[2026-06-03T20:17:59] Launching Arriba 2.4.0
[2026-06-03T20:17:59] Loading assembly from 'ref_genome.fa' 
[2026-06-03T20:18:13] Loading annotation from 'ref_annot.gtf' 
[2026-06-03T20:18:18] Reading chimeric alignments from 'aih-tih-sc-fe8311-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam' (total=10436951)
[2026-06-03T20:26:27] Marking multi-mapping alignments (marked=6574333)
[2026-06-03T20:26:31] Detecting strandedness (reverse)
[2026-06-03T20:26:31] Assigning strands to alignments 
[2026-06-03T20:26:33] Annotating alignments 
[2026-06-03T20:27:03] Filtering duplicates (remaining=6759681)
[2026-06-03T20:27:09] 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=6348451)
[2026-06-03T20:27:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6348451)
[2026-06-03T20:27:13] Filtering viral contigs with expression lower than the top 5 (remaining=6348451)
[2026-06-03T20:27:17] Filtering viral contigs with less than 5% coverage (remaining=6348451)
[2026-06-03T20:27:19] Estimating fragment length (mate gap mean=-86.9754, mate gap stddev=29.405, read length mean=130.198)
[2026-06-03T20:27:19] Filtering read-through fragments with a distance <=10000bp (remaining=5931330)
[2026-06-03T20:27:21] Filtering inconsistently clipped mates (remaining=5802888)
[2026-06-03T20:27:23] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5645792)
[2026-06-03T20:27:27] Filtering fragments with small insert size (remaining=5644253)
[2026-06-03T20:27:28] Filtering alignments with long gaps (remaining=5644251)
[2026-06-03T20:27:30] Filtering fragments with both mates in the same gene (remaining=5642989)
[2026-06-03T20:27:32] Filtering fusions arising from hairpin structures (remaining=5247523)
[2026-06-03T20:27:35] Filtering reads with a mismatch p-value <=0.01 (remaining=2264034)
[2026-06-03T20:27:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=1174098)
[2026-06-03T20:27:59] Finding fusions and counting supporting reads (total=875721)
[2026-06-03T20:28:14] Merging adjacent fusion breakpoints (remaining=862205)
[2026-06-03T20:28:15] Filtering multi-mapping fusions by alignment score and read support (remaining=551955)
[2026-06-03T20:28:44] Estimating expected number of fusions by random chance (e-value) 
[2026-06-03T20:28:50] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=548900)
[2026-06-03T20:28:51] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=314631)
[2026-06-03T20:28:52] Filtering fusions with <2 supporting reads (remaining=38691)
[2026-06-03T20:28:52] Filtering fusions with an e-value >=0.3 (remaining=9445)
[2026-06-03T20:28:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9513)
[2026-06-03T20:28:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9345)
[2026-06-03T20:28:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9347)
[2026-06-03T20:28:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7934)
[2026-06-03T20:29:03] Searching for fusions with spliced split reads (remaining=8077)
[2026-06-03T20:29:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=5161)
[2026-06-03T20:29:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5076)
[2026-06-03T20:29:10] Searching for fusions with >=4 spliced events (remaining=5934)
[2026-06-03T20:29:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2112)
[2026-06-03T20:29:37] Filtering fusions with anchors <=23nt (remaining=1475)
[2026-06-03T20:29:37] Filtering end-to-end fusions with low support (remaining=1427)
[2026-06-03T20:29:38] Filtering fusions with no coverage around the breakpoints (remaining=1398)
[2026-06-03T20:29:39] Indexing gene sequences 
[2026-06-03T20:29:44] Filtering genes with >=30% identity (remaining=421)
[2026-06-03T20:29:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=189)
[2026-06-03T20:29:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=177)
[2026-06-03T20:29:54] Searching for additional isoforms (remaining=207)
[2026-06-03T20:29:55] Assigning confidence scores to events 
[2026-06-03T20:29:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-03T20:29:59] Writing fusions to file 'aih-tih-sc-fe8311-R1_A23YTGFLT4_1.arriba.fusions.tsv' 
[2026-06-03T20:30:00] Writing discarded fusions to file 'aih-tih-sc-fe8311-R1_A23YTGFLT4_1.arriba.fusions.discarded.tsv'
[2026-06-03T20:30:30] Freeing resources
[2026-06-03T20:30:46] Done (elapsed time=00:12:47, CPU time=00:12:46, peak memory=15.3gb)