file 'FFPE_V4_0002_RNA_0001_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:53] Freeing resources
[2026-06-08T09:06:15] Done (elapsed time=00:13:27, CPU time=00:13:26, peak memory=17.7gb)