[2026-06-08T08:32:31] Launching Arriba 2.4.0
[2026-06-08T08:32:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:49] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_05_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=10869206)
[2026-06-08T08:39:07] Marking multi-mapping alignments (marked=7017652)
[2026-06-08T08:39:11] Detecting strandedness (reverse)
[2026-06-08T08:39:11] Assigning strands to alignments 
[2026-06-08T08:39:13] Annotating alignments 
[2026-06-08T08:39:44] Filtering duplicates (remaining=3729679)
[2026-06-08T08:39:49] 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=3555124)
[2026-06-08T08:39:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3555124)
[2026-06-08T08:39:52] Filtering viral contigs with expression lower than the top 5 (remaining=3555124)
[2026-06-08T08:39:56] Filtering viral contigs with less than 5% coverage (remaining=3555124)
[2026-06-08T08:39:58] Estimating fragment length (mate gap mean=-87.1646, mate gap stddev=28.1963, read length mean=129.661)
[2026-06-08T08:39:58] Filtering read-through fragments with a distance <=10000bp (remaining=3393244)
[2026-06-08T08:40:00] Filtering inconsistently clipped mates (remaining=3343116)
[2026-06-08T08:40:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3234887)
[2026-06-08T08:40:05] Filtering fragments with small insert size (remaining=3234343)
[2026-06-08T08:40:07] Filtering alignments with long gaps (remaining=3234342)
[2026-06-08T08:40:08] Filtering fragments with both mates in the same gene (remaining=3233793)
[2026-06-08T08:40:10] Filtering fusions arising from hairpin structures (remaining=3118994)
[2026-06-08T08:40:12] Filtering reads with a mismatch p-value <=0.01 (remaining=1420325)
[2026-06-08T08:40:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=397604)
[2026-06-08T08:40:27] Finding fusions and counting supporting reads (total=347370)
[2026-06-08T08:40:41] Merging adjacent fusion breakpoints (remaining=344673)
[2026-06-08T08:40:42] Filtering multi-mapping fusions by alignment score and read support (remaining=200131)
[2026-06-08T08:41:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=198882)
[2026-06-08T08:41:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=115892)
[2026-06-08T08:41:17] Filtering fusions with <2 supporting reads (remaining=10940)
[2026-06-08T08:41:18] Filtering fusions with an e-value >=0.3 (remaining=2884)
[2026-06-08T08:41:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2906)
[2026-06-08T08:41:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2828)
[2026-06-08T08:41:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2828)
[2026-06-08T08:41:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2643)
[2026-06-08T08:41:29] Searching for fusions with spliced split reads (remaining=2715)
[2026-06-08T08:41:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=2018)
[2026-06-08T08:41:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1974)
[2026-06-08T08:41:36] Searching for fusions with >=4 spliced events (remaining=2222)
[2026-06-08T08:41:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=795)
[2026-06-08T08:41:54] Filtering fusions with anchors <=23nt (remaining=679)
[2026-06-08T08:41:54] Filtering end-to-end fusions with low support (remaining=660)
[2026-06-08T08:41:55] Filtering fusions with no coverage around the breakpoints (remaining=641)
[2026-06-08T08:41:55] Indexing gene sequences 
[2026-06-08T08:42:00] Filtering genes with >=30% identity (remaining=281)
[2026-06-08T08:42:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=196)
[2026-06-08T08:42:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=160)
[2026-06-08T08:42:05] Searching for additional isoforms (remaining=198)
[2026-06-08T08:42:06] Assigning confidence scores to events 
[2026-06-08T08:42:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:08] Writing fusions to file 'BVT_FFPE_TRNA_bst_05_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:42:10] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_05_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:31] Freeing resources
[2026-06-08T08:42:49] Done (elapsed time=00:10:18, CPU time=00:10:17, peak memory=14.9gb)