[2026-06-08T08:54:06] Launching Arriba 2.4.0
[2026-06-08T08:54:06] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:14] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:54:18] Reading chimeric alignments from 'aih-tih-sc-884b4c-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=14272020)
[2026-06-08T09:01:33] Marking multi-mapping alignments (marked=9744330)
[2026-06-08T09:01:38] Detecting strandedness (reverse)
[2026-06-08T09:01:38] Assigning strands to alignments 
[2026-06-08T09:01:41] Annotating alignments 
[2026-06-08T09:02:25] Filtering duplicates (remaining=6125331)
[2026-06-08T09:02:34] 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=5618357)
[2026-06-08T09:02:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5618357)
[2026-06-08T09:02:40] Filtering viral contigs with expression lower than the top 5 (remaining=5618357)
[2026-06-08T09:02:47] Filtering viral contigs with less than 5% coverage (remaining=5618357)
[2026-06-08T09:02:50] Estimating fragment length (mate gap mean=-85.9554, mate gap stddev=29.573, read length mean=129.359)
[2026-06-08T09:02:50] Filtering read-through fragments with a distance <=10000bp (remaining=5414859)
[2026-06-08T09:02:53] Filtering inconsistently clipped mates (remaining=5318582)
[2026-06-08T09:02:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5168632)
[2026-06-08T09:03:00] Filtering fragments with small insert size (remaining=5167755)
[2026-06-08T09:03:03] Filtering alignments with long gaps (remaining=5167755)
[2026-06-08T09:03:06] Filtering fragments with both mates in the same gene (remaining=5166853)
[2026-06-08T09:03:09] Filtering fusions arising from hairpin structures (remaining=4922215)
[2026-06-08T09:03:12] Filtering reads with a mismatch p-value <=0.01 (remaining=2082384)
[2026-06-08T09:03:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=567567)
[2026-06-08T09:03:35] Finding fusions and counting supporting reads (total=431050)
[2026-06-08T09:03:54] Merging adjacent fusion breakpoints (remaining=426969)
[2026-06-08T09:03:55] Filtering multi-mapping fusions by alignment score and read support (remaining=252838)
[2026-06-08T09:04:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=250751)
[2026-06-08T09:04:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=141976)
[2026-06-08T09:04:49] Filtering fusions with <2 supporting reads (remaining=17122)
[2026-06-08T09:04:50] Filtering fusions with an e-value >=0.3 (remaining=4963)
[2026-06-08T09:04:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5024)
[2026-06-08T09:04:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4945)
[2026-06-08T09:04:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4949)
[2026-06-08T09:04:57] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4284)
[2026-06-08T09:05:03] Searching for fusions with spliced split reads (remaining=4383)
[2026-06-08T09:05:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=3052)
[2026-06-08T09:05:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3001)
[2026-06-08T09:05:11] Searching for fusions with >=4 spliced events (remaining=3412)
[2026-06-08T09:05:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1302)
[2026-06-08T09:05:29] Filtering fusions with anchors <=23nt (remaining=957)
[2026-06-08T09:05:30] Filtering end-to-end fusions with low support (remaining=933)
[2026-06-08T09:05:30] Filtering fusions with no coverage around the breakpoints (remaining=912)
[2026-06-08T09:05:31] Indexing gene sequences 
[2026-06-08T09:05:36] Filtering genes with >=30% identity (remaining=308)
[2026-06-08T09:05:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=169)
[2026-06-08T09:05:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=144)
[2026-06-08T09:05:43] Searching for additional isoforms (remaining=180)
[2026-06-08T09:05:44] Assigning confidence scores to events 
[2026-06-08T09:05:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:47] Writing fusions to file 'aih-tih-sc-884b4c-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:48] Writing discarded fusions to file 'aih-tih-sc-884b4c-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:06:13] Freeing resources
[2026-06-08T09:06:34] Done (elapsed time=00:12:28, CPU time=00:12:27, peak memory=18.4gb)