[2026-06-08T08:38:47] Launching Arriba 2.4.0
[2026-06-08T08:38:47] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:38:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:00] Reading chimeric alignments from 'aih-tih-sc-8d3f7c-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam' (total=8200387)
[2026-06-08T08:43:20] Marking multi-mapping alignments (marked=5503240)
[2026-06-08T08:43:23] Detecting strandedness (reverse)
[2026-06-08T08:43:23] Assigning strands to alignments 
[2026-06-08T08:43:25] Annotating alignments 
[2026-06-08T08:43:51] Filtering duplicates (remaining=3794265)
[2026-06-08T08:43:55] 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=3610098)
[2026-06-08T08:43:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3610098)
[2026-06-08T08:43:58] Filtering viral contigs with expression lower than the top 5 (remaining=3610098)
[2026-06-08T08:44:01] Filtering viral contigs with less than 5% coverage (remaining=3610098)
[2026-06-08T08:44:03] Estimating fragment length (mate gap mean=-84.019, mate gap stddev=26.7408, read length mean=121.334)
[2026-06-08T08:44:03] Filtering read-through fragments with a distance <=10000bp (remaining=3429818)
[2026-06-08T08:44:05] Filtering inconsistently clipped mates (remaining=3376824)
[2026-06-08T08:44:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3258737)
[2026-06-08T08:44:09] Filtering fragments with small insert size (remaining=3258061)
[2026-06-08T08:44:10] Filtering alignments with long gaps (remaining=3258060)
[2026-06-08T08:44:11] Filtering fragments with both mates in the same gene (remaining=3257146)
[2026-06-08T08:44:13] Filtering fusions arising from hairpin structures (remaining=3148541)
[2026-06-08T08:44:15] Filtering reads with a mismatch p-value <=0.01 (remaining=1327342)
[2026-06-08T08:44:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=413943)
[2026-06-08T08:44:28] Finding fusions and counting supporting reads (total=348715)
[2026-06-08T08:44:39] Merging adjacent fusion breakpoints (remaining=345639)
[2026-06-08T08:44:40] Filtering multi-mapping fusions by alignment score and read support (remaining=189233)
[2026-06-08T08:45:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:45:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=188463)
[2026-06-08T08:45:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=117982)
[2026-06-08T08:45:10] Filtering fusions with <2 supporting reads (remaining=11526)
[2026-06-08T08:45:11] Filtering fusions with an e-value >=0.3 (remaining=2903)
[2026-06-08T08:45:11] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2930)
[2026-06-08T08:45:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2867)
[2026-06-08T08:45:14] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2867)
[2026-06-08T08:45:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2821)
[2026-06-08T08:45:19] Searching for fusions with spliced split reads (remaining=2878)
[2026-06-08T08:45:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=2077)
[2026-06-08T08:45:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2058)
[2026-06-08T08:45:24] Searching for fusions with >=4 spliced events (remaining=2331)
[2026-06-08T08:45:25] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=980)
[2026-06-08T08:45:38] Filtering fusions with anchors <=23nt (remaining=838)
[2026-06-08T08:45:38] Filtering end-to-end fusions with low support (remaining=813)
[2026-06-08T08:45:39] Filtering fusions with no coverage around the breakpoints (remaining=796)
[2026-06-08T08:45:39] Indexing gene sequences 
[2026-06-08T08:45:43] Filtering genes with >=30% identity (remaining=247)
[2026-06-08T08:45:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=128)
[2026-06-08T08:45:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=117)
[2026-06-08T08:45:47] Searching for additional isoforms (remaining=140)
[2026-06-08T08:45:48] Assigning confidence scores to events 
[2026-06-08T08:45:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:45:50] Writing fusions to file 'aih-tih-sc-8d3f7c-R1_B23WHYVLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:45:51] Writing discarded fusions to file 'aih-tih-sc-8d3f7c-R1_B23WHYVLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:46:09] Freeing resources
[2026-06-08T08:46:21] Done (elapsed time=00:07:34, CPU time=00:07:33, peak memory=12.4gb)