[2026-06-08T09:07:31] Launching Arriba 2.4.0
[2026-06-08T09:07:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:07:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:07:43] Reading chimeric alignments from 'aih-tih-sc-6fcd81-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=12049409)
[2026-06-08T09:14:58] Marking multi-mapping alignments (marked=7841293)
[2026-06-08T09:15:04] Detecting strandedness (reverse)
[2026-06-08T09:15:04] Assigning strands to alignments 
[2026-06-08T09:15:06] Annotating alignments 
[2026-06-08T09:15:50] Filtering duplicates (remaining=6151496)
[2026-06-08T09:15:59] 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=5810981)
[2026-06-08T09:16:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5810981)
[2026-06-08T09:16:04] Filtering viral contigs with expression lower than the top 5 (remaining=5810981)
[2026-06-08T09:16:10] Filtering viral contigs with less than 5% coverage (remaining=5810981)
[2026-06-08T09:16:13] Estimating fragment length (mate gap mean=-88.0336, mate gap stddev=28.4979, read length mean=130.113)
[2026-06-08T09:16:13] Filtering read-through fragments with a distance <=10000bp (remaining=5464171)
[2026-06-08T09:16:15] Filtering inconsistently clipped mates (remaining=5370247)
[2026-06-08T09:16:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5253964)
[2026-06-08T09:16:23] Filtering fragments with small insert size (remaining=5253210)
[2026-06-08T09:16:26] Filtering alignments with long gaps (remaining=5253210)
[2026-06-08T09:16:29] Filtering fragments with both mates in the same gene (remaining=5252336)
[2026-06-08T09:16:32] Filtering fusions arising from hairpin structures (remaining=4926408)
[2026-06-08T09:16:35] Filtering reads with a mismatch p-value <=0.01 (remaining=2061681)
[2026-06-08T09:16:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=870732)
[2026-06-08T09:16:59] Finding fusions and counting supporting reads (total=689274)
[2026-06-08T09:17:19] Merging adjacent fusion breakpoints (remaining=678369)
[2026-06-08T09:17:21] Filtering multi-mapping fusions by alignment score and read support (remaining=430405)
[2026-06-08T09:18:03] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:18:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=427812)
[2026-06-08T09:18:12] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=226065)
[2026-06-08T09:18:13] Filtering fusions with <2 supporting reads (remaining=30244)
[2026-06-08T09:18:13] Filtering fusions with an e-value >=0.3 (remaining=8774)
[2026-06-08T09:18:14] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8822)
[2026-06-08T09:18:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8703)
[2026-06-08T09:18:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8703)
[2026-06-08T09:18:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6937)
[2026-06-08T09:18:26] Searching for fusions with spliced split reads (remaining=7043)
[2026-06-08T09:18:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=4518)
[2026-06-08T09:18:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4458)
[2026-06-08T09:18:34] Searching for fusions with >=4 spliced events (remaining=5218)
[2026-06-08T09:18:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2057)
[2026-06-08T09:18:53] Filtering fusions with anchors <=23nt (remaining=1487)
[2026-06-08T09:18:54] Filtering end-to-end fusions with low support (remaining=1428)
[2026-06-08T09:18:55] Filtering fusions with no coverage around the breakpoints (remaining=1388)
[2026-06-08T09:18:55] Indexing gene sequences 
[2026-06-08T09:19:01] Filtering genes with >=30% identity (remaining=431)
[2026-06-08T09:19:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=183)
[2026-06-08T09:19:06] Selecting best breakpoints from genes with multiple breakpoints (remaining=166)
[2026-06-08T09:19:07] Searching for additional isoforms (remaining=190)
[2026-06-08T09:19:08] Assigning confidence scores to events 
[2026-06-08T09:19:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:19:12] Writing fusions to file 'aih-tih-sc-6fcd81-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:19:13] Writing discarded fusions to file 'aih-tih-sc-6fcd81-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:19:44] Freeing resources
[2026-06-08T09:20:04] Done (elapsed time=00:12:33, CPU time=00:12:31, peak memory=16.9gb)