[2026-05-28T00:05:44] Launching Arriba 2.4.0
[2026-05-28T00:05:44] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:53] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:05:57] Reading chimeric alignments from 'tih_rna_sample_00161_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3517645)
[2026-05-28T00:08:19] Marking multi-mapping alignments (marked=2267358)
[2026-05-28T00:08:20] Detecting strandedness (reverse)
[2026-05-28T00:08:20] Assigning strands to alignments 
[2026-05-28T00:08:21] Annotating alignments 
[2026-05-28T00:08:34] Filtering duplicates (remaining=2224730)
[2026-05-28T00:08:36] 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=2099554)
[2026-05-28T00:08:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2099554)
[2026-05-28T00:08:38] Filtering viral contigs with expression lower than the top 5 (remaining=2099554)
[2026-05-28T00:08:39] Filtering viral contigs with less than 5% coverage (remaining=2099554)
[2026-05-28T00:08:40] Estimating fragment length (mate gap mean=-88.5443, mate gap stddev=27.796, read length mean=130.95)
[2026-05-28T00:08:40] Filtering read-through fragments with a distance <=10000bp (remaining=1927473)
[2026-05-28T00:08:41] Filtering inconsistently clipped mates (remaining=1892684)
[2026-05-28T00:08:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1849502)
[2026-05-28T00:08:44] Filtering fragments with small insert size (remaining=1849164)
[2026-05-28T00:08:45] Filtering alignments with long gaps (remaining=1849164)
[2026-05-28T00:08:46] Filtering fragments with both mates in the same gene (remaining=1848779)
[2026-05-28T00:08:47] Filtering fusions arising from hairpin structures (remaining=1741309)
[2026-05-28T00:08:48] Filtering reads with a mismatch p-value <=0.01 (remaining=752813)
[2026-05-28T00:08:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=364738)
[2026-05-28T00:08:57] Finding fusions and counting supporting reads (total=314541)
[2026-05-28T00:09:04] Merging adjacent fusion breakpoints (remaining=312363)
[2026-05-28T00:09:04] Filtering multi-mapping fusions by alignment score and read support (remaining=191950)
[2026-05-28T00:09:19] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:09:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=190921)
[2026-05-28T00:09:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=97955)
[2026-05-28T00:09:22] Filtering fusions with <2 supporting reads (remaining=11029)
[2026-05-28T00:09:23] Filtering fusions with an e-value >=0.3 (remaining=3026)
[2026-05-28T00:09:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3069)
[2026-05-28T00:09:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3034)
[2026-05-28T00:09:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3034)
[2026-05-28T00:09:25] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2704)
[2026-05-28T00:09:27] Searching for fusions with spliced split reads (remaining=2748)
[2026-05-28T00:09:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=2070)
[2026-05-28T00:09:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2045)
[2026-05-28T00:09:30] Searching for fusions with >=4 spliced events (remaining=2317)
[2026-05-28T00:09:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=931)
[2026-05-28T00:09:41] Filtering fusions with anchors <=23nt (remaining=807)
[2026-05-28T00:09:42] Filtering end-to-end fusions with low support (remaining=788)
[2026-05-28T00:09:42] Filtering fusions with no coverage around the breakpoints (remaining=764)
[2026-05-28T00:09:42] Indexing gene sequences 
[2026-05-28T00:09:48] Filtering genes with >=30% identity (remaining=414)
[2026-05-28T00:09:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=317)
[2026-05-28T00:09:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=255)
[2026-05-28T00:09:54] Searching for additional isoforms (remaining=309)
[2026-05-28T00:09:55] Assigning confidence scores to events 
[2026-05-28T00:09:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:09:56] Writing fusions to file 'tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:09:58] Writing discarded fusions to file 'tih_rna_sample_00161_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:10:15] Freeing resources
[2026-05-28T00:10:22] Done (elapsed time=00:04:38, CPU time=00:04:36, peak memory=7.88gb)