[2026-05-28T00:14:41] Launching Arriba 2.4.0
[2026-05-28T00:14:41] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:14:54] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:14:59] Reading chimeric alignments from 'tih_rna_sample_00163_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3193214)
[2026-05-28T00:17:43] Marking multi-mapping alignments (marked=2000389)
[2026-05-28T00:17:45] Detecting strandedness (reverse)
[2026-05-28T00:17:45] Assigning strands to alignments 
[2026-05-28T00:17:45] Annotating alignments 
[2026-05-28T00:17:57] Filtering duplicates (remaining=2248810)
[2026-05-28T00:18:00] 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=2171581)
[2026-05-28T00:18:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2171581)
[2026-05-28T00:18:01] Filtering viral contigs with expression lower than the top 5 (remaining=2171581)
[2026-05-28T00:18:02] Filtering viral contigs with less than 5% coverage (remaining=2171581)
[2026-05-28T00:18:03] Estimating fragment length (mate gap mean=-85.7789, mate gap stddev=29.3698, read length mean=132.864)
[2026-05-28T00:18:03] Filtering read-through fragments with a distance <=10000bp (remaining=2017815)
[2026-05-28T00:18:04] Filtering inconsistently clipped mates (remaining=1984531)
[2026-05-28T00:18:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1937625)
[2026-05-28T00:18:06] Filtering fragments with small insert size (remaining=1937321)
[2026-05-28T00:18:06] Filtering alignments with long gaps (remaining=1937321)
[2026-05-28T00:18:07] Filtering fragments with both mates in the same gene (remaining=1936914)
[2026-05-28T00:18:07] Filtering fusions arising from hairpin structures (remaining=1821924)
[2026-05-28T00:18:08] Filtering reads with a mismatch p-value <=0.01 (remaining=859945)
[2026-05-28T00:18:12] Filtering reads with low entropy (k-mer content >=60%) (remaining=374441)
[2026-05-28T00:18:16] Finding fusions and counting supporting reads (total=316539)
[2026-05-28T00:18:22] Merging adjacent fusion breakpoints (remaining=314589)
[2026-05-28T00:18:22] Filtering multi-mapping fusions by alignment score and read support (remaining=200379)
[2026-05-28T00:18:33] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:18:35] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=199144)
[2026-05-28T00:18:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=103812)
[2026-05-28T00:18:36] Filtering fusions with <2 supporting reads (remaining=13757)
[2026-05-28T00:18:36] Filtering fusions with an e-value >=0.3 (remaining=5203)
[2026-05-28T00:18:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5247)
[2026-05-28T00:18:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5222)
[2026-05-28T00:18:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5222)
[2026-05-28T00:18:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3363)
[2026-05-28T00:18:40] Searching for fusions with spliced split reads (remaining=3405)
[2026-05-28T00:18:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=2289)
[2026-05-28T00:18:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2263)
[2026-05-28T00:18:43] Searching for fusions with >=4 spliced events (remaining=2493)
[2026-05-28T00:18:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=810)
[2026-05-28T00:18:59] Filtering fusions with anchors <=23nt (remaining=664)
[2026-05-28T00:18:59] Filtering end-to-end fusions with low support (remaining=652)
[2026-05-28T00:19:00] Filtering fusions with no coverage around the breakpoints (remaining=630)
[2026-05-28T00:19:00] Indexing gene sequences 
[2026-05-28T00:19:03] Filtering genes with >=30% identity (remaining=229)
[2026-05-28T00:19:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=136)
[2026-05-28T00:19:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=128)
[2026-05-28T00:19:13] Searching for additional isoforms (remaining=163)
[2026-05-28T00:19:13] Assigning confidence scores to events 
[2026-05-28T00:19:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:19:14] Writing fusions to file 'tih_rna_sample_00163_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:19:15] Writing discarded fusions to file 'tih_rna_sample_00163_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:19:29] Freeing resources
[2026-05-28T00:19:36] Done (elapsed time=00:04:55, CPU time=00:04:54, peak memory=7.51gb)