[2026-06-08T09:03:10] Launching Arriba 2.4.0
[2026-06-08T09:03:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:03:21] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:03:27] Reading chimeric alignments from 'aih-tih-sc-d12f1f-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=10260243)
[2026-06-08T09:11:04] Marking multi-mapping alignments (marked=6102731)
[2026-06-08T09:11:08] Detecting strandedness (reverse)
[2026-06-08T09:11:08] Assigning strands to alignments 
[2026-06-08T09:11:11] Annotating alignments 
[2026-06-08T09:11:48] Filtering duplicates (remaining=7371984)
[2026-06-08T09:11:57] 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=7128581)
[2026-06-08T09:12:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7128581)
[2026-06-08T09:12:02] Filtering viral contigs with expression lower than the top 5 (remaining=7128581)
[2026-06-08T09:12:07] Filtering viral contigs with less than 5% coverage (remaining=7128581)
[2026-06-08T09:12:10] Estimating fragment length (mate gap mean=-85.0121, mate gap stddev=30.0132, read length mean=135.587)
[2026-06-08T09:12:10] Filtering read-through fragments with a distance <=10000bp (remaining=6780110)
[2026-06-08T09:12:12] Filtering inconsistently clipped mates (remaining=6714223)
[2026-06-08T09:12:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6577319)
[2026-06-08T09:12:19] Filtering fragments with small insert size (remaining=6576864)
[2026-06-08T09:12:22] Filtering alignments with long gaps (remaining=6576864)
[2026-06-08T09:12:24] Filtering fragments with both mates in the same gene (remaining=6575698)
[2026-06-08T09:12:27] Filtering fusions arising from hairpin structures (remaining=6368535)
[2026-06-08T09:12:29] Filtering reads with a mismatch p-value <=0.01 (remaining=3506599)
[2026-06-08T09:12:46] Filtering reads with low entropy (k-mer content >=60%) (remaining=1401581)
[2026-06-08T09:12:59] Finding fusions and counting supporting reads (total=872516)
[2026-06-08T09:13:18] Merging adjacent fusion breakpoints (remaining=866073)
[2026-06-08T09:13:20] Filtering multi-mapping fusions by alignment score and read support (remaining=589502)
[2026-06-08T09:13:55] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:14:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=587158)
[2026-06-08T09:14:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=389763)
[2026-06-08T09:14:06] Filtering fusions with <2 supporting reads (remaining=52619)
[2026-06-08T09:14:07] Filtering fusions with an e-value >=0.3 (remaining=12008)
[2026-06-08T09:14:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12055)
[2026-06-08T09:14:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12004)
[2026-06-08T09:14:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12004)
[2026-06-08T09:14:14] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=10022)
[2026-06-08T09:14:20] Searching for fusions with spliced split reads (remaining=10124)
[2026-06-08T09:14:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=5463)
[2026-06-08T09:14:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5409)
[2026-06-08T09:14:28] Searching for fusions with >=4 spliced events (remaining=7022)
[2026-06-08T09:14:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2601)
[2026-06-08T09:14:46] Filtering fusions with anchors <=23nt (remaining=2219)
[2026-06-08T09:14:47] Filtering end-to-end fusions with low support (remaining=2184)
[2026-06-08T09:14:48] Filtering fusions with no coverage around the breakpoints (remaining=2144)
[2026-06-08T09:14:48] Indexing gene sequences 
[2026-06-08T09:14:56] Filtering genes with >=30% identity (remaining=678)
[2026-06-08T09:15:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=384)
[2026-06-08T09:15:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=296)
[2026-06-08T09:15:06] Searching for additional isoforms (remaining=477)
[2026-06-08T09:15:08] Assigning confidence scores to events 
[2026-06-08T09:15:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:15:12] Writing fusions to file 'aih-tih-sc-d12f1f-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:15:17] Writing discarded fusions to file 'aih-tih-sc-d12f1f-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:15:49] Freeing resources
[2026-06-08T09:16:06] Done (elapsed time=00:12:56, CPU time=00:12:55, peak memory=14.6gb)