[2026-05-28T00:02:05] Launching Arriba 2.4.0
[2026-05-28T00:02:05] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:02:14] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:02:19] Reading chimeric alignments from 'tih_rna_sample_00116_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=4126664)
[2026-05-28T00:04:50] Marking multi-mapping alignments (marked=2619025)
[2026-05-28T00:04:52] Detecting strandedness (reverse)
[2026-05-28T00:04:52] Assigning strands to alignments 
[2026-05-28T00:04:53] Annotating alignments 
[2026-05-28T00:05:11] Filtering duplicates (remaining=2469912)
[2026-05-28T00:05:16] 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=2336867)
[2026-05-28T00:05:17] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2336867)
[2026-05-28T00:05:18] Filtering viral contigs with expression lower than the top 5 (remaining=2336867)
[2026-05-28T00:05:20] Filtering viral contigs with less than 5% coverage (remaining=2336867)
[2026-05-28T00:05:21] Estimating fragment length (mate gap mean=-86.5287, mate gap stddev=26.9363, read length mean=123.898)
[2026-05-28T00:05:21] Filtering read-through fragments with a distance <=10000bp (remaining=2140666)
[2026-05-28T00:05:22] Filtering inconsistently clipped mates (remaining=2099326)
[2026-05-28T00:05:23] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2054000)
[2026-05-28T00:05:25] Filtering fragments with small insert size (remaining=2053491)
[2026-05-28T00:05:26] Filtering alignments with long gaps (remaining=2053491)
[2026-05-28T00:05:27] Filtering fragments with both mates in the same gene (remaining=2053036)
[2026-05-28T00:05:28] Filtering fusions arising from hairpin structures (remaining=1943188)
[2026-05-28T00:05:30] Filtering reads with a mismatch p-value <=0.01 (remaining=797449)
[2026-05-28T00:05:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=403819)
[2026-05-28T00:05:40] Finding fusions and counting supporting reads (total=362838)
[2026-05-28T00:05:53] Merging adjacent fusion breakpoints (remaining=358846)
[2026-05-28T00:05:55] Filtering multi-mapping fusions by alignment score and read support (remaining=222482)
[2026-05-28T00:06:16] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:06:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=221842)
[2026-05-28T00:06:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=110477)
[2026-05-28T00:06:20] Filtering fusions with <2 supporting reads (remaining=12062)
[2026-05-28T00:06:21] Filtering fusions with an e-value >=0.3 (remaining=3112)
[2026-05-28T00:06:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3156)
[2026-05-28T00:06:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3112)
[2026-05-28T00:06:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3112)
[2026-05-28T00:06:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3043)
[2026-05-28T00:06:27] Searching for fusions with spliced split reads (remaining=3077)
[2026-05-28T00:06:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=2345)
[2026-05-28T00:06:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2314)
[2026-05-28T00:06:32] Searching for fusions with >=4 spliced events (remaining=2522)
[2026-05-28T00:06:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=927)
[2026-05-28T00:06:53] Filtering fusions with anchors <=23nt (remaining=697)
[2026-05-28T00:06:54] Filtering end-to-end fusions with low support (remaining=673)
[2026-05-28T00:06:54] Filtering fusions with no coverage around the breakpoints (remaining=649)
[2026-05-28T00:06:55] Indexing gene sequences 
[2026-05-28T00:06:59] Filtering genes with >=30% identity (remaining=228)
[2026-05-28T00:07:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=91)
[2026-05-28T00:07:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=91)
[2026-05-28T00:07:02] Searching for additional isoforms (remaining=106)
[2026-05-28T00:07:03] Assigning confidence scores to events 
[2026-05-28T00:07:05] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:07:05] Writing fusions to file 'tih_rna_sample_00116_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:07:06] Writing discarded fusions to file 'tih_rna_sample_00116_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:07:25] Freeing resources
[2026-05-28T00:07:34] Done (elapsed time=00:05:29, CPU time=00:05:27, peak memory=8.47gb)