[2026-06-08T08:51:44] Launching Arriba 2.4.0
[2026-06-08T08:51:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:51:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:52:00] Reading chimeric alignments from 'aih-tih-sc-804b22-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=9739289)
[2026-06-08T08:59:18] Marking multi-mapping alignments (marked=6068232)
[2026-06-08T08:59:23] Detecting strandedness (reverse)
[2026-06-08T08:59:23] Assigning strands to alignments 
[2026-06-08T08:59:25] Annotating alignments 
[2026-06-08T09:00:02] Filtering duplicates (remaining=5035669)
[2026-06-08T09:00:09] 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=4748036)
[2026-06-08T09:00:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4748036)
[2026-06-08T09:00:13] Filtering viral contigs with expression lower than the top 5 (remaining=4748036)
[2026-06-08T09:00:19] Filtering viral contigs with less than 5% coverage (remaining=4748036)
[2026-06-08T09:00:22] Estimating fragment length (mate gap mean=-88.4535, mate gap stddev=29.408, read length mean=134.547)
[2026-06-08T09:00:23] Filtering read-through fragments with a distance <=10000bp (remaining=4490803)
[2026-06-08T09:00:26] Filtering inconsistently clipped mates (remaining=4411222)
[2026-06-08T09:00:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4300902)
[2026-06-08T09:00:35] Filtering fragments with small insert size (remaining=4300141)
[2026-06-08T09:00:37] Filtering alignments with long gaps (remaining=4300141)
[2026-06-08T09:00:40] Filtering fragments with both mates in the same gene (remaining=4299271)
[2026-06-08T09:00:42] Filtering fusions arising from hairpin structures (remaining=4028476)
[2026-06-08T09:00:47] Filtering reads with a mismatch p-value <=0.01 (remaining=1772419)
[2026-06-08T09:01:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=716513)
[2026-06-08T09:01:09] Finding fusions and counting supporting reads (total=535876)
[2026-06-08T09:01:31] Merging adjacent fusion breakpoints (remaining=530800)
[2026-06-08T09:01:33] Filtering multi-mapping fusions by alignment score and read support (remaining=342593)
[2026-06-08T09:02:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:02:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=340304)
[2026-06-08T09:02:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=190724)
[2026-06-08T09:02:29] Filtering fusions with <2 supporting reads (remaining=27544)
[2026-06-08T09:02:30] Filtering fusions with an e-value >=0.3 (remaining=8382)
[2026-06-08T09:02:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8441)
[2026-06-08T09:02:35] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8382)
[2026-06-08T09:02:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8382)
[2026-06-08T09:02:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5891)
[2026-06-08T09:02:42] Searching for fusions with spliced split reads (remaining=5987)
[2026-06-08T09:02:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=3922)
[2026-06-08T09:02:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3870)
[2026-06-08T09:02:49] Searching for fusions with >=4 spliced events (remaining=4398)
[2026-06-08T09:02:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1372)
[2026-06-08T09:03:06] Filtering fusions with anchors <=23nt (remaining=1071)
[2026-06-08T09:03:06] Filtering end-to-end fusions with low support (remaining=1012)
[2026-06-08T09:03:07] Filtering fusions with no coverage around the breakpoints (remaining=980)
[2026-06-08T09:03:08] Indexing gene sequences 
[2026-06-08T09:03:12] Filtering genes with >=30% identity (remaining=294)
[2026-06-08T09:03:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=178)
[2026-06-08T09:03:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=170)
[2026-06-08T09:03:20] Searching for additional isoforms (remaining=200)
[2026-06-08T09:03:21] Assigning confidence scores to events 
[2026-06-08T09:03:24] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:03:24] Writing fusions to file 'aih-tih-sc-804b22-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:03:26] Writing discarded fusions to file 'aih-tih-sc-804b22-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:03:54] Freeing resources
[2026-06-08T09:04:12] Done (elapsed time=00:12:28, CPU time=00:12:27, peak memory=14.3gb)