[2026-05-28T00:04:52] Launching Arriba 2.4.0
[2026-05-28T00:04:52] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:00] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:05:04] Reading chimeric alignments from 'tih_rna_sample_00096_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3201924)
[2026-05-28T00:07:17] Marking multi-mapping alignments (marked=2031959)
[2026-05-28T00:07:19] Detecting strandedness (reverse)
[2026-05-28T00:07:19] Assigning strands to alignments 
[2026-05-28T00:07:19] Annotating alignments 
[2026-05-28T00:07:31] Filtering duplicates (remaining=2337108)
[2026-05-28T00:07:33] 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=2230922)
[2026-05-28T00:07:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2230922)
[2026-05-28T00:07:34] Filtering viral contigs with expression lower than the top 5 (remaining=2230922)
[2026-05-28T00:07:36] Filtering viral contigs with less than 5% coverage (remaining=2230922)
[2026-05-28T00:07:37] Estimating fragment length (mate gap mean=-88.2424, mate gap stddev=29.0054, read length mean=134.039)
[2026-05-28T00:07:37] Filtering read-through fragments with a distance <=10000bp (remaining=2066501)
[2026-05-28T00:07:37] Filtering inconsistently clipped mates (remaining=2027840)
[2026-05-28T00:07:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1979661)
[2026-05-28T00:07:39] Filtering fragments with small insert size (remaining=1979373)
[2026-05-28T00:07:40] Filtering alignments with long gaps (remaining=1979373)
[2026-05-28T00:07:41] Filtering fragments with both mates in the same gene (remaining=1978910)
[2026-05-28T00:07:41] Filtering fusions arising from hairpin structures (remaining=1845467)
[2026-05-28T00:07:42] Filtering reads with a mismatch p-value <=0.01 (remaining=846078)
[2026-05-28T00:07:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=385669)
[2026-05-28T00:07:50] Finding fusions and counting supporting reads (total=325280)
[2026-05-28T00:07:56] Merging adjacent fusion breakpoints (remaining=323417)
[2026-05-28T00:07:57] Filtering multi-mapping fusions by alignment score and read support (remaining=208094)
[2026-05-28T00:08:08] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=206801)
[2026-05-28T00:08:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=105696)
[2026-05-28T00:08:11] Filtering fusions with <2 supporting reads (remaining=12112)
[2026-05-28T00:08:11] Filtering fusions with an e-value >=0.3 (remaining=4450)
[2026-05-28T00:08:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4500)
[2026-05-28T00:08:13] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4464)
[2026-05-28T00:08:13] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4464)
[2026-05-28T00:08:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2843)
[2026-05-28T00:08:15] Searching for fusions with spliced split reads (remaining=2903)
[2026-05-28T00:08:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=2052)
[2026-05-28T00:08:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2028)
[2026-05-28T00:08:18] Searching for fusions with >=4 spliced events (remaining=2289)
[2026-05-28T00:08:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=863)
[2026-05-28T00:08:30] Filtering fusions with anchors <=23nt (remaining=698)
[2026-05-28T00:08:30] Filtering end-to-end fusions with low support (remaining=679)
[2026-05-28T00:08:30] Filtering fusions with no coverage around the breakpoints (remaining=652)
[2026-05-28T00:08:31] Indexing gene sequences 
[2026-05-28T00:08:34] Filtering genes with >=30% identity (remaining=232)
[2026-05-28T00:08:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=135)
[2026-05-28T00:08:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=130)
[2026-05-28T00:08:38] Searching for additional isoforms (remaining=155)
[2026-05-28T00:08:38] Assigning confidence scores to events 
[2026-05-28T00:08:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:39] Writing fusions to file 'tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:08:40] Writing discarded fusions to file 'tih_rna_sample_00096_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:08:53] Freeing resources
[2026-05-28T00:08:59] Done (elapsed time=00:04:07, CPU time=00:04:07, peak memory=7.58gb)