[2026-06-08T08:43:20] Launching Arriba 2.4.0
[2026-06-08T08:43:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:43:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:43:44] Reading chimeric alignments from 'aih-tih-sc-6832bb-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10506295)
[2026-06-08T08:55:09] Marking multi-mapping alignments (marked=6385883)
[2026-06-08T08:55:14] Detecting strandedness (reverse)
[2026-06-08T08:55:14] Assigning strands to alignments 
[2026-06-08T08:55:16] Annotating alignments 
[2026-06-08T08:55:56] Filtering duplicates (remaining=6010253)
[2026-06-08T08:56:05] 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=5763545)
[2026-06-08T08:56:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5763545)
[2026-06-08T08:56:09] Filtering viral contigs with expression lower than the top 5 (remaining=5763545)
[2026-06-08T08:56:14] Filtering viral contigs with less than 5% coverage (remaining=5763545)
[2026-06-08T08:56:17] Estimating fragment length (mate gap mean=-86.0261, mate gap stddev=27.9003, read length mean=129.186)
[2026-06-08T08:56:17] Filtering read-through fragments with a distance <=10000bp (remaining=5325602)
[2026-06-08T08:56:20] Filtering inconsistently clipped mates (remaining=5234737)
[2026-06-08T08:56:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5133975)
[2026-06-08T08:56:26] Filtering fragments with small insert size (remaining=5132951)
[2026-06-08T08:56:28] Filtering alignments with long gaps (remaining=5132951)
[2026-06-08T08:56:31] Filtering fragments with both mates in the same gene (remaining=5131990)
[2026-06-08T08:56:33] Filtering fusions arising from hairpin structures (remaining=4852392)
[2026-06-08T08:56:36] Filtering reads with a mismatch p-value <=0.01 (remaining=2270368)
[2026-06-08T08:56:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1060330)
[2026-06-08T08:57:06] Finding fusions and counting supporting reads (total=823736)
[2026-06-08T08:57:25] Merging adjacent fusion breakpoints (remaining=816195)
[2026-06-08T08:57:27] Filtering multi-mapping fusions by alignment score and read support (remaining=539599)
[2026-06-08T08:58:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=538225)
[2026-06-08T08:58:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=269737)
[2026-06-08T08:58:22] Filtering fusions with <2 supporting reads (remaining=36857)
[2026-06-08T08:58:22] Filtering fusions with an e-value >=0.3 (remaining=8885)
[2026-06-08T08:58:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8929)
[2026-06-08T08:58:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8861)
[2026-06-08T08:58:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8861)
[2026-06-08T08:58:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8055)
[2026-06-08T08:58:34] Searching for fusions with spliced split reads (remaining=8169)
[2026-06-08T08:58:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=5095)
[2026-06-08T08:58:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5034)
[2026-06-08T08:58:41] Searching for fusions with >=4 spliced events (remaining=6056)
[2026-06-08T08:58:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2294)
[2026-06-08T08:59:10] Filtering fusions with anchors <=23nt (remaining=1921)
[2026-06-08T08:59:11] Filtering end-to-end fusions with low support (remaining=1873)
[2026-06-08T08:59:11] Filtering fusions with no coverage around the breakpoints (remaining=1829)
[2026-06-08T08:59:12] Indexing gene sequences 
[2026-06-08T08:59:21] Filtering genes with >=30% identity (remaining=602)
[2026-06-08T08:59:25] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=245)
[2026-06-08T08:59:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=209)
[2026-06-08T08:59:54] Searching for additional isoforms (remaining=254)
[2026-06-08T08:59:55] Assigning confidence scores to events 
[2026-06-08T08:59:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:59] Writing fusions to file 'aih-tih-sc-6832bb-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:02] Writing discarded fusions to file 'aih-tih-sc-6832bb-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:41] Freeing resources
[2026-06-08T09:01:05] Done (elapsed time=00:17:45, CPU time=00:17:44, peak memory=15.2gb)