[2026-06-08T08:48:25] Launching Arriba 2.4.0
[2026-06-08T08:48:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:38] Reading chimeric alignments from 'aih-tih-sc-fee548-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9296115)
[2026-06-08T08:55:25] Marking multi-mapping alignments (marked=5716397)
[2026-06-08T08:55:29] Detecting strandedness (reverse)
[2026-06-08T08:55:29] Assigning strands to alignments 
[2026-06-08T08:55:31] Annotating alignments 
[2026-06-08T08:56:04] Filtering duplicates (remaining=5699682)
[2026-06-08T08:56:11] 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=5506923)
[2026-06-08T08:56:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5506923)
[2026-06-08T08:56:15] Filtering viral contigs with expression lower than the top 5 (remaining=5506923)
[2026-06-08T08:56:19] Filtering viral contigs with less than 5% coverage (remaining=5506923)
[2026-06-08T08:56:22] Estimating fragment length (mate gap mean=-86.7265, mate gap stddev=29.7341, read length mean=134.315)
[2026-06-08T08:56:22] Filtering read-through fragments with a distance <=10000bp (remaining=5181600)
[2026-06-08T08:56:24] Filtering inconsistently clipped mates (remaining=5106514)
[2026-06-08T08:56:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4996455)
[2026-06-08T08:56:30] Filtering fragments with small insert size (remaining=4995924)
[2026-06-08T08:56:33] Filtering alignments with long gaps (remaining=4995924)
[2026-06-08T08:56:35] Filtering fragments with both mates in the same gene (remaining=4995135)
[2026-06-08T08:56:37] Filtering fusions arising from hairpin structures (remaining=4728850)
[2026-06-08T08:56:39] Filtering reads with a mismatch p-value <=0.01 (remaining=2213660)
[2026-06-08T08:56:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=836825)
[2026-06-08T08:57:02] Finding fusions and counting supporting reads (total=654697)
[2026-06-08T08:57:18] Merging adjacent fusion breakpoints (remaining=648821)
[2026-06-08T08:57:20] Filtering multi-mapping fusions by alignment score and read support (remaining=440290)
[2026-06-08T08:57:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=438360)
[2026-06-08T08:57:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=235333)
[2026-06-08T08:58:00] Filtering fusions with <2 supporting reads (remaining=37828)
[2026-06-08T08:58:01] Filtering fusions with an e-value >=0.3 (remaining=16761)
[2026-06-08T08:58:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=16815)
[2026-06-08T08:58:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16762)
[2026-06-08T08:58:06] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=16762)
[2026-06-08T08:58:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6959)
[2026-06-08T08:58:12] Searching for fusions with spliced split reads (remaining=6991)
[2026-06-08T08:58:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=3816)
[2026-06-08T08:58:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3768)
[2026-06-08T08:58:18] Searching for fusions with >=4 spliced events (remaining=4703)
[2026-06-08T08:58:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1911)
[2026-06-08T08:58:33] Filtering fusions with anchors <=23nt (remaining=1512)
[2026-06-08T08:58:34] Filtering end-to-end fusions with low support (remaining=1478)
[2026-06-08T08:58:34] Filtering fusions with no coverage around the breakpoints (remaining=1445)
[2026-06-08T08:58:35] Indexing gene sequences 
[2026-06-08T08:58:40] Filtering genes with >=30% identity (remaining=389)
[2026-06-08T08:58:42] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=166)
[2026-06-08T08:58:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=135)
[2026-06-08T08:58:48] Searching for additional isoforms (remaining=168)
[2026-06-08T08:58:50] Assigning confidence scores to events 
[2026-06-08T08:58:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:53] Writing fusions to file 'aih-tih-sc-fee548-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:55] Writing discarded fusions to file 'aih-tih-sc-fee548-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:25] Freeing resources
[2026-06-08T08:59:42] Done (elapsed time=00:11:17, CPU time=00:11:15, peak memory=13.8gb)