[2026-05-28T00:05:46] Launching Arriba 2.4.0
[2026-05-28T00:05:46] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:05:54] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:05:58] Reading chimeric alignments from 'tih_rna_sample_00451_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=3596185)
[2026-05-28T00:08:19] Marking multi-mapping alignments (marked=2254590)
[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=2348161)
[2026-05-28T00:08:37] 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=2266097)
[2026-05-28T00:08:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2266097)
[2026-05-28T00:08:39] Filtering viral contigs with expression lower than the top 5 (remaining=2266097)
[2026-05-28T00:08:40] Filtering viral contigs with less than 5% coverage (remaining=2266097)
[2026-05-28T00:08:41] Estimating fragment length (mate gap mean=-88.6449, mate gap stddev=27.4929, read length mean=130.405)
[2026-05-28T00:08:41] Filtering read-through fragments with a distance <=10000bp (remaining=2055137)
[2026-05-28T00:08:42] Filtering inconsistently clipped mates (remaining=2016164)
[2026-05-28T00:08:43] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1967092)
[2026-05-28T00:08:45] Filtering fragments with small insert size (remaining=1966770)
[2026-05-28T00:08:46] Filtering alignments with long gaps (remaining=1966770)
[2026-05-28T00:08:46] Filtering fragments with both mates in the same gene (remaining=1966387)
[2026-05-28T00:08:47] Filtering fusions arising from hairpin structures (remaining=1851728)
[2026-05-28T00:08:48] Filtering reads with a mismatch p-value <=0.01 (remaining=828949)
[2026-05-28T00:08:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=440274)
[2026-05-28T00:08:58] Finding fusions and counting supporting reads (total=378978)
[2026-05-28T00:09:05] Merging adjacent fusion breakpoints (remaining=376421)
[2026-05-28T00:09:06] Filtering multi-mapping fusions by alignment score and read support (remaining=229368)
[2026-05-28T00:09:20] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:09:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=228061)
[2026-05-28T00:09:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=119334)
[2026-05-28T00:09:24] Filtering fusions with <2 supporting reads (remaining=14103)
[2026-05-28T00:09:24] Filtering fusions with an e-value >=0.3 (remaining=3898)
[2026-05-28T00:09:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3943)
[2026-05-28T00:09:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3913)
[2026-05-28T00:09:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3913)
[2026-05-28T00:09:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3768)
[2026-05-28T00:09:29] Searching for fusions with spliced split reads (remaining=3818)
[2026-05-28T00:09:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=2697)
[2026-05-28T00:09:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2651)
[2026-05-28T00:09:31] Searching for fusions with >=4 spliced events (remaining=2945)
[2026-05-28T00:09:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=966)
[2026-05-28T00:09:44] Filtering fusions with anchors <=23nt (remaining=813)
[2026-05-28T00:09:44] Filtering end-to-end fusions with low support (remaining=797)
[2026-05-28T00:09:44] Filtering fusions with no coverage around the breakpoints (remaining=770)
[2026-05-28T00:09:45] Indexing gene sequences 
[2026-05-28T00:09:48] Filtering genes with >=30% identity (remaining=253)
[2026-05-28T00:09:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=145)
[2026-05-28T00:09:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=136)
[2026-05-28T00:09:51] Searching for additional isoforms (remaining=166)
[2026-05-28T00:09:51] Assigning confidence scores to events 
[2026-05-28T00:09:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:09:53] Writing fusions to file 'tih_rna_sample_00451_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-05-28T00:09:54] Writing discarded fusions to file 'tih_rna_sample_00451_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T00:10:10] Freeing resources
[2026-05-28T00:10:18] Done (elapsed time=00:04:32, CPU time=00:04:32, peak memory=7.99gb)