[2026-06-08T08:36:02] Launching Arriba 2.4.0
[2026-06-08T08:36:02] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:17] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:21] Reading chimeric alignments from 'aih-tih-sc-d113b5-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=12304285)
[2026-06-08T08:45:42] Marking multi-mapping alignments (marked=7828195)
[2026-06-08T08:45:49] Detecting strandedness (reverse)
[2026-06-08T08:45:49] Assigning strands to alignments 
[2026-06-08T08:45:52] Annotating alignments 
[2026-06-08T08:46:51] Filtering duplicates (remaining=5304224)
[2026-06-08T08:47:02] 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=5038683)
[2026-06-08T08:47:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5038683)
[2026-06-08T08:47:08] Filtering viral contigs with expression lower than the top 5 (remaining=5038683)
[2026-06-08T08:47:15] Filtering viral contigs with less than 5% coverage (remaining=5038683)
[2026-06-08T08:47:19] Estimating fragment length (mate gap mean=-84.8884, mate gap stddev=27.8515, read length mean=125.332)
[2026-06-08T08:47:19] Filtering read-through fragments with a distance <=10000bp (remaining=4749165)
[2026-06-08T08:47:22] Filtering inconsistently clipped mates (remaining=4673958)
[2026-06-08T08:47:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4555402)
[2026-06-08T08:47:31] Filtering fragments with small insert size (remaining=4554539)
[2026-06-08T08:47:34] Filtering alignments with long gaps (remaining=4554539)
[2026-06-08T08:47:37] Filtering fragments with both mates in the same gene (remaining=4553615)
[2026-06-08T08:47:42] Filtering fusions arising from hairpin structures (remaining=4369077)
[2026-06-08T08:47:46] Filtering reads with a mismatch p-value <=0.01 (remaining=1912289)
[2026-06-08T08:48:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=628167)
[2026-06-08T08:48:20] Finding fusions and counting supporting reads (total=500877)
[2026-06-08T08:48:55] Merging adjacent fusion breakpoints (remaining=491688)
[2026-06-08T08:48:57] Filtering multi-mapping fusions by alignment score and read support (remaining=293863)
[2026-06-08T08:49:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:05] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=292684)
[2026-06-08T08:50:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=163089)
[2026-06-08T08:50:07] Filtering fusions with <2 supporting reads (remaining=21531)
[2026-06-08T08:50:08] Filtering fusions with an e-value >=0.3 (remaining=5157)
[2026-06-08T08:50:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5214)
[2026-06-08T08:50:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5136)
[2026-06-08T08:50:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5136)
[2026-06-08T08:50:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4981)
[2026-06-08T08:50:28] Searching for fusions with spliced split reads (remaining=5060)
[2026-06-08T08:50:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=3514)
[2026-06-08T08:50:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3461)
[2026-06-08T08:50:40] Searching for fusions with >=4 spliced events (remaining=3930)
[2026-06-08T08:50:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1469)
[2026-06-08T08:51:12] Filtering fusions with anchors <=23nt (remaining=1157)
[2026-06-08T08:51:13] Filtering end-to-end fusions with low support (remaining=1130)
[2026-06-08T08:51:14] Filtering fusions with no coverage around the breakpoints (remaining=1102)
[2026-06-08T08:51:15] Indexing gene sequences 
[2026-06-08T08:51:28] Filtering genes with >=30% identity (remaining=343)
[2026-06-08T08:51:31] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=157)
[2026-06-08T08:51:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=150)
[2026-06-08T08:51:35] Searching for additional isoforms (remaining=193)
[2026-06-08T08:51:37] Assigning confidence scores to events 
[2026-06-08T08:51:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:41] Writing fusions to file 'aih-tih-sc-d113b5-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:42] Writing discarded fusions to file 'aih-tih-sc-d113b5-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:52:21] Freeing resources
[2026-06-08T08:53:01] Done (elapsed time=00:16:59, CPU time=00:16:58, peak memory=16.5gb)