[2026-06-08T09:05:24] Launching Arriba 2.4.0
[2026-06-08T09:05:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:05:33] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:05:37] Reading chimeric alignments from 'aih-tih-sc-4c132f-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11011893)
[2026-06-08T09:12:33] Marking multi-mapping alignments (marked=6902861)
[2026-06-08T09:12:37] Detecting strandedness (reverse)
[2026-06-08T09:12:37] Assigning strands to alignments 
[2026-06-08T09:12:39] Annotating alignments 
[2026-06-08T09:13:14] Filtering duplicates (remaining=5406661)
[2026-06-08T09:13:20] 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=5169647)
[2026-06-08T09:13:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5169647)
[2026-06-08T09:13:24] Filtering viral contigs with expression lower than the top 5 (remaining=5169647)
[2026-06-08T09:13:29] Filtering viral contigs with less than 5% coverage (remaining=5169647)
[2026-06-08T09:13:31] Estimating fragment length (mate gap mean=-86.8288, mate gap stddev=27.4852, read length mean=127.567)
[2026-06-08T09:13:31] Filtering read-through fragments with a distance <=10000bp (remaining=4770030)
[2026-06-08T09:13:33] Filtering inconsistently clipped mates (remaining=4672379)
[2026-06-08T09:13:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4548972)
[2026-06-08T09:13:40] Filtering fragments with small insert size (remaining=4547866)
[2026-06-08T09:13:42] Filtering alignments with long gaps (remaining=4547865)
[2026-06-08T09:13:44] Filtering fragments with both mates in the same gene (remaining=4546935)
[2026-06-08T09:13:46] Filtering fusions arising from hairpin structures (remaining=4270106)
[2026-06-08T09:13:49] Filtering reads with a mismatch p-value <=0.01 (remaining=1885379)
[2026-06-08T09:14:02] Filtering reads with low entropy (k-mer content >=60%) (remaining=857031)
[2026-06-08T09:14:11] Finding fusions and counting supporting reads (total=709039)
[2026-06-08T09:14:28] Merging adjacent fusion breakpoints (remaining=699480)
[2026-06-08T09:14:30] Filtering multi-mapping fusions by alignment score and read support (remaining=414758)
[2026-06-08T09:15:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:15:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=412923)
[2026-06-08T09:15:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=220747)
[2026-06-08T09:15:13] Filtering fusions with <2 supporting reads (remaining=26109)
[2026-06-08T09:15:13] Filtering fusions with an e-value >=0.3 (remaining=6350)
[2026-06-08T09:15:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6399)
[2026-06-08T09:15:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6290)
[2026-06-08T09:15:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6290)
[2026-06-08T09:15:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5400)
[2026-06-08T09:15:25] Searching for fusions with spliced split reads (remaining=5489)
[2026-06-08T09:15:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=3628)
[2026-06-08T09:15:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3588)
[2026-06-08T09:15:32] Searching for fusions with >=4 spliced events (remaining=4263)
[2026-06-08T09:15:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1698)
[2026-06-08T09:15:46] Filtering fusions with anchors <=23nt (remaining=1476)
[2026-06-08T09:15:47] Filtering end-to-end fusions with low support (remaining=1446)
[2026-06-08T09:15:48] Filtering fusions with no coverage around the breakpoints (remaining=1423)
[2026-06-08T09:15:48] Indexing gene sequences 
[2026-06-08T09:15:54] Filtering genes with >=30% identity (remaining=382)
[2026-06-08T09:15:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=129)
[2026-06-08T09:15:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=127)
[2026-06-08T09:15:59] Searching for additional isoforms (remaining=151)
[2026-06-08T09:16:01] Assigning confidence scores to events 
[2026-06-08T09:16:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:16:04] Writing fusions to file 'aih-tih-sc-4c132f-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:16:05] Writing discarded fusions to file 'aih-tih-sc-4c132f-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:16:32] Freeing resources
[2026-06-08T09:16:51] Done (elapsed time=00:11:27, CPU time=00:11:26, peak memory=15.7gb)