[2026-06-08T08:51:39] Launching Arriba 2.4.0
[2026-06-08T08:51:39] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:51:55] Reading chimeric alignments from 'FFPE_V4_0002_RNA_0001_A23T55JLT4_1.Aligned.sortedByCoord.out.bam' (total=13612821)
[2026-06-08T09:00:01] Marking multi-mapping alignments (marked=8882321)
[2026-06-08T09:00:07] Detecting strandedness (reverse)
[2026-06-08T09:00:07] Assigning strands to alignments 
[2026-06-08T09:00:10] Annotating alignments 
[2026-06-08T09:00:58] Filtering duplicates (remaining=8330866)
[2026-06-08T09:01:09] 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=8034743)
[2026-06-08T09:01:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8034743)
[2026-06-08T09:01:16] Filtering viral contigs with expression lower than the top 5 (remaining=8034743)
[2026-06-08T09:01:23] Filtering viral contigs with less than 5% coverage (remaining=8034743)
[2026-06-08T09:01:26] Estimating fragment length (mate gap mean=-82.809, mate gap stddev=35.1432, read length mean=138.995)
[2026-06-08T09:01:27] Filtering read-through fragments with a distance <=10000bp (remaining=7793007)
[2026-06-08T09:01:30] Filtering inconsistently clipped mates (remaining=7694404)
[2026-06-08T09:01:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7434708)
[2026-06-08T09:01:38] Filtering fragments with small insert size (remaining=7433995)
[2026-06-08T09:01:42] Filtering alignments with long gaps (remaining=7433995)
[2026-06-08T09:01:45] Filtering fragments with both mates in the same gene (remaining=7433038)
[2026-06-08T09:01:48] Filtering fusions arising from hairpin structures (remaining=7114225)
[2026-06-08T09:01:52] Filtering reads with a mismatch p-value <=0.01 (remaining=3275791)
[2026-06-08T09:02:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=929620)
[2026-06-08T09:02:26] Finding fusions and counting supporting reads (total=709253)
[2026-06-08T09:02:56] Merging adjacent fusion breakpoints (remaining=704250)
[2026-06-08T09:02:59] Filtering multi-mapping fusions by alignment score and read support (remaining=441505)
[2026-06-08T09:03:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=438997)
[2026-06-08T09:04:05] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=265575)
[2026-06-08T09:04:08] Filtering fusions with <2 supporting reads (remaining=32398)
[2026-06-08T09:04:09] Filtering fusions with an e-value >=0.3 (remaining=11228)
[2026-06-08T09:04:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11272)
[2026-06-08T09:04:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11178)
[2026-06-08T09:04:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11191)
[2026-06-08T09:04:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7874)
[2026-06-08T09:04:30] Searching for fusions with spliced split reads (remaining=8005)
[2026-06-08T09:04:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=4123)
[2026-06-08T09:04:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4078)
[2026-06-08T09:04:40] Searching for fusions with >=4 spliced events (remaining=4937)
[2026-06-08T09:04:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1956)
[2026-06-08T09:04:58] Filtering fusions with anchors <=23nt (remaining=1472)
[2026-06-08T09:04:59] Filtering end-to-end fusions with low support (remaining=1415)
[2026-06-08T09:05:00] Filtering fusions with no coverage around the breakpoints (remaining=1369)
[2026-06-08T09:05:01] Indexing gene sequences 
[2026-06-08T09:05:08] Filtering genes with >=30% identity (remaining=330)
[2026-06-08T09:05:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=102)
[2026-06-08T09:05:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=96)
[2026-06-08T09:05:16] Searching for additional isoforms (remaining=131)
[2026-06-08T09:05:18] 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_A23T55JLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:24] Writing discarded fusions to file 'FFPE_V4_0002_RNA_0001_A23T55JLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:00] Freeing resources
[2026-06-08T09:06:24] Done (elapsed time=00:14:45, CPU time=00:14:44, peak memory=17.8gb)