[2026-05-28T00:04:45] Launching Arriba 2.4.0
[2026-05-28T00:04:45] Loading assembly from 'ref_genome.fa' 
[2026-05-28T00:04:54] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T00:04:58] Reading chimeric alignments from 'tih_rna_sample_00451_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=3675513)
[2026-05-28T00:07:13] Marking multi-mapping alignments (marked=2323578)
[2026-05-28T00:07:14] Detecting strandedness (reverse)
[2026-05-28T00:07:14] Assigning strands to alignments 
[2026-05-28T00:07:15] Annotating alignments 
[2026-05-28T00:07:28] Filtering duplicates (remaining=2714723)
[2026-05-28T00:07:30] 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=2618331)
[2026-05-28T00:07:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2618331)
[2026-05-28T00:07:32] Filtering viral contigs with expression lower than the top 5 (remaining=2618331)
[2026-05-28T00:07:33] Filtering viral contigs with less than 5% coverage (remaining=2618331)
[2026-05-28T00:07:34] Estimating fragment length (mate gap mean=-87.5472, mate gap stddev=27.6699, read length mean=129.475)
[2026-05-28T00:07:34] Filtering read-through fragments with a distance <=10000bp (remaining=2368874)
[2026-05-28T00:07:35] Filtering inconsistently clipped mates (remaining=2322694)
[2026-05-28T00:07:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2270546)
[2026-05-28T00:07:37] Filtering fragments with small insert size (remaining=2270108)
[2026-05-28T00:07:38] Filtering alignments with long gaps (remaining=2270108)
[2026-05-28T00:07:39] Filtering fragments with both mates in the same gene (remaining=2269657)
[2026-05-28T00:07:40] Filtering fusions arising from hairpin structures (remaining=2131353)
[2026-05-28T00:07:41] Filtering reads with a mismatch p-value <=0.01 (remaining=963321)
[2026-05-28T00:07:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=520189)
[2026-05-28T00:07:51] Finding fusions and counting supporting reads (total=441366)
[2026-05-28T00:07:58] Merging adjacent fusion breakpoints (remaining=438149)
[2026-05-28T00:07:58] Filtering multi-mapping fusions by alignment score and read support (remaining=267350)
[2026-05-28T00:08:11] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T00:08:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=265833)
[2026-05-28T00:08:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=143779)
[2026-05-28T00:08:15] Filtering fusions with <2 supporting reads (remaining=16786)
[2026-05-28T00:08:15] Filtering fusions with an e-value >=0.3 (remaining=4419)
[2026-05-28T00:08:16] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4471)
[2026-05-28T00:08:17] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4435)
[2026-05-28T00:08:17] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4435)
[2026-05-28T00:08:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4239)
[2026-05-28T00:08:20] Searching for fusions with spliced split reads (remaining=4321)
[2026-05-28T00:08:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=2997)
[2026-05-28T00:08:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2951)
[2026-05-28T00:08:23] Searching for fusions with >=4 spliced events (remaining=3381)
[2026-05-28T00:08:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1218)
[2026-05-28T00:08:36] Filtering fusions with anchors <=23nt (remaining=1052)
[2026-05-28T00:08:36] Filtering end-to-end fusions with low support (remaining=1022)
[2026-05-28T00:08:36] Filtering fusions with no coverage around the breakpoints (remaining=978)
[2026-05-28T00:08:37] Indexing gene sequences 
[2026-05-28T00:08:41] Filtering genes with >=30% identity (remaining=330)
[2026-05-28T00:08:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=185)
[2026-05-28T00:08:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=168)
[2026-05-28T00:08:44] Searching for additional isoforms (remaining=210)
[2026-05-28T00:08:45] Assigning confidence scores to events 
[2026-05-28T00:08:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T00:08:47] Writing fusions to file 'tih_rna_sample_00451_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-05-28T00:08:48] Writing discarded fusions to file 'tih_rna_sample_00451_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T00:09:04] Freeing resources
[2026-05-28T00:09:11] Done (elapsed time=00:04:26, CPU time=00:04:24, peak memory=8.11gb)