[2026-06-08T10:00:46] Launching Arriba 2.4.0
[2026-06-08T10:00:46] Loading assembly from 'ref_genome.fa' 
[2026-06-08T10:00:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T10:00:58] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_05_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=12749016)
[2026-06-08T10:07:47] Marking multi-mapping alignments (marked=8126811)
[2026-06-08T10:07:52] Detecting strandedness (reverse)
[2026-06-08T10:07:52] Assigning strands to alignments 
[2026-06-08T10:07:54] Annotating alignments 
[2026-06-08T10:08:31] Filtering duplicates (remaining=5809525)
[2026-06-08T10:08:37] 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=5565058)
[2026-06-08T10:08:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5565058)
[2026-06-08T10:08:42] Filtering viral contigs with expression lower than the top 5 (remaining=5565058)
[2026-06-08T10:08:48] Filtering viral contigs with less than 5% coverage (remaining=5565058)
[2026-06-08T10:08:50] Estimating fragment length (mate gap mean=-87.7401, mate gap stddev=28.4095, read length mean=130.352)
[2026-06-08T10:08:51] Filtering read-through fragments with a distance <=10000bp (remaining=5214533)
[2026-06-08T10:08:53] Filtering inconsistently clipped mates (remaining=5121043)
[2026-06-08T10:08:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4951677)
[2026-06-08T10:09:00] Filtering fragments with small insert size (remaining=4950956)
[2026-06-08T10:09:02] Filtering alignments with long gaps (remaining=4950956)
[2026-06-08T10:09:05] Filtering fragments with both mates in the same gene (remaining=4950104)
[2026-06-08T10:09:07] Filtering fusions arising from hairpin structures (remaining=4698279)
[2026-06-08T10:09:10] Filtering reads with a mismatch p-value <=0.01 (remaining=2254116)
[2026-06-08T10:09:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=806855)
[2026-06-08T10:09:32] Finding fusions and counting supporting reads (total=662295)
[2026-06-08T10:09:50] Merging adjacent fusion breakpoints (remaining=655394)
[2026-06-08T10:09:51] Filtering multi-mapping fusions by alignment score and read support (remaining=385598)
[2026-06-08T10:10:30] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T10:10:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=383451)
[2026-06-08T10:10:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=216100)
[2026-06-08T10:10:40] Filtering fusions with <2 supporting reads (remaining=24292)
[2026-06-08T10:10:41] Filtering fusions with an e-value >=0.3 (remaining=6198)
[2026-06-08T10:10:41] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6238)
[2026-06-08T10:10:46] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6125)
[2026-06-08T10:10:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6125)
[2026-06-08T10:10:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5483)
[2026-06-08T10:10:54] Searching for fusions with spliced split reads (remaining=5611)
[2026-06-08T10:11:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=3854)
[2026-06-08T10:11:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3770)
[2026-06-08T10:11:02] Searching for fusions with >=4 spliced events (remaining=4567)
[2026-06-08T10:11:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1831)
[2026-06-08T10:11:19] Filtering fusions with anchors <=23nt (remaining=1534)
[2026-06-08T10:11:20] Filtering end-to-end fusions with low support (remaining=1497)
[2026-06-08T10:11:21] Filtering fusions with no coverage around the breakpoints (remaining=1458)
[2026-06-08T10:11:22] Indexing gene sequences 
[2026-06-08T10:11:29] Filtering genes with >=30% identity (remaining=561)
[2026-06-08T10:11:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=345)
[2026-06-08T10:11:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=255)
[2026-06-08T10:11:40] Searching for additional isoforms (remaining=337)
[2026-06-08T10:11:41] Assigning confidence scores to events 
[2026-06-08T10:11:44] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T10:11:44] Writing fusions to file 'BVT_FFPE_TRNA_bst_05_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T10:11:47] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_05_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T10:12:12] Freeing resources
[2026-06-08T10:12:34] Done (elapsed time=00:11:48, CPU time=00:11:46, peak memory=17.2gb)