[2026-06-08T08:25:54] Launching Arriba 2.4.0
[2026-06-08T08:25:54] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:07] Reading chimeric alignments from 'aih-tih-sc-762402-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=7617630)
[2026-06-08T08:32:24] Marking multi-mapping alignments (marked=4649643)
[2026-06-08T08:32:28] Detecting strandedness (reverse)
[2026-06-08T08:32:28] Assigning strands to alignments 
[2026-06-08T08:32:31] Annotating alignments 
[2026-06-08T08:33:09] Filtering duplicates (remaining=4842229)
[2026-06-08T08:33:17] 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=4683633)
[2026-06-08T08:33:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4683633)
[2026-06-08T08:33:21] Filtering viral contigs with expression lower than the top 5 (remaining=4683633)
[2026-06-08T08:33:26] Filtering viral contigs with less than 5% coverage (remaining=4683633)
[2026-06-08T08:33:29] Estimating fragment length (mate gap mean=-87.1791, mate gap stddev=28.9911, read length mean=133.976)
[2026-06-08T08:33:29] Filtering read-through fragments with a distance <=10000bp (remaining=4440157)
[2026-06-08T08:33:32] Filtering inconsistently clipped mates (remaining=4374423)
[2026-06-08T08:33:34] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4288812)
[2026-06-08T08:33:38] Filtering fragments with small insert size (remaining=4287976)
[2026-06-08T08:33:41] Filtering alignments with long gaps (remaining=4287975)
[2026-06-08T08:33:43] Filtering fragments with both mates in the same gene (remaining=4287178)
[2026-06-08T08:33:46] Filtering fusions arising from hairpin structures (remaining=4090739)
[2026-06-08T08:33:48] Filtering reads with a mismatch p-value <=0.01 (remaining=1955720)
[2026-06-08T08:34:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=704133)
[2026-06-08T08:34:11] Finding fusions and counting supporting reads (total=488878)
[2026-06-08T08:34:30] Merging adjacent fusion breakpoints (remaining=482571)
[2026-06-08T08:34:31] Filtering multi-mapping fusions by alignment score and read support (remaining=319626)
[2026-06-08T08:35:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=318579)
[2026-06-08T08:35:14] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=186689)
[2026-06-08T08:35:16] Filtering fusions with <2 supporting reads (remaining=25890)
[2026-06-08T08:35:17] Filtering fusions with an e-value >=0.3 (remaining=6500)
[2026-06-08T08:35:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6576)
[2026-06-08T08:35:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6506)
[2026-06-08T08:35:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6506)
[2026-06-08T08:35:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5564)
[2026-06-08T08:35:29] Searching for fusions with spliced split reads (remaining=5667)
[2026-06-08T08:35:34] Selecting best breakpoints from genes with multiple breakpoints (remaining=3815)
[2026-06-08T08:35:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3763)
[2026-06-08T08:35:36] Searching for fusions with >=4 spliced events (remaining=4316)
[2026-06-08T08:35:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1439)
[2026-06-08T08:35:58] Filtering fusions with anchors <=23nt (remaining=1144)
[2026-06-08T08:35:59] Filtering end-to-end fusions with low support (remaining=1119)
[2026-06-08T08:36:00] Filtering fusions with no coverage around the breakpoints (remaining=1085)
[2026-06-08T08:36:01] Indexing gene sequences 
[2026-06-08T08:36:07] Filtering genes with >=30% identity (remaining=339)
[2026-06-08T08:36:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=182)
[2026-06-08T08:36:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=173)
[2026-06-08T08:36:17] Searching for additional isoforms (remaining=199)
[2026-06-08T08:36:19] Assigning confidence scores to events 
[2026-06-08T08:36:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:22] Writing fusions to file 'aih-tih-sc-762402-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:36:24] Writing discarded fusions to file 'aih-tih-sc-762402-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:58] Freeing resources
[2026-06-08T08:37:18] Done (elapsed time=00:11:24, CPU time=00:11:22, peak memory=11.8gb)