[2026-06-08T07:31:10] Launching Arriba 2.4.0
[2026-06-08T07:31:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:31:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:31:35] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=1339191)
[2026-06-08T07:32:25] Marking multi-mapping alignments (marked=965446)
[2026-06-08T07:32:26] Detecting strandedness (reverse)
[2026-06-08T07:32:26] Assigning strands to alignments 
[2026-06-08T07:32:26] Annotating alignments 
[2026-06-08T07:32:32] Filtering duplicates (remaining=392133)
[2026-06-08T07:32:33] 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=365159)
[2026-06-08T07:32:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=365159)
[2026-06-08T07:32:34] Filtering viral contigs with expression lower than the top 5 (remaining=365159)
[2026-06-08T07:32:34] Filtering viral contigs with less than 5% coverage (remaining=365159)
[2026-06-08T07:32:35] Estimating fragment length (mate gap mean=-75.0142, mate gap stddev=27.7078, read length mean=110.006)
[2026-06-08T07:32:35] Filtering read-through fragments with a distance <=10000bp (remaining=349073)
[2026-06-08T07:32:36] Filtering inconsistently clipped mates (remaining=336230)
[2026-06-08T07:32:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=322242)
[2026-06-08T07:32:37] Filtering fragments with small insert size (remaining=321826)
[2026-06-08T07:32:37] Filtering alignments with long gaps (remaining=321826)
[2026-06-08T07:32:37] Filtering fragments with both mates in the same gene (remaining=321729)
[2026-06-08T07:32:37] Filtering fusions arising from hairpin structures (remaining=303951)
[2026-06-08T07:32:38] Filtering reads with a mismatch p-value <=0.01 (remaining=100408)
[2026-06-08T07:32:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=34226)
[2026-06-08T07:32:40] Finding fusions and counting supporting reads (total=35949)
[2026-06-08T07:32:42] Merging adjacent fusion breakpoints (remaining=35811)
[2026-06-08T07:32:42] Filtering multi-mapping fusions by alignment score and read support (remaining=17217)
[2026-06-08T07:32:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:32:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=17123)
[2026-06-08T07:32:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=11589)
[2026-06-08T07:32:48] Filtering fusions with <2 supporting reads (remaining=492)
[2026-06-08T07:32:48] Filtering fusions with an e-value >=0.3 (remaining=187)
[2026-06-08T07:32:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=192)
[2026-06-08T07:32:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=185)
[2026-06-08T07:32:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=185)
[2026-06-08T07:32:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=169)
[2026-06-08T07:32:50] Searching for fusions with spliced split reads (remaining=171)
[2026-06-08T07:32:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=152)
[2026-06-08T07:32:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=150)
[2026-06-08T07:32:50] Searching for fusions with >=4 spliced events (remaining=150)
[2026-06-08T07:32:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=69)
[2026-06-08T07:33:12] Filtering fusions with anchors <=23nt (remaining=61)
[2026-06-08T07:33:12] Filtering end-to-end fusions with low support (remaining=42)
[2026-06-08T07:33:12] Filtering fusions with no coverage around the breakpoints (remaining=25)
[2026-06-08T07:33:13] Indexing gene sequences 
[2026-06-08T07:33:13] Filtering genes with >=30% identity (remaining=13)
[2026-06-08T07:33:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-06-08T07:33:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-06-08T07:33:14] Searching for additional isoforms (remaining=6)
[2026-06-08T07:33:14] Assigning confidence scores to events 
[2026-06-08T07:33:14] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:33:14] Writing fusions to file 'BVT_FFPE_TRNA_utn_01_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T07:33:14] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_01_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T07:33:17] Freeing resources
[2026-06-08T07:33:21] Done (elapsed time=00:02:11, CPU time=00:02:10, peak memory=5.44gb)