[2026-06-08T08:49:08] Launching Arriba 2.4.0
[2026-06-08T08:49:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:22] Reading chimeric alignments from 'FFPE_HD789_01_RNA_13_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11121182)
[2026-06-08T08:56:59] Marking multi-mapping alignments (marked=7129229)
[2026-06-08T08:57:04] Detecting strandedness (reverse)
[2026-06-08T08:57:04] Assigning strands to alignments 
[2026-06-08T08:57:06] Annotating alignments 
[2026-06-08T08:57:46] Filtering duplicates (remaining=7641828)
[2026-06-08T08:57:54] 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=7356125)
[2026-06-08T08:57:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7356125)
[2026-06-08T08:57:59] Filtering viral contigs with expression lower than the top 5 (remaining=7356125)
[2026-06-08T08:58:04] Filtering viral contigs with less than 5% coverage (remaining=7356125)
[2026-06-08T08:58:06] Estimating fragment length (mate gap mean=-85.4122, mate gap stddev=32.9853, read length mean=141.045)
[2026-06-08T08:58:07] Filtering read-through fragments with a distance <=10000bp (remaining=7098025)
[2026-06-08T08:58:09] Filtering inconsistently clipped mates (remaining=7024687)
[2026-06-08T08:58:11] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6836780)
[2026-06-08T08:58:16] Filtering fragments with small insert size (remaining=6836460)
[2026-06-08T08:58:18] Filtering alignments with long gaps (remaining=6836459)
[2026-06-08T08:58:20] Filtering fragments with both mates in the same gene (remaining=6835308)
[2026-06-08T08:58:23] Filtering fusions arising from hairpin structures (remaining=6536009)
[2026-06-08T08:58:25] Filtering reads with a mismatch p-value <=0.01 (remaining=3265810)
[2026-06-08T08:58:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=987797)
[2026-06-08T08:58:54] Finding fusions and counting supporting reads (total=681168)
[2026-06-08T08:59:14] Merging adjacent fusion breakpoints (remaining=676253)
[2026-06-08T08:59:16] Filtering multi-mapping fusions by alignment score and read support (remaining=449635)
[2026-06-08T08:59:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=445806)
[2026-06-08T09:00:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=267778)
[2026-06-08T09:00:04] Filtering fusions with <2 supporting reads (remaining=41897)
[2026-06-08T09:00:05] Filtering fusions with an e-value >=0.3 (remaining=15216)
[2026-06-08T09:00:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=15272)
[2026-06-08T09:00:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=15202)
[2026-06-08T09:00:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15211)
[2026-06-08T09:00:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9426)
[2026-06-08T09:00:19] Searching for fusions with spliced split reads (remaining=9465)
[2026-06-08T09:00:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=4950)
[2026-06-08T09:00:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4908)
[2026-06-08T09:00:27] Searching for fusions with >=4 spliced events (remaining=5983)
[2026-06-08T09:00:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2361)
[2026-06-08T09:00:44] Filtering fusions with anchors <=23nt (remaining=1901)
[2026-06-08T09:00:45] Filtering end-to-end fusions with low support (remaining=1855)
[2026-06-08T09:00:46] Filtering fusions with no coverage around the breakpoints (remaining=1808)
[2026-06-08T09:00:47] Indexing gene sequences 
[2026-06-08T09:00:54] Filtering genes with >=30% identity (remaining=643)
[2026-06-08T09:00:58] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=373)
[2026-06-08T09:01:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=272)
[2026-06-08T09:01:04] Searching for additional isoforms (remaining=391)
[2026-06-08T09:01:06] Assigning confidence scores to events 
[2026-06-08T09:01:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:10] Writing fusions to file 'FFPE_HD789_01_RNA_13_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:13] Writing discarded fusions to file 'FFPE_HD789_01_RNA_13_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:49] Freeing resources
[2026-06-08T09:02:11] Done (elapsed time=00:13:03, CPU time=00:13:02, peak memory=15.4gb)