[2026-06-08T07:52:43] Launching Arriba 2.4.0
[2026-06-08T07:52:43] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:52:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:53:00] Reading chimeric alignments from 'aih-tih-sc-2482ef-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=1669954)
[2026-06-08T07:54:02] Marking multi-mapping alignments (marked=1190793)
[2026-06-08T07:54:03] Detecting strandedness (reverse)
[2026-06-08T07:54:03] Assigning strands to alignments 
[2026-06-08T07:54:04] Annotating alignments 
[2026-06-08T07:54:12] Filtering duplicates (remaining=516283)
[2026-06-08T07:54:13] 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=450736)
[2026-06-08T07:54:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=450736)
[2026-06-08T07:54:14] Filtering viral contigs with expression lower than the top 5 (remaining=450736)
[2026-06-08T07:54:14] Filtering viral contigs with less than 5% coverage (remaining=450736)
[2026-06-08T07:54:15] Estimating fragment length (mate gap mean=-81.6167, mate gap stddev=29.0165, read length mean=119.893)
[2026-06-08T07:54:15] Filtering read-through fragments with a distance <=10000bp (remaining=436800)
[2026-06-08T07:54:16] Filtering inconsistently clipped mates (remaining=426901)
[2026-06-08T07:54:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=415839)
[2026-06-08T07:54:17] Filtering fragments with small insert size (remaining=415688)
[2026-06-08T07:54:17] Filtering alignments with long gaps (remaining=415688)
[2026-06-08T07:54:18] Filtering fragments with both mates in the same gene (remaining=415553)
[2026-06-08T07:54:18] Filtering fusions arising from hairpin structures (remaining=393087)
[2026-06-08T07:54:19] Filtering reads with a mismatch p-value <=0.01 (remaining=142126)
[2026-06-08T07:54:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=42906)
[2026-06-08T07:54:21] Finding fusions and counting supporting reads (total=40883)
[2026-06-08T07:54:25] Merging adjacent fusion breakpoints (remaining=40665)
[2026-06-08T07:54:25] Filtering multi-mapping fusions by alignment score and read support (remaining=21585)
[2026-06-08T07:54:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:54:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=21311)
[2026-06-08T07:54:33] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=12574)
[2026-06-08T07:54:33] Filtering fusions with <2 supporting reads (remaining=771)
[2026-06-08T07:54:33] Filtering fusions with an e-value >=0.3 (remaining=267)
[2026-06-08T07:54:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=276)
[2026-06-08T07:54:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=268)
[2026-06-08T07:54:34] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=268)
[2026-06-08T07:54:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=258)
[2026-06-08T07:54:35] Searching for fusions with spliced split reads (remaining=272)
[2026-06-08T07:54:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=218)
[2026-06-08T07:54:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=215)
[2026-06-08T07:54:36] Searching for fusions with >=4 spliced events (remaining=217)
[2026-06-08T07:54:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=61)
[2026-06-08T07:54:52] Filtering fusions with anchors <=23nt (remaining=46)
[2026-06-08T07:54:52] Filtering end-to-end fusions with low support (remaining=44)
[2026-06-08T07:54:52] Filtering fusions with no coverage around the breakpoints (remaining=40)
[2026-06-08T07:54:52] Indexing gene sequences 
[2026-06-08T07:54:53] Filtering genes with >=30% identity (remaining=21)
[2026-06-08T07:54:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=12)
[2026-06-08T07:54:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=12)
[2026-06-08T07:54:53] Searching for additional isoforms (remaining=13)
[2026-06-08T07:54:53] Assigning confidence scores to events 
[2026-06-08T07:54:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:54:54] Writing fusions to file 'aih-tih-sc-2482ef-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:54:54] Writing discarded fusions to file 'aih-tih-sc-2482ef-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:54:58] Freeing resources
[2026-06-08T07:55:03] Done (elapsed time=00:02:20, CPU time=00:02:19, peak memory=5.8gb)