[2026-06-04T21:15:46] Launching Arriba 2.4.0
[2026-06-04T21:15:46] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:15:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:15:58] Reading chimeric alignments from 'FFPE_HD789_02_RNA_0014_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=11601475)
[2026-06-04T21:22:55] Marking multi-mapping alignments (marked=7477591)
[2026-06-04T21:22:59] Detecting strandedness (reverse)
[2026-06-04T21:22:59] Assigning strands to alignments 
[2026-06-04T21:23:01] Annotating alignments 
[2026-06-04T21:23:35] Filtering duplicates (remaining=8038442)
[2026-06-04T21:23:43] 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=7516004)
[2026-06-04T21:23:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7516004)
[2026-06-04T21:23:47] Filtering viral contigs with expression lower than the top 5 (remaining=7516004)
[2026-06-04T21:23:53] Filtering viral contigs with less than 5% coverage (remaining=7516004)
[2026-06-04T21:23:55] Estimating fragment length (mate gap mean=-82.1779, mate gap stddev=33.4096, read length mean=134.98)
[2026-06-04T21:23:55] Filtering read-through fragments with a distance <=10000bp (remaining=7201893)
[2026-06-04T21:23:58] Filtering inconsistently clipped mates (remaining=7106936)
[2026-06-04T21:24:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6910534)
[2026-06-04T21:24:04] Filtering fragments with small insert size (remaining=6909681)
[2026-06-04T21:24:07] Filtering alignments with long gaps (remaining=6909680)
[2026-06-04T21:24:09] Filtering fragments with both mates in the same gene (remaining=6908177)
[2026-06-04T21:24:12] Filtering fusions arising from hairpin structures (remaining=6496903)
[2026-06-04T21:24:15] Filtering reads with a mismatch p-value <=0.01 (remaining=3513409)
[2026-06-04T21:24:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=1252588)
[2026-06-04T21:24:44] Finding fusions and counting supporting reads (total=889917)
[2026-06-04T21:25:02] Merging adjacent fusion breakpoints (remaining=883821)
[2026-06-04T21:25:04] Filtering multi-mapping fusions by alignment score and read support (remaining=582085)
[2026-06-04T21:25:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:25:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=576707)
[2026-06-04T21:25:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=351236)
[2026-06-04T21:25:50] Filtering fusions with <2 supporting reads (remaining=49323)
[2026-06-04T21:25:51] Filtering fusions with an e-value >=0.3 (remaining=17876)
[2026-06-04T21:25:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17934)
[2026-06-04T21:25:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=17853)
[2026-06-04T21:25:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17866)
[2026-06-04T21:25:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9823)
[2026-06-04T21:26:04] Searching for fusions with spliced split reads (remaining=9875)
[2026-06-04T21:26:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=5008)
[2026-06-04T21:26:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4959)
[2026-06-04T21:26:13] Searching for fusions with >=4 spliced events (remaining=6197)
[2026-06-04T21:26:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2535)
[2026-06-04T21:26:28] Filtering fusions with anchors <=23nt (remaining=2020)
[2026-06-04T21:26:29] Filtering end-to-end fusions with low support (remaining=1962)
[2026-06-04T21:26:30] Filtering fusions with no coverage around the breakpoints (remaining=1920)
[2026-06-04T21:26:31] Indexing gene sequences 
[2026-06-04T21:26:38] Filtering genes with >=30% identity (remaining=701)
[2026-06-04T21:26:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=438)
[2026-06-04T21:26:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=303)
[2026-06-04T21:26:50] Searching for additional isoforms (remaining=453)
[2026-06-04T21:26:51] Assigning confidence scores to events 
[2026-06-04T21:26:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:26:55] Writing fusions to file 'FFPE_HD789_02_RNA_0014_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:26:59] Writing discarded fusions to file 'FFPE_HD789_02_RNA_0014_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:27:29] Freeing resources
[2026-06-04T21:27:49] Done (elapsed time=00:12:03, CPU time=00:12:02, peak memory=16.2gb)