[2026-06-08T08:14:59] Launching Arriba 2.4.0
[2026-06-08T08:14:59] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:12] Reading chimeric alignments from 'tih_rna_sample_00158_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=6184534)
[2026-06-08T08:18:49] Marking multi-mapping alignments (marked=4098854)
[2026-06-08T08:18:52] Detecting strandedness (reverse)
[2026-06-08T08:18:52] Assigning strands to alignments 
[2026-06-08T08:18:53] Annotating alignments 
[2026-06-08T08:19:13] Filtering duplicates (remaining=2835046)
[2026-06-08T08:19:16] 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=2666499)
[2026-06-08T08:19:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2666499)
[2026-06-08T08:19:18] Filtering viral contigs with expression lower than the top 5 (remaining=2666499)
[2026-06-08T08:19:21] Filtering viral contigs with less than 5% coverage (remaining=2666499)
[2026-06-08T08:19:22] Estimating fragment length (mate gap mean=-85.2177, mate gap stddev=29.957, read length mean=132.208)
[2026-06-08T08:19:22] Filtering read-through fragments with a distance <=10000bp (remaining=2530392)
[2026-06-08T08:19:24] Filtering inconsistently clipped mates (remaining=2492204)
[2026-06-08T08:19:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2410459)
[2026-06-08T08:19:27] Filtering fragments with small insert size (remaining=2409975)
[2026-06-08T08:19:28] Filtering alignments with long gaps (remaining=2409975)
[2026-06-08T08:19:29] Filtering fragments with both mates in the same gene (remaining=2409552)
[2026-06-08T08:19:30] Filtering fusions arising from hairpin structures (remaining=2298254)
[2026-06-08T08:19:31] Filtering reads with a mismatch p-value <=0.01 (remaining=972098)
[2026-06-08T08:19:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=338375)
[2026-06-08T08:19:42] Finding fusions and counting supporting reads (total=280438)
[2026-06-08T08:19:51] Merging adjacent fusion breakpoints (remaining=278668)
[2026-06-08T08:19:52] Filtering multi-mapping fusions by alignment score and read support (remaining=163997)
[2026-06-08T08:20:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:20:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=162421)
[2026-06-08T08:20:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90546)
[2026-06-08T08:20:14] Filtering fusions with <2 supporting reads (remaining=11595)
[2026-06-08T08:20:15] Filtering fusions with an e-value >=0.3 (remaining=3847)
[2026-06-08T08:20:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3873)
[2026-06-08T08:20:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3827)
[2026-06-08T08:20:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3828)
[2026-06-08T08:20:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2903)
[2026-06-08T08:20:20] Searching for fusions with spliced split reads (remaining=2949)
[2026-06-08T08:20:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=2036)
[2026-06-08T08:20:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2012)
[2026-06-08T08:20:24] Searching for fusions with >=4 spliced events (remaining=2184)
[2026-06-08T08:20:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=548)
[2026-06-08T08:20:37] Filtering fusions with anchors <=23nt (remaining=418)
[2026-06-08T08:20:37] Filtering end-to-end fusions with low support (remaining=403)
[2026-06-08T08:20:37] Filtering fusions with no coverage around the breakpoints (remaining=393)
[2026-06-08T08:20:38] Indexing gene sequences 
[2026-06-08T08:20:40] Filtering genes with >=30% identity (remaining=118)
[2026-06-08T08:20:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=43)
[2026-06-08T08:20:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=39)
[2026-06-08T08:20:42] Searching for additional isoforms (remaining=55)
[2026-06-08T08:20:43] Assigning confidence scores to events 
[2026-06-08T08:20:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:20:44] Writing fusions to file 'tih_rna_sample_00158_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:20:45] Writing discarded fusions to file 'tih_rna_sample_00158_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:20:58] Freeing resources
[2026-06-08T08:21:08] Done (elapsed time=00:06:09, CPU time=00:06:08, peak memory=10.4gb)