[2026-06-08T08:49:30] Launching Arriba 2.4.0
[2026-06-08T08:49:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:47] Reading chimeric alignments from 'aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10336843)
[2026-06-08T08:57:27] Marking multi-mapping alignments (marked=6966744)
[2026-06-08T08:57:32] Detecting strandedness (reverse)
[2026-06-08T08:57:32] Assigning strands to alignments 
[2026-06-08T08:57:34] Annotating alignments 
[2026-06-08T08:58:08] Filtering duplicates (remaining=7195451)
[2026-06-08T08:58:16] 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=6734493)
[2026-06-08T08:58:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6734493)
[2026-06-08T08:58:20] Filtering viral contigs with expression lower than the top 5 (remaining=6734493)
[2026-06-08T08:58:25] Filtering viral contigs with less than 5% coverage (remaining=6734493)
[2026-06-08T08:58:27] Estimating fragment length (mate gap mean=-85.0558, mate gap stddev=29.9134, read length mean=131.872)
[2026-06-08T08:58:28] Filtering read-through fragments with a distance <=10000bp (remaining=6274405)
[2026-06-08T08:58:30] Filtering inconsistently clipped mates (remaining=6154321)
[2026-06-08T08:58:32] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5994333)
[2026-06-08T08:58:38] Filtering fragments with small insert size (remaining=5993513)
[2026-06-08T08:58:40] Filtering alignments with long gaps (remaining=5993513)
[2026-06-08T08:58:42] Filtering fragments with both mates in the same gene (remaining=5992337)
[2026-06-08T08:58:44] Filtering fusions arising from hairpin structures (remaining=5530018)
[2026-06-08T08:58:47] Filtering reads with a mismatch p-value <=0.01 (remaining=2478791)
[2026-06-08T08:59:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=1179724)
[2026-06-08T08:59:13] Finding fusions and counting supporting reads (total=911619)
[2026-06-08T08:59:31] Merging adjacent fusion breakpoints (remaining=900832)
[2026-06-08T08:59:33] Filtering multi-mapping fusions by alignment score and read support (remaining=558302)
[2026-06-08T09:00:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=555304)
[2026-06-08T09:00:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=334550)
[2026-06-08T09:00:19] Filtering fusions with <2 supporting reads (remaining=33722)
[2026-06-08T09:00:20] Filtering fusions with an e-value >=0.3 (remaining=11499)
[2026-06-08T09:00:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11567)
[2026-06-08T09:00:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11457)
[2026-06-08T09:00:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11457)
[2026-06-08T09:00:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7613)
[2026-06-08T09:00:33] Searching for fusions with spliced split reads (remaining=7638)
[2026-06-08T09:00:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=3985)
[2026-06-08T09:00:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3941)
[2026-06-08T09:00:41] Searching for fusions with >=4 spliced events (remaining=4721)
[2026-06-08T09:00:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1905)
[2026-06-08T09:00:58] Filtering fusions with anchors <=23nt (remaining=1461)
[2026-06-08T09:00:59] Filtering end-to-end fusions with low support (remaining=1407)
[2026-06-08T09:01:00] Filtering fusions with no coverage around the breakpoints (remaining=1383)
[2026-06-08T09:01:01] Indexing gene sequences 
[2026-06-08T09:01:06] Filtering genes with >=30% identity (remaining=423)
[2026-06-08T09:01:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=177)
[2026-06-08T09:01:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=161)
[2026-06-08T09:01:13] Searching for additional isoforms (remaining=211)
[2026-06-08T09:01:15] Assigning confidence scores to events 
[2026-06-08T09:01:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:19] Writing fusions to file 'aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:01:21] Writing discarded fusions to file 'aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:58] Freeing resources
[2026-06-08T09:02:18] Done (elapsed time=00:12:48, CPU time=00:12:46, peak memory=15.3gb)