[2026-06-08T09:07:23] Launching Arriba 2.4.0
[2026-06-08T09:07:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:07:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:07:43] Reading chimeric alignments from 'aih-tih-sc-c8485b-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10705953)
[2026-06-08T09:15:55] Marking multi-mapping alignments (marked=6831474)
[2026-06-08T09:15:59] Detecting strandedness (reverse)
[2026-06-08T09:15:59] Assigning strands to alignments 
[2026-06-08T09:16:01] Annotating alignments 
[2026-06-08T09:16:34] Filtering duplicates (remaining=5356388)
[2026-06-08T09:16:39] 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=5125609)
[2026-06-08T09:16:41] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5125609)
[2026-06-08T09:16:43] Filtering viral contigs with expression lower than the top 5 (remaining=5125609)
[2026-06-08T09:16:47] Filtering viral contigs with less than 5% coverage (remaining=5125609)
[2026-06-08T09:16:49] Estimating fragment length (mate gap mean=-85.3656, mate gap stddev=28.6376, read length mean=129.245)
[2026-06-08T09:16:49] Filtering read-through fragments with a distance <=10000bp (remaining=4849464)
[2026-06-08T09:16:51] Filtering inconsistently clipped mates (remaining=4757524)
[2026-06-08T09:16:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4634960)
[2026-06-08T09:16:56] Filtering fragments with small insert size (remaining=4634065)
[2026-06-08T09:16:58] Filtering alignments with long gaps (remaining=4634065)
[2026-06-08T09:17:00] Filtering fragments with both mates in the same gene (remaining=4633050)
[2026-06-08T09:17:02] Filtering fusions arising from hairpin structures (remaining=4366558)
[2026-06-08T09:17:04] Filtering reads with a mismatch p-value <=0.01 (remaining=1965623)
[2026-06-08T09:17:16] Filtering reads with low entropy (k-mer content >=60%) (remaining=735452)
[2026-06-08T09:17:25] Finding fusions and counting supporting reads (total=578950)
[2026-06-08T09:17:40] Merging adjacent fusion breakpoints (remaining=572947)
[2026-06-08T09:17:42] Filtering multi-mapping fusions by alignment score and read support (remaining=351421)
[2026-06-08T09:18:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:18:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=349141)
[2026-06-08T09:18:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=194339)
[2026-06-08T09:18:20] Filtering fusions with <2 supporting reads (remaining=24903)
[2026-06-08T09:18:21] Filtering fusions with an e-value >=0.3 (remaining=6868)
[2026-06-08T09:18:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6917)
[2026-06-08T09:18:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6781)
[2026-06-08T09:18:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6781)
[2026-06-08T09:18:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5184)
[2026-06-08T09:18:31] Searching for fusions with spliced split reads (remaining=5298)
[2026-06-08T09:18:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=3429)
[2026-06-08T09:18:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3380)
[2026-06-08T09:18:37] Searching for fusions with >=4 spliced events (remaining=3969)
[2026-06-08T09:18:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1490)
[2026-06-08T09:18:56] Filtering fusions with anchors <=23nt (remaining=1262)
[2026-06-08T09:18:56] Filtering end-to-end fusions with low support (remaining=1224)
[2026-06-08T09:18:57] Filtering fusions with no coverage around the breakpoints (remaining=1201)
[2026-06-08T09:18:58] Indexing gene sequences 
[2026-06-08T09:19:03] Filtering genes with >=30% identity (remaining=354)
[2026-06-08T09:19:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=165)
[2026-06-08T09:19:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=154)
[2026-06-08T09:19:09] Searching for additional isoforms (remaining=186)
[2026-06-08T09:19:11] Assigning confidence scores to events 
[2026-06-08T09:19:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:19:14] Writing fusions to file 'aih-tih-sc-c8485b-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:19:15] Writing discarded fusions to file 'aih-tih-sc-c8485b-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:19:42] Freeing resources
[2026-06-08T09:20:00] Done (elapsed time=00:12:37, CPU time=00:12:35, peak memory=15.2gb)