[2026-06-08T08:36:56] Launching Arriba 2.4.0
[2026-06-08T08:36:56] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:37:05] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:37:10] Reading chimeric alignments from 'FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=10256503)
[2026-06-08T08:46:53] Marking multi-mapping alignments (marked=6503243)
[2026-06-08T08:47:00] Detecting strandedness (reverse)
[2026-06-08T08:47:00] Assigning strands to alignments 
[2026-06-08T08:47:04] Annotating alignments 
[2026-06-08T08:47:59] Filtering duplicates (remaining=7089557)
[2026-06-08T08:48:11] 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=6649134)
[2026-06-08T08:48:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6649134)
[2026-06-08T08:48:18] Filtering viral contigs with expression lower than the top 5 (remaining=6649134)
[2026-06-08T08:48:26] Filtering viral contigs with less than 5% coverage (remaining=6649134)
[2026-06-08T08:48:30] Estimating fragment length (mate gap mean=-83.748, mate gap stddev=34.3235, read length mean=139.466)
[2026-06-08T08:48:30] Filtering read-through fragments with a distance <=10000bp (remaining=6305194)
[2026-06-08T08:48:34] Filtering inconsistently clipped mates (remaining=6222767)
[2026-06-08T08:48:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5997589)
[2026-06-08T08:48:46] Filtering fragments with small insert size (remaining=5997057)
[2026-06-08T08:48:49] Filtering alignments with long gaps (remaining=5997057)
[2026-06-08T08:48:53] Filtering fragments with both mates in the same gene (remaining=5995661)
[2026-06-08T08:48:58] Filtering fusions arising from hairpin structures (remaining=5607868)
[2026-06-08T08:49:03] Filtering reads with a mismatch p-value <=0.01 (remaining=3123134)
[2026-06-08T08:49:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=1225111)
[2026-06-08T08:49:46] Finding fusions and counting supporting reads (total=862324)
[2026-06-08T08:50:24] Merging adjacent fusion breakpoints (remaining=853723)
[2026-06-08T08:50:28] Filtering multi-mapping fusions by alignment score and read support (remaining=564174)
[2026-06-08T08:51:25] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:51:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=556337)
[2026-06-08T08:51:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=310362)
[2026-06-08T08:51:42] Filtering fusions with <2 supporting reads (remaining=55614)
[2026-06-08T08:51:44] Filtering fusions with an e-value >=0.3 (remaining=24418)
[2026-06-08T08:51:45] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=24473)
[2026-06-08T08:51:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=24368)
[2026-06-08T08:51:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=24377)
[2026-06-08T08:51:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=11624)
[2026-06-08T08:52:04] Searching for fusions with spliced split reads (remaining=11715)
[2026-06-08T08:52:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=5423)
[2026-06-08T08:52:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5370)
[2026-06-08T08:52:16] Searching for fusions with >=4 spliced events (remaining=6819)
[2026-06-08T08:52:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2716)
[2026-06-08T08:52:45] Filtering fusions with anchors <=23nt (remaining=2282)
[2026-06-08T08:52:47] Filtering end-to-end fusions with low support (remaining=2218)
[2026-06-08T08:52:48] Filtering fusions with no coverage around the breakpoints (remaining=2158)
[2026-06-08T08:52:49] Indexing gene sequences 
[2026-06-08T08:53:08] Filtering genes with >=30% identity (remaining=761)
[2026-06-08T08:53:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=454)
[2026-06-08T08:53:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=308)
[2026-06-08T08:53:31] Searching for additional isoforms (remaining=491)
[2026-06-08T08:53:34] Assigning confidence scores to events 
[2026-06-08T08:53:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:41] Writing fusions to file 'FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:48] Writing discarded fusions to file 'FFPE_HD789_02_RNA_0015_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:49] Freeing resources
[2026-06-08T08:55:24] Done (elapsed time=00:18:28, CPU time=00:18:27, peak memory=15.1gb)