[2026-06-08T08:42:01] Launching Arriba 2.4.0
[2026-06-08T08:42:01] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:15] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:20] Reading chimeric alignments from 'aih-tih-sc-431fe7-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=8324502)
[2026-06-08T08:47:11] Marking multi-mapping alignments (marked=5691240)
[2026-06-08T08:47:14] Detecting strandedness (reverse)
[2026-06-08T08:47:14] Assigning strands to alignments 
[2026-06-08T08:47:16] Annotating alignments 
[2026-06-08T08:47:40] Filtering duplicates (remaining=3083991)
[2026-06-08T08:47:44] 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=2789353)
[2026-06-08T08:47:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2789353)
[2026-06-08T08:47:47] Filtering viral contigs with expression lower than the top 5 (remaining=2789353)
[2026-06-08T08:47:50] Filtering viral contigs with less than 5% coverage (remaining=2789353)
[2026-06-08T08:47:52] Estimating fragment length (mate gap mean=-86.2365, mate gap stddev=28.8256, read length mean=126.277)
[2026-06-08T08:47:52] Filtering read-through fragments with a distance <=10000bp (remaining=2678701)
[2026-06-08T08:47:53] Filtering inconsistently clipped mates (remaining=2613900)
[2026-06-08T08:47:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2523410)
[2026-06-08T08:47:57] Filtering fragments with small insert size (remaining=2522817)
[2026-06-08T08:47:59] Filtering alignments with long gaps (remaining=2522817)
[2026-06-08T08:48:00] Filtering fragments with both mates in the same gene (remaining=2522217)
[2026-06-08T08:48:02] Filtering fusions arising from hairpin structures (remaining=2365393)
[2026-06-08T08:48:04] Filtering reads with a mismatch p-value <=0.01 (remaining=977548)
[2026-06-08T08:48:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=319959)
[2026-06-08T08:48:15] Finding fusions and counting supporting reads (total=257935)
[2026-06-08T08:48:25] Merging adjacent fusion breakpoints (remaining=255896)
[2026-06-08T08:48:26] Filtering multi-mapping fusions by alignment score and read support (remaining=144870)
[2026-06-08T08:48:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:48:51] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=143691)
[2026-06-08T08:48:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=84276)
[2026-06-08T08:48:52] Filtering fusions with <2 supporting reads (remaining=8756)
[2026-06-08T08:48:52] Filtering fusions with an e-value >=0.3 (remaining=2633)
[2026-06-08T08:48:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2672)
[2026-06-08T08:48:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2614)
[2026-06-08T08:48:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2614)
[2026-06-08T08:48:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2116)
[2026-06-08T08:48:59] Searching for fusions with spliced split reads (remaining=2155)
[2026-06-08T08:49:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=1553)
[2026-06-08T08:49:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1519)
[2026-06-08T08:49:02] Searching for fusions with >=4 spliced events (remaining=1661)
[2026-06-08T08:49:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=513)
[2026-06-08T08:49:15] Filtering fusions with anchors <=23nt (remaining=417)
[2026-06-08T08:49:15] Filtering end-to-end fusions with low support (remaining=396)
[2026-06-08T08:49:15] Filtering fusions with no coverage around the breakpoints (remaining=381)
[2026-06-08T08:49:16] Indexing gene sequences 
[2026-06-08T08:49:18] Filtering genes with >=30% identity (remaining=123)
[2026-06-08T08:49:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=51)
[2026-06-08T08:49:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=51)
[2026-06-08T08:49:20] Searching for additional isoforms (remaining=56)
[2026-06-08T08:49:21] Assigning confidence scores to events 
[2026-06-08T08:49:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:49:22] Writing fusions to file 'aih-tih-sc-431fe7-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:49:23] Writing discarded fusions to file 'aih-tih-sc-431fe7-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:49:36] Freeing resources
[2026-06-08T08:49:48] Done (elapsed time=00:07:47, CPU time=00:07:45, peak memory=12.7gb)