[2026-06-03T20:14:50] Launching Arriba 2.4.0
[2026-06-03T20:14:50] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:15:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:15:08] Reading chimeric alignments from 'aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10336843)
[2026-06-03T20:23:54] Marking multi-mapping alignments (marked=6966744)
[2026-06-03T20:23:59] Detecting strandedness (reverse)
[2026-06-03T20:23:59] Assigning strands to alignments 
[2026-06-03T20:24:01] Annotating alignments 
[2026-06-03T20:24:33] Filtering duplicates (remaining=7195451)
[2026-06-03T20:24:41] 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)
[2026-06-03T20:24:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6734493)
[2026-06-03T20:24:45] Filtering viral contigs with expression lower than the top 5 (remaining=6734493)
[2026-06-03T20:24:50] Filtering viral contigs with less than 5% coverage (remaining=6734493)
[2026-06-03T20:24:52] Estimating fragment length (mate gap mean=-85.0558, mate gap stddev=29.9134, read length mean=131.872)
[2026-06-03T20:24:53] Filtering read-through fragments with a distance <=10000bp (remaining=6274405)
[2026-06-03T20:24:55] Filtering inconsistently clipped mates (remaining=6154321)
[2026-06-03T20:24:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5994333)
[2026-06-03T20:25:01] Filtering fragments with small insert size (remaining=5993513)
[2026-06-03T20:25:03] Filtering alignments with long gaps (remaining=5993513)
[2026-06-03T20:25:06] Filtering fragments with both mates in the same gene (remaining=5992337)
[2026-06-03T20:25:08] Filtering fusions arising from hairpin structures (remaining=5530018)
[2026-06-03T20:25:10] Filtering reads with a mismatch p-value <=0.01 (remaining=2478791)
[2026-06-03T20:25:25] Filtering reads with low entropy (k-mer content >=60%) (remaining=1179724)
[2026-06-03T20:25:37] Finding fusions and counting supporting reads (total=911619)
[2026-06-03T20:25:54] Merging adjacent fusion breakpoints (remaining=900832)
[2026-06-03T20:25:56] Filtering multi-mapping fusions by alignment score and read support (remaining=558302)
[2026-06-03T20:26:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:26:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=555304)
[2026-06-03T20:26:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=334550)
[2026-06-03T20:26:37] Filtering fusions with <2 supporting reads (remaining=33722)
[2026-06-03T20:26:38] Filtering fusions with an e-value >=0.3 (remaining=11499)
[2026-06-03T20:26:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11567)
[2026-06-03T20:26:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11457)
[2026-06-03T20:26:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11457)
[2026-06-03T20:26:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7613)
[2026-06-03T20:26:49] Searching for fusions with spliced split reads (remaining=7638)
[2026-06-03T20:26:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=3985)
[2026-06-03T20:26:55] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3941)
[2026-06-03T20:26:56] Searching for fusions with >=4 spliced events (remaining=4721)
[2026-06-03T20:26:57] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1905)
[2026-06-03T20:27:15] Filtering fusions with anchors <=23nt (remaining=1461)
[2026-06-03T20:27:16] Filtering end-to-end fusions with low support (remaining=1407)
[2026-06-03T20:27:17] Filtering fusions with no coverage around the breakpoints (remaining=1383)
[2026-06-03T20:27:17] Indexing gene sequences 
[2026-06-03T20:27:23] Filtering genes with >=30% identity (remaining=423)
[2026-06-03T20:27:25] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=177)
[2026-06-03T20:27:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=161)
[2026-06-03T20:27:29] Searching for additional isoforms (remaining=211)
[2026-06-03T20:27:30] Assigning confidence scores to events 
[2026-06-03T20:27:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:27:34] Writing fusions to file 'aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:27:35] Writing discarded fusions to file 'aih-tih-sc-a9fe91-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:28:09] Freeing resources
[2026-06-03T20:28:28] Done (elapsed time=00:13:38, CPU time=00:13:37, peak memory=15.3gb)