[2026-06-04T21:15:10] Launching Arriba 2.4.0
[2026-06-04T21:15:10] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:15:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:15:21] Reading chimeric alignments from 'FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.Aligned.sortedByCoord.out.bam' (total=10789522)
[2026-06-04T21:22:06] Marking multi-mapping alignments (marked=6828827)
[2026-06-04T21:22:10] Detecting strandedness (reverse)
[2026-06-04T21:22:10] Assigning strands to alignments 
[2026-06-04T21:22:13] Annotating alignments 
[2026-06-04T21:22:44] Filtering duplicates (remaining=6184743)
[2026-06-04T21:22:51] 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=5819662)
[2026-06-04T21:22:53] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5819662)
[2026-06-04T21:22:55] Filtering viral contigs with expression lower than the top 5 (remaining=5819662)
[2026-06-04T21:23:00] Filtering viral contigs with less than 5% coverage (remaining=5819662)
[2026-06-04T21:23:02] Estimating fragment length (mate gap mean=-89.3198, mate gap stddev=30.9626, read length mean=134.515)
[2026-06-04T21:23:03] Filtering read-through fragments with a distance <=10000bp (remaining=5561642)
[2026-06-04T21:23:05] Filtering inconsistently clipped mates (remaining=5470567)
[2026-06-04T21:23:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5293988)
[2026-06-04T21:23:11] Filtering fragments with small insert size (remaining=5293331)
[2026-06-04T21:23:13] Filtering alignments with long gaps (remaining=5293331)
[2026-06-04T21:23:16] Filtering fragments with both mates in the same gene (remaining=5292495)
[2026-06-04T21:23:18] Filtering fusions arising from hairpin structures (remaining=4977559)
[2026-06-04T21:23:21] Filtering reads with a mismatch p-value <=0.01 (remaining=2545044)
[2026-06-04T21:23:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=1032025)
[2026-06-04T21:23:48] Finding fusions and counting supporting reads (total=725189)
[2026-06-04T21:24:07] Merging adjacent fusion breakpoints (remaining=715172)
[2026-06-04T21:24:09] Filtering multi-mapping fusions by alignment score and read support (remaining=474926)
[2026-06-04T21:24:41] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:24:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=472878)
[2026-06-04T21:24:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=243197)
[2026-06-04T21:24:49] Filtering fusions with <2 supporting reads (remaining=33961)
[2026-06-04T21:24:49] Filtering fusions with an e-value >=0.3 (remaining=9611)
[2026-06-04T21:24:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9654)
[2026-06-04T21:24:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9556)
[2026-06-04T21:24:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9587)
[2026-06-04T21:24:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7492)
[2026-06-04T21:25:01] Searching for fusions with spliced split reads (remaining=7597)
[2026-06-04T21:25:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=4370)
[2026-06-04T21:25:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4329)
[2026-06-04T21:25:08] Searching for fusions with >=4 spliced events (remaining=5195)
[2026-06-04T21:25:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2115)
[2026-06-04T21:25:24] Filtering fusions with anchors <=23nt (remaining=1526)
[2026-06-04T21:25:24] Filtering end-to-end fusions with low support (remaining=1468)
[2026-06-04T21:25:25] Filtering fusions with no coverage around the breakpoints (remaining=1424)
[2026-06-04T21:25:26] Indexing gene sequences 
[2026-06-04T21:25:31] Filtering genes with >=30% identity (remaining=369)
[2026-06-04T21:25:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=121)
[2026-06-04T21:25:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=108)
[2026-06-04T21:25:38] Searching for additional isoforms (remaining=149)
[2026-06-04T21:25:39] Assigning confidence scores to events 
[2026-06-04T21:25:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:25:43] Writing fusions to file 'FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.arriba.fusions.tsv' 
[2026-06-04T21:25:44] Writing discarded fusions to file 'FFPE_V4_0001_RNA_0003_B23MHV2LT4_2.arriba.fusions.discarded.tsv'
[2026-06-04T21:26:07] Freeing resources
[2026-06-04T21:26:26] Done (elapsed time=00:11:16, CPU time=00:11:16, peak memory=15.5gb)