[2026-06-08T08:38:58] Launching Arriba 2.4.0
[2026-06-08T08:38:58] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:06] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:10] Reading chimeric alignments from 'aih-tih-sc-910896-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10856149)
[2026-06-08T08:44:44] Marking multi-mapping alignments (marked=7399605)
[2026-06-08T08:44:49] Detecting strandedness (reverse)
[2026-06-08T08:44:49] Assigning strands to alignments 
[2026-06-08T08:44:51] Annotating alignments 
[2026-06-08T08:45:25] Filtering duplicates (remaining=5004382)
[2026-06-08T08:45:31] 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=4697639)
[2026-06-08T08:45:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4697639)
[2026-06-08T08:45:36] Filtering viral contigs with expression lower than the top 5 (remaining=4697639)
[2026-06-08T08:45:40] Filtering viral contigs with less than 5% coverage (remaining=4697639)
[2026-06-08T08:45:43] Estimating fragment length (mate gap mean=-85.8462, mate gap stddev=28.3031, read length mean=129.825)
[2026-06-08T08:45:43] Filtering read-through fragments with a distance <=10000bp (remaining=4519175)
[2026-06-08T08:45:45] Filtering inconsistently clipped mates (remaining=4434948)
[2026-06-08T08:45:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4236559)
[2026-06-08T08:45:51] Filtering fragments with small insert size (remaining=4235951)
[2026-06-08T08:45:53] Filtering alignments with long gaps (remaining=4235951)
[2026-06-08T08:45:55] Filtering fragments with both mates in the same gene (remaining=4235129)
[2026-06-08T08:45:57] Filtering fusions arising from hairpin structures (remaining=4002418)
[2026-06-08T08:46:00] Filtering reads with a mismatch p-value <=0.01 (remaining=1820938)
[2026-06-08T08:46:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=531685)
[2026-06-08T08:46:20] Finding fusions and counting supporting reads (total=410776)
[2026-06-08T08:46:35] Merging adjacent fusion breakpoints (remaining=405791)
[2026-06-08T08:46:36] Filtering multi-mapping fusions by alignment score and read support (remaining=230608)
[2026-06-08T08:47:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:47:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=229222)
[2026-06-08T08:47:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=135374)
[2026-06-08T08:47:18] Filtering fusions with <2 supporting reads (remaining=16633)
[2026-06-08T08:47:19] Filtering fusions with an e-value >=0.3 (remaining=4500)
[2026-06-08T08:47:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4545)
[2026-06-08T08:47:23] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4457)
[2026-06-08T08:47:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4457)
[2026-06-08T08:47:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4248)
[2026-06-08T08:47:29] Searching for fusions with spliced split reads (remaining=4317)
[2026-06-08T08:47:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=3075)
[2026-06-08T08:47:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3027)
[2026-06-08T08:47:35] Searching for fusions with >=4 spliced events (remaining=3386)
[2026-06-08T08:47:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1195)
[2026-06-08T08:47:50] Filtering fusions with anchors <=23nt (remaining=985)
[2026-06-08T08:47:50] Filtering end-to-end fusions with low support (remaining=944)
[2026-06-08T08:47:51] Filtering fusions with no coverage around the breakpoints (remaining=901)
[2026-06-08T08:47:52] Indexing gene sequences 
[2026-06-08T08:47:56] Filtering genes with >=30% identity (remaining=292)
[2026-06-08T08:47:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=149)
[2026-06-08T08:47:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=147)
[2026-06-08T08:48:00] Searching for additional isoforms (remaining=174)
[2026-06-08T08:48:01] Assigning confidence scores to events 
[2026-06-08T08:48:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:04] Writing fusions to file 'aih-tih-sc-910896-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:05] Writing discarded fusions to file 'aih-tih-sc-910896-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:28] Freeing resources
[2026-06-08T08:48:45] Done (elapsed time=00:09:47, CPU time=00:09:47, peak memory=15.1gb)