[2026-06-08T08:58:20] Launching Arriba 2.4.0
[2026-06-08T08:58:20] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:58:35] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:58:40] Reading chimeric alignments from 'aih-tih-sc-98fc22-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=10218433)
[2026-06-08T09:06:42] Marking multi-mapping alignments (marked=6668272)
[2026-06-08T09:06:47] Detecting strandedness (reverse)
[2026-06-08T09:06:47] Assigning strands to alignments 
[2026-06-08T09:06:49] Annotating alignments 
[2026-06-08T09:07:24] Filtering duplicates (remaining=5507536)
[2026-06-08T09:07:30] 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=5249396)
[2026-06-08T09:07:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5249396)
[2026-06-08T09:07:35] Filtering viral contigs with expression lower than the top 5 (remaining=5249396)
[2026-06-08T09:07:40] Filtering viral contigs with less than 5% coverage (remaining=5249396)
[2026-06-08T09:07:42] Estimating fragment length (mate gap mean=-86.5326, mate gap stddev=28.421, read length mean=126.955)
[2026-06-08T09:07:43] Filtering read-through fragments with a distance <=10000bp (remaining=4875464)
[2026-06-08T09:07:45] Filtering inconsistently clipped mates (remaining=4785721)
[2026-06-08T09:07:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4678369)
[2026-06-08T09:07:51] Filtering fragments with small insert size (remaining=4677597)
[2026-06-08T09:07:54] Filtering alignments with long gaps (remaining=4677597)
[2026-06-08T09:07:56] Filtering fragments with both mates in the same gene (remaining=4676724)
[2026-06-08T09:07:58] Filtering fusions arising from hairpin structures (remaining=4404300)
[2026-06-08T09:08:01] Filtering reads with a mismatch p-value <=0.01 (remaining=1947957)
[2026-06-08T09:08:14] Filtering reads with low entropy (k-mer content >=60%) (remaining=787980)
[2026-06-08T09:08:25] Finding fusions and counting supporting reads (total=635302)
[2026-06-08T09:08:43] Merging adjacent fusion breakpoints (remaining=626823)
[2026-06-08T09:08:44] Filtering multi-mapping fusions by alignment score and read support (remaining=393222)
[2026-06-08T09:09:19] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:09:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=391475)
[2026-06-08T09:09:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=206303)
[2026-06-08T09:09:26] Filtering fusions with <2 supporting reads (remaining=24217)
[2026-06-08T09:09:27] Filtering fusions with an e-value >=0.3 (remaining=6060)
[2026-06-08T09:09:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6108)
[2026-06-08T09:09:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6021)
[2026-06-08T09:09:32] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6021)
[2026-06-08T09:09:33] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5594)
[2026-06-08T09:09:38] Searching for fusions with spliced split reads (remaining=5700)
[2026-06-08T09:09:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=3814)
[2026-06-08T09:09:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3774)
[2026-06-08T09:09:45] Searching for fusions with >=4 spliced events (remaining=4407)
[2026-06-08T09:09:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1775)
[2026-06-08T09:10:06] Filtering fusions with anchors <=23nt (remaining=1345)
[2026-06-08T09:10:06] Filtering end-to-end fusions with low support (remaining=1299)
[2026-06-08T09:10:07] Filtering fusions with no coverage around the breakpoints (remaining=1268)
[2026-06-08T09:10:07] Indexing gene sequences 
[2026-06-08T09:10:13] Filtering genes with >=30% identity (remaining=366)
[2026-06-08T09:10:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=93)
[2026-06-08T09:10:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=88)
[2026-06-08T09:10:18] Searching for additional isoforms (remaining=127)
[2026-06-08T09:10:19] Assigning confidence scores to events 
[2026-06-08T09:10:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:10:23] Writing fusions to file 'aih-tih-sc-98fc22-R1_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:10:24] Writing discarded fusions to file 'aih-tih-sc-98fc22-R1_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:56] Freeing resources
[2026-06-08T09:11:14] Done (elapsed time=00:12:54, CPU time=00:12:53, peak memory=14.9gb)