[2026-05-28T00:04:49] Launching Arriba 2.4.0
[2026-05-28T00:04:49] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:04:58] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:05:02] Reading chimeric alignments from 'FFPE_HD789_01_RNA_13_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3059429)
[2026-05-28T00:07:17] Marking multi-mapping alignments (marked=1967982)
[2026-05-28T00:07:19] Detecting strandedness (reverse)
[2026-05-28T00:07:19] Assigning strands to alignments 
[2026-05-28T00:07:19] Annotating alignments 
[2026-05-28T00:07:30] Filtering duplicates (remaining=2411270)
[2026-05-28T00:07:32] 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=2275313)
[2026-05-28T00:07:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2275313)
[2026-05-28T00:07:33] Filtering viral contigs with expression lower than the top 5 (remaining=2275313)
[2026-05-28T00:07:34] Filtering viral contigs with less than 5% coverage (remaining=2275313)
[2026-05-28T00:07:35] Estimating fragment length (mate gap mean=-84.7239, mate gap stddev=33.324, read length mean=139.526)
[2026-05-28T00:07:36] Filtering read-through fragments with a distance <=10000bp (remaining=2163109)
[2026-05-28T00:07:36] Filtering inconsistently clipped mates (remaining=2131794)
[2026-05-28T00:07:37] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2070917)
[2026-05-28T00:07:38] Filtering fragments with small insert size (remaining=2070749)
[2026-05-28T00:07:39] Filtering alignments with long gaps (remaining=2070749)
[2026-05-28T00:07:39] Filtering fragments with both mates in the same gene (remaining=2070322)
[2026-05-28T00:07:40] Filtering fusions arising from hairpin structures (remaining=1925816)
[2026-05-28T00:07:41] Filtering reads with a mismatch p-value <=0.01 (remaining=949796)
[2026-05-28T00:07:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=396231)
[2026-05-28T00:07:49] Finding fusions and counting supporting reads (total=312908)
[2026-05-28T00:07:55] Merging adjacent fusion breakpoints (remaining=310943)
[2026-05-28T00:07:56] Filtering multi-mapping fusions by alignment score and read support (remaining=205975)
[2026-05-28T00:08:06] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=203738)
[2026-05-28T00:08:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=119352)
[2026-05-28T00:08:09] Filtering fusions with <2 supporting reads (remaining=18211)
[2026-05-28T00:08:09] Filtering fusions with an e-value >=0.3 (remaining=7847)
[2026-05-28T00:08:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7898)
[2026-05-28T00:08:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7872)
[2026-05-28T00:08:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7874)
[2026-05-28T00:08:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4543)
[2026-05-28T00:08:13] Searching for fusions with spliced split reads (remaining=4624)
[2026-05-28T00:08:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=2741)
[2026-05-28T00:08:15] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2713)
[2026-05-28T00:08:16] Searching for fusions with >=4 spliced events (remaining=3056)
[2026-05-28T00:08:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1035)
[2026-05-28T00:08:27] Filtering fusions with anchors <=23nt (remaining=808)
[2026-05-28T00:08:28] Filtering end-to-end fusions with low support (remaining=779)
[2026-05-28T00:08:28] Filtering fusions with no coverage around the breakpoints (remaining=753)
[2026-05-28T00:08:28] Indexing gene sequences 
[2026-05-28T00:08:32] Filtering genes with >=30% identity (remaining=306)
[2026-05-28T00:08:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=211)
[2026-05-28T00:08:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=167)
[2026-05-28T00:08:35] Searching for additional isoforms (remaining=231)
[2026-05-28T00:08:36] Assigning confidence scores to events 
[2026-05-28T00:08:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:37] Writing fusions to file 'FFPE_HD789_01_RNA_13_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:08:39] Writing discarded fusions to file 'FFPE_HD789_01_RNA_13_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:51] Freeing resources
[2026-05-28T00:08:56] Done (elapsed time=00:04:07, CPU time=00:04:06, peak memory=7.36gb)