[2026-06-08T09:02:23] Launching Arriba 2.4.0
[2026-06-08T09:02:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:02:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:02:43] Reading chimeric alignments from 'aih-tih-sc-ced210-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11415767)
[2026-06-08T09:11:16] Marking multi-mapping alignments (marked=7326968)
[2026-06-08T09:11:21] Detecting strandedness (reverse)
[2026-06-08T09:11:21] Assigning strands to alignments 
[2026-06-08T09:11:23] Annotating alignments 
[2026-06-08T09:12:03] Filtering duplicates (remaining=6250981)
[2026-06-08T09:12:11] 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=5885495)
[2026-06-08T09:12:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5885495)
[2026-06-08T09:12:15] Filtering viral contigs with expression lower than the top 5 (remaining=5885495)
[2026-06-08T09:12:20] Filtering viral contigs with less than 5% coverage (remaining=5885495)
[2026-06-08T09:12:23] Estimating fragment length (mate gap mean=-86.9744, mate gap stddev=29.2625, read length mean=130.471)
[2026-06-08T09:12:23] Filtering read-through fragments with a distance <=10000bp (remaining=5490821)
[2026-06-08T09:12:25] Filtering inconsistently clipped mates (remaining=5388252)
[2026-06-08T09:12:28] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5246495)
[2026-06-08T09:12:32] Filtering fragments with small insert size (remaining=5245602)
[2026-06-08T09:12:35] Filtering alignments with long gaps (remaining=5245602)
[2026-06-08T09:12:37] Filtering fragments with both mates in the same gene (remaining=5244584)
[2026-06-08T09:12:40] Filtering fusions arising from hairpin structures (remaining=4944197)
[2026-06-08T09:12:42] Filtering reads with a mismatch p-value <=0.01 (remaining=2144969)
[2026-06-08T09:12:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=973347)
[2026-06-08T09:13:08] Finding fusions and counting supporting reads (total=760301)
[2026-06-08T09:13:26] Merging adjacent fusion breakpoints (remaining=750902)
[2026-06-08T09:13:28] Filtering multi-mapping fusions by alignment score and read support (remaining=454214)
[2026-06-08T09:14:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:14:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=451524)
[2026-06-08T09:14:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=249174)
[2026-06-08T09:14:13] Filtering fusions with <2 supporting reads (remaining=33507)
[2026-06-08T09:14:14] Filtering fusions with an e-value >=0.3 (remaining=9520)
[2026-06-08T09:14:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9588)
[2026-06-08T09:14:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9389)
[2026-06-08T09:14:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9389)
[2026-06-08T09:14:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8126)
[2026-06-08T09:14:26] Searching for fusions with spliced split reads (remaining=8274)
[2026-06-08T09:14:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=5335)
[2026-06-08T09:14:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5250)
[2026-06-08T09:14:33] Searching for fusions with >=4 spliced events (remaining=6191)
[2026-06-08T09:14:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2532)
[2026-06-08T09:15:03] Filtering fusions with anchors <=23nt (remaining=1823)
[2026-06-08T09:15:03] Filtering end-to-end fusions with low support (remaining=1746)
[2026-06-08T09:15:04] Filtering fusions with no coverage around the breakpoints (remaining=1694)
[2026-06-08T09:15:05] Indexing gene sequences 
[2026-06-08T09:15:13] Filtering genes with >=30% identity (remaining=572)
[2026-06-08T09:15:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=296)
[2026-06-08T09:15:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=248)
[2026-06-08T09:15:24] Searching for additional isoforms (remaining=297)
[2026-06-08T09:15:25] Assigning confidence scores to events 
[2026-06-08T09:15:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:15:29] Writing fusions to file 'aih-tih-sc-ced210-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:15:32] Writing discarded fusions to file 'aih-tih-sc-ced210-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:16:03] Freeing resources
[2026-06-08T09:16:21] Done (elapsed time=00:13:58, CPU time=00:13:56, peak memory=16.2gb)