[2026-06-08T08:19:56] Launching Arriba 2.4.0
[2026-06-08T08:19:56] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:12] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:16] Reading chimeric alignments from 'aih-tih-sc-a70f1e-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=11497700)
[2026-06-08T08:27:14] Marking multi-mapping alignments (marked=7761880)
[2026-06-08T08:27:19] Detecting strandedness (reverse)
[2026-06-08T08:27:19] Assigning strands to alignments 
[2026-06-08T08:27:21] Annotating alignments 
[2026-06-08T08:28:04] Filtering duplicates (remaining=4005181)
[2026-06-08T08:28:11] 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=3802924)
[2026-06-08T08:28:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3802924)
[2026-06-08T08:28:16] Filtering viral contigs with expression lower than the top 5 (remaining=3802924)
[2026-06-08T08:28:21] Filtering viral contigs with less than 5% coverage (remaining=3802924)
[2026-06-08T08:28:24] Estimating fragment length (mate gap mean=-82.2513, mate gap stddev=26.8514, read length mean=118.744)
[2026-06-08T08:28:24] Filtering read-through fragments with a distance <=10000bp (remaining=3633954)
[2026-06-08T08:28:26] Filtering inconsistently clipped mates (remaining=3574930)
[2026-06-08T08:28:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3423128)
[2026-06-08T08:28:32] Filtering fragments with small insert size (remaining=3422256)
[2026-06-08T08:28:35] Filtering alignments with long gaps (remaining=3422254)
[2026-06-08T08:28:38] Filtering fragments with both mates in the same gene (remaining=3421345)
[2026-06-08T08:28:41] Filtering fusions arising from hairpin structures (remaining=3303123)
[2026-06-08T08:28:44] Filtering reads with a mismatch p-value <=0.01 (remaining=1332850)
[2026-06-08T08:28:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=452515)
[2026-06-08T08:29:02] Finding fusions and counting supporting reads (total=363626)
[2026-06-08T08:29:19] Merging adjacent fusion breakpoints (remaining=359618)
[2026-06-08T08:29:20] Filtering multi-mapping fusions by alignment score and read support (remaining=184587)
[2026-06-08T08:29:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:30:03] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=183884)
[2026-06-08T08:30:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=120096)
[2026-06-08T08:30:05] Filtering fusions with <2 supporting reads (remaining=14739)
[2026-06-08T08:30:05] Filtering fusions with an e-value >=0.3 (remaining=3512)
[2026-06-08T08:30:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3547)
[2026-06-08T08:30:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3492)
[2026-06-08T08:30:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3494)
[2026-06-08T08:30:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3485)
[2026-06-08T08:30:15] Searching for fusions with spliced split reads (remaining=3525)
[2026-06-08T08:30:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=2484)
[2026-06-08T08:30:21] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2434)
[2026-06-08T08:30:22] Searching for fusions with >=4 spliced events (remaining=2722)
[2026-06-08T08:30:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=948)
[2026-06-08T08:30:41] Filtering fusions with anchors <=23nt (remaining=813)
[2026-06-08T08:30:41] Filtering end-to-end fusions with low support (remaining=794)
[2026-06-08T08:30:42] Filtering fusions with no coverage around the breakpoints (remaining=777)
[2026-06-08T08:30:42] Indexing gene sequences 
[2026-06-08T08:30:46] Filtering genes with >=30% identity (remaining=235)
[2026-06-08T08:30:48] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=57)
[2026-06-08T08:30:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=57)
[2026-06-08T08:30:50] Searching for additional isoforms (remaining=74)
[2026-06-08T08:30:51] Assigning confidence scores to events 
[2026-06-08T08:30:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:54] Writing fusions to file 'aih-tih-sc-a70f1e-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:30:55] Writing discarded fusions to file 'aih-tih-sc-a70f1e-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:31:22] Freeing resources
[2026-06-08T08:31:45] Done (elapsed time=00:11:49, CPU time=00:11:48, peak memory=15.6gb)