[2026-06-08T08:15:04] Launching Arriba 2.4.0
[2026-06-08T08:15:04] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:23] Reading chimeric alignments from 'aih-tih-sc-176637-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=7569400)
[2026-06-08T08:20:37] Marking multi-mapping alignments (marked=4735568)
[2026-06-08T08:20:40] Detecting strandedness (reverse)
[2026-06-08T08:20:40] Assigning strands to alignments 
[2026-06-08T08:20:41] Annotating alignments 
[2026-06-08T08:21:04] Filtering duplicates (remaining=5286242)
[2026-06-08T08:21:09] 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=5140096)
[2026-06-08T08:21:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5140096)
[2026-06-08T08:21:12] Filtering viral contigs with expression lower than the top 5 (remaining=5140096)
[2026-06-08T08:21:15] Filtering viral contigs with less than 5% coverage (remaining=5140096)
[2026-06-08T08:21:17] Estimating fragment length (mate gap mean=-85.4897, mate gap stddev=29.5834, read length mean=135.741)
[2026-06-08T08:21:17] Filtering read-through fragments with a distance <=10000bp (remaining=4881221)
[2026-06-08T08:21:18] Filtering inconsistently clipped mates (remaining=4822874)
[2026-06-08T08:21:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4724626)
[2026-06-08T08:21:22] Filtering fragments with small insert size (remaining=4724212)
[2026-06-08T08:21:24] Filtering alignments with long gaps (remaining=4724211)
[2026-06-08T08:21:25] Filtering fragments with both mates in the same gene (remaining=4723415)
[2026-06-08T08:21:26] Filtering fusions arising from hairpin structures (remaining=4536810)
[2026-06-08T08:21:28] Filtering reads with a mismatch p-value <=0.01 (remaining=2324776)
[2026-06-08T08:21:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=763312)
[2026-06-08T08:21:48] Finding fusions and counting supporting reads (total=587220)
[2026-06-08T08:22:01] Merging adjacent fusion breakpoints (remaining=583250)
[2026-06-08T08:22:02] Filtering multi-mapping fusions by alignment score and read support (remaining=372773)
[2026-06-08T08:22:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:22:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=370956)
[2026-06-08T08:22:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=216602)
[2026-06-08T08:22:36] Filtering fusions with <2 supporting reads (remaining=25884)
[2026-06-08T08:22:36] Filtering fusions with an e-value >=0.3 (remaining=8187)
[2026-06-08T08:22:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8230)
[2026-06-08T08:22:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8190)
[2026-06-08T08:22:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8190)
[2026-06-08T08:22:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6068)
[2026-06-08T08:22:45] Searching for fusions with spliced split reads (remaining=6189)
[2026-06-08T08:22:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=3673)
[2026-06-08T08:22:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3618)
[2026-06-08T08:22:51] Searching for fusions with >=4 spliced events (remaining=4109)
[2026-06-08T08:22:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1575)
[2026-06-08T08:23:10] Filtering fusions with anchors <=23nt (remaining=1293)
[2026-06-08T08:23:11] Filtering end-to-end fusions with low support (remaining=1263)
[2026-06-08T08:23:12] Filtering fusions with no coverage around the breakpoints (remaining=1242)
[2026-06-08T08:23:12] Indexing gene sequences 
[2026-06-08T08:23:20] Filtering genes with >=30% identity (remaining=496)
[2026-06-08T08:23:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=313)
[2026-06-08T08:23:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=264)
[2026-06-08T08:23:31] Searching for additional isoforms (remaining=330)
[2026-06-08T08:23:32] Assigning confidence scores to events 
[2026-06-08T08:23:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:23:35] Writing fusions to file 'aih-tih-sc-176637-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:23:39] Writing discarded fusions to file 'aih-tih-sc-176637-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:24:06] Freeing resources
[2026-06-08T08:24:19] Done (elapsed time=00:09:15, CPU time=00:09:14, peak memory=11.8gb)