[2026-05-28T00:05:47] Launching Arriba 2.4.0
[2026-05-28T00:05:47] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:56] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:06:00] Reading chimeric alignments from 'tih_rna_sample_00480_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3514673)
[2026-05-28T00:08:14] Marking multi-mapping alignments (marked=2354759)
[2026-05-28T00:08:15] Detecting strandedness (reverse)
[2026-05-28T00:08:15] Assigning strands to alignments 
[2026-05-28T00:08:16] Annotating alignments 
[2026-05-28T00:08:28] Filtering duplicates (remaining=2119342)
[2026-05-28T00:08:31] 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=1976760)
[2026-05-28T00:08:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1976760)
[2026-05-28T00:08:32] Filtering viral contigs with expression lower than the top 5 (remaining=1976760)
[2026-05-28T00:08:33] Filtering viral contigs with less than 5% coverage (remaining=1976760)
[2026-05-28T00:08:34] Estimating fragment length (mate gap mean=-87.4018, mate gap stddev=28.6183, read length mean=131.176)
[2026-05-28T00:08:35] Filtering read-through fragments with a distance <=10000bp (remaining=1857174)
[2026-05-28T00:08:35] Filtering inconsistently clipped mates (remaining=1822378)
[2026-05-28T00:08:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1770760)
[2026-05-28T00:08:37] Filtering fragments with small insert size (remaining=1770431)
[2026-05-28T00:08:38] Filtering alignments with long gaps (remaining=1770431)
[2026-05-28T00:08:39] Filtering fragments with both mates in the same gene (remaining=1770101)
[2026-05-28T00:08:40] Filtering fusions arising from hairpin structures (remaining=1662190)
[2026-05-28T00:08:40] Filtering reads with a mismatch p-value <=0.01 (remaining=718461)
[2026-05-28T00:08:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=302385)
[2026-05-28T00:08:48] Finding fusions and counting supporting reads (total=258119)
[2026-05-28T00:08:55] Merging adjacent fusion breakpoints (remaining=256856)
[2026-05-28T00:08:55] Filtering multi-mapping fusions by alignment score and read support (remaining=155247)
[2026-05-28T00:09:07] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:09:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=154293)
[2026-05-28T00:09:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=84734)
[2026-05-28T00:09:10] Filtering fusions with <2 supporting reads (remaining=9856)
[2026-05-28T00:09:11] Filtering fusions with an e-value >=0.3 (remaining=2991)
[2026-05-28T00:09:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3028)
[2026-05-28T00:09:12] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3002)
[2026-05-28T00:09:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3002)
[2026-05-28T00:09:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2684)
[2026-05-28T00:09:15] Searching for fusions with spliced split reads (remaining=2734)
[2026-05-28T00:09:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=2056)
[2026-05-28T00:09:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2027)
[2026-05-28T00:09:17] Searching for fusions with >=4 spliced events (remaining=2261)
[2026-05-28T00:09:18] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=819)
[2026-05-28T00:09:29] Filtering fusions with anchors <=23nt (remaining=693)
[2026-05-28T00:09:29] Filtering end-to-end fusions with low support (remaining=677)
[2026-05-28T00:09:30] Filtering fusions with no coverage around the breakpoints (remaining=649)
[2026-05-28T00:09:30] Indexing gene sequences 
[2026-05-28T00:09:34] Filtering genes with >=30% identity (remaining=341)
[2026-05-28T00:09:36] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=255)
[2026-05-28T00:09:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=175)
[2026-05-28T00:09:38] Searching for additional isoforms (remaining=243)
[2026-05-28T00:09:38] Assigning confidence scores to events 
[2026-05-28T00:09:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:09:40] Writing fusions to file 'tih_rna_sample_00480_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:09:41] Writing discarded fusions to file 'tih_rna_sample_00480_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:53] Freeing resources
[2026-05-28T00:10:00] Done (elapsed time=00:04:13, CPU time=00:04:12, peak memory=7.83gb)