[2026-06-08T08:47:30] Launching Arriba 2.4.0
[2026-06-08T08:47:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:47] Reading chimeric alignments from 'tih_rna_sample_00089_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam' (total=10147463)
[2026-06-08T08:55:43] Marking multi-mapping alignments (marked=6576040)
[2026-06-08T08:55:48] Detecting strandedness (reverse)
[2026-06-08T08:55:48] Assigning strands to alignments 
[2026-06-08T08:55:50] Annotating alignments 
[2026-06-08T08:56:26] Filtering duplicates (remaining=5911759)
[2026-06-08T08:56:32] 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=5630812)
[2026-06-08T08:56:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5630812)
[2026-06-08T08:56:37] Filtering viral contigs with expression lower than the top 5 (remaining=5630812)
[2026-06-08T08:56:42] Filtering viral contigs with less than 5% coverage (remaining=5630812)
[2026-06-08T08:56:44] Estimating fragment length (mate gap mean=-86.9766, mate gap stddev=29.4654, read length mean=134.192)
[2026-06-08T08:56:44] Filtering read-through fragments with a distance <=10000bp (remaining=5229292)
[2026-06-08T08:56:47] Filtering inconsistently clipped mates (remaining=5140169)
[2026-06-08T08:56:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4997116)
[2026-06-08T08:56:54] Filtering fragments with small insert size (remaining=4996245)
[2026-06-08T08:56:56] Filtering alignments with long gaps (remaining=4996245)
[2026-06-08T08:56:58] Filtering fragments with both mates in the same gene (remaining=4995366)
[2026-06-08T08:57:00] Filtering fusions arising from hairpin structures (remaining=4693823)
[2026-06-08T08:57:03] Filtering reads with a mismatch p-value <=0.01 (remaining=2108238)
[2026-06-08T08:57:15] Filtering reads with low entropy (k-mer content >=60%) (remaining=945026)
[2026-06-08T08:57:26] Finding fusions and counting supporting reads (total=738506)
[2026-06-08T08:57:44] Merging adjacent fusion breakpoints (remaining=729719)
[2026-06-08T08:57:46] Filtering multi-mapping fusions by alignment score and read support (remaining=453569)
[2026-06-08T08:58:20] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=450712)
[2026-06-08T08:58:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=235253)
[2026-06-08T08:58:29] Filtering fusions with <2 supporting reads (remaining=33987)
[2026-06-08T08:58:30] Filtering fusions with an e-value >=0.3 (remaining=11473)
[2026-06-08T08:58:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11526)
[2026-06-08T08:58:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11435)
[2026-06-08T08:58:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11436)
[2026-06-08T08:58:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6820)
[2026-06-08T08:58:41] Searching for fusions with spliced split reads (remaining=6951)
[2026-06-08T08:58:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=4282)
[2026-06-08T08:58:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4231)
[2026-06-08T08:58:48] Searching for fusions with >=4 spliced events (remaining=5030)
[2026-06-08T08:58:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2065)
[2026-06-08T08:59:04] Filtering fusions with anchors <=23nt (remaining=1679)
[2026-06-08T08:59:05] Filtering end-to-end fusions with low support (remaining=1636)
[2026-06-08T08:59:05] Filtering fusions with no coverage around the breakpoints (remaining=1607)
[2026-06-08T08:59:06] Indexing gene sequences 
[2026-06-08T08:59:12] Filtering genes with >=30% identity (remaining=543)
[2026-06-08T08:59:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=240)
[2026-06-08T08:59:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=204)
[2026-06-08T08:59:21] Searching for additional isoforms (remaining=268)
[2026-06-08T08:59:22] Assigning confidence scores to events 
[2026-06-08T08:59:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:26] Writing fusions to file 'tih_rna_sample_00089_B23WHTKLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:59:28] Writing discarded fusions to file 'tih_rna_sample_00089_B23WHTKLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:57] Freeing resources
[2026-06-08T09:00:15] Done (elapsed time=00:12:45, CPU time=00:12:43, peak memory=14.8gb)