[2026-06-03T20:13:57] Launching Arriba 2.4.0
[2026-06-03T20:13:57] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:14:05] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:14:09] Reading chimeric alignments from 'aih-tih-sc-b8457f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10465702)
[2026-06-03T20:21:13] Marking multi-mapping alignments (marked=6892731)
[2026-06-03T20:21:18] Detecting strandedness (reverse)
[2026-06-03T20:21:18] Assigning strands to alignments 
[2026-06-03T20:21:21] Annotating alignments 
[2026-06-03T20:21:56] Filtering duplicates (remaining=7732520)
[2026-06-03T20:22:04] 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=7318174)
[2026-06-03T20:22:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7318174)
[2026-06-03T20:22:09] Filtering viral contigs with expression lower than the top 5 (remaining=7318174)
[2026-06-03T20:22:14] Filtering viral contigs with less than 5% coverage (remaining=7318174)
[2026-06-03T20:22:16] Estimating fragment length (mate gap mean=-84.282, mate gap stddev=30.5704, read length mean=134.132)
[2026-06-03T20:22:16] Filtering read-through fragments with a distance <=10000bp (remaining=6856431)
[2026-06-03T20:22:18] Filtering inconsistently clipped mates (remaining=6734209)
[2026-06-03T20:22:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6536456)
[2026-06-03T20:22:25] Filtering fragments with small insert size (remaining=6535792)
[2026-06-03T20:22:27] Filtering alignments with long gaps (remaining=6535792)
[2026-06-03T20:22:30] Filtering fragments with both mates in the same gene (remaining=6534604)
[2026-06-03T20:22:32] Filtering fusions arising from hairpin structures (remaining=6095491)
[2026-06-03T20:22:35] Filtering reads with a mismatch p-value <=0.01 (remaining=2837844)
[2026-06-03T20:22:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=1417644)
[2026-06-03T20:23:04] Finding fusions and counting supporting reads (total=1067156)
[2026-06-03T20:23:22] Merging adjacent fusion breakpoints (remaining=1055567)
[2026-06-03T20:23:24] Filtering multi-mapping fusions by alignment score and read support (remaining=664115)
[2026-06-03T20:23:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:24:07] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=660382)
[2026-06-03T20:24:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=405532)
[2026-06-03T20:24:09] Filtering fusions with <2 supporting reads (remaining=44502)
[2026-06-03T20:24:10] Filtering fusions with an e-value >=0.3 (remaining=13602)
[2026-06-03T20:24:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=13652)
[2026-06-03T20:24:15] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=13550)
[2026-06-03T20:24:16] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=13550)
[2026-06-03T20:24:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8671)
[2026-06-03T20:24:24] Searching for fusions with spliced split reads (remaining=8693)
[2026-06-03T20:24:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=4773)
[2026-06-03T20:24:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4736)
[2026-06-03T20:24:32] Searching for fusions with >=4 spliced events (remaining=5950)
[2026-06-03T20:24:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2479)
[2026-06-03T20:24:50] Filtering fusions with anchors <=23nt (remaining=1961)
[2026-06-03T20:24:51] Filtering end-to-end fusions with low support (remaining=1896)
[2026-06-03T20:24:52] Filtering fusions with no coverage around the breakpoints (remaining=1854)
[2026-06-03T20:24:53] Indexing gene sequences 
[2026-06-03T20:25:00] Filtering genes with >=30% identity (remaining=614)
[2026-06-03T20:25:05] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=340)
[2026-06-03T20:25:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=207)
[2026-06-03T20:25:11] Searching for additional isoforms (remaining=314)
[2026-06-03T20:25:12] Assigning confidence scores to events 
[2026-06-03T20:25:17] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:25:18] Writing fusions to file 'aih-tih-sc-b8457f-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:25:21] Writing discarded fusions to file 'aih-tih-sc-b8457f-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:26:02] Freeing resources
[2026-06-03T20:26:29] Done (elapsed time=00:12:32, CPU time=00:12:31, peak memory=15.4gb)