[2026-06-08T08:19:30] Launching Arriba 2.4.0
[2026-06-08T08:19:30] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:53] Reading chimeric alignments from 'BVT_FFPE_TRNA_brn_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=10925861)
[2026-06-08T08:26:18] Marking multi-mapping alignments (marked=7385124)
[2026-06-08T08:26:23] Detecting strandedness (reverse)
[2026-06-08T08:26:23] Assigning strands to alignments 
[2026-06-08T08:26:25] Annotating alignments 
[2026-06-08T08:27:05] Filtering duplicates (remaining=3175190)
[2026-06-08T08:27:11] 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=2937576)
[2026-06-08T08:27:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2937576)
[2026-06-08T08:27:15] Filtering viral contigs with expression lower than the top 5 (remaining=2937576)
[2026-06-08T08:27:20] Filtering viral contigs with less than 5% coverage (remaining=2937576)
[2026-06-08T08:27:23] Estimating fragment length (mate gap mean=-84.1949, mate gap stddev=27.9933, read length mean=121.802)
[2026-06-08T08:27:23] Filtering read-through fragments with a distance <=10000bp (remaining=2826385)
[2026-06-08T08:27:25] Filtering inconsistently clipped mates (remaining=2764877)
[2026-06-08T08:27:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2660905)
[2026-06-08T08:27:31] Filtering fragments with small insert size (remaining=2659985)
[2026-06-08T08:27:33] Filtering alignments with long gaps (remaining=2659985)
[2026-06-08T08:27:35] Filtering fragments with both mates in the same gene (remaining=2659335)
[2026-06-08T08:27:38] Filtering fusions arising from hairpin structures (remaining=2527289)
[2026-06-08T08:27:40] Filtering reads with a mismatch p-value <=0.01 (remaining=1114684)
[2026-06-08T08:27:48] Filtering reads with low entropy (k-mer content >=60%) (remaining=314544)
[2026-06-08T08:27:56] Finding fusions and counting supporting reads (total=285409)
[2026-06-08T08:28:11] Merging adjacent fusion breakpoints (remaining=283205)
[2026-06-08T08:28:12] Filtering multi-mapping fusions by alignment score and read support (remaining=152720)
[2026-06-08T08:28:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=151851)
[2026-06-08T08:28:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=90152)
[2026-06-08T08:28:57] Filtering fusions with <2 supporting reads (remaining=7188)
[2026-06-08T08:28:57] Filtering fusions with an e-value >=0.3 (remaining=1740)
[2026-06-08T08:28:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1758)
[2026-06-08T08:29:01] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1688)
[2026-06-08T08:29:01] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1688)
[2026-06-08T08:29:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1669)
[2026-06-08T08:29:06] Searching for fusions with spliced split reads (remaining=1779)
[2026-06-08T08:29:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=1376)
[2026-06-08T08:29:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1351)
[2026-06-08T08:29:11] Searching for fusions with >=4 spliced events (remaining=1467)
[2026-06-08T08:29:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=539)
[2026-06-08T08:29:28] Filtering fusions with anchors <=23nt (remaining=469)
[2026-06-08T08:29:29] Filtering end-to-end fusions with low support (remaining=448)
[2026-06-08T08:29:29] Filtering fusions with no coverage around the breakpoints (remaining=424)
[2026-06-08T08:29:29] Indexing gene sequences 
[2026-06-08T08:29:33] Filtering genes with >=30% identity (remaining=158)
[2026-06-08T08:29:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=87)
[2026-06-08T08:29:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=84)
[2026-06-08T08:29:40] Searching for additional isoforms (remaining=103)
[2026-06-08T08:29:40] Assigning confidence scores to events 
[2026-06-08T08:29:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:42] Writing fusions to file 'BVT_FFPE_TRNA_brn_01_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:29:43] Writing discarded fusions to file 'BVT_FFPE_TRNA_brn_01_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:30:02] Freeing resources
[2026-06-08T08:30:20] Done (elapsed time=00:10:50, CPU time=00:10:48, peak memory=15gb)