[2026-06-08T08:47:35] Launching Arriba 2.4.0
[2026-06-08T08:47:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:52] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=13150358)
[2026-06-08T08:54:55] Marking multi-mapping alignments (marked=8384785)
[2026-06-08T08:55:01] Detecting strandedness (reverse)
[2026-06-08T08:55:01] Assigning strands to alignments 
[2026-06-08T08:55:03] Annotating alignments 
[2026-06-08T08:55:50] Filtering duplicates (remaining=3476530)
[2026-06-08T08:55:56] 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=3288576)
[2026-06-08T08:55:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3288576)
[2026-06-08T08:56:02] Filtering viral contigs with expression lower than the top 5 (remaining=3288576)
[2026-06-08T08:56:07] Filtering viral contigs with less than 5% coverage (remaining=3288576)
[2026-06-08T08:56:11] Estimating fragment length (mate gap mean=-85.4673, mate gap stddev=26.1629, read length mean=122.551)
[2026-06-08T08:56:11] Filtering read-through fragments with a distance <=10000bp (remaining=3093740)
[2026-06-08T08:56:14] Filtering inconsistently clipped mates (remaining=3043352)
[2026-06-08T08:56:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2942493)
[2026-06-08T08:56:20] Filtering fragments with small insert size (remaining=2941781)
[2026-06-08T08:56:23] Filtering alignments with long gaps (remaining=2941781)
[2026-06-08T08:56:26] Filtering fragments with both mates in the same gene (remaining=2941111)
[2026-06-08T08:56:28] Filtering fusions arising from hairpin structures (remaining=2839601)
[2026-06-08T08:56:31] Filtering reads with a mismatch p-value <=0.01 (remaining=1186383)
[2026-06-08T08:56:40] Filtering reads with low entropy (k-mer content >=60%) (remaining=403497)
[2026-06-08T08:56:48] Finding fusions and counting supporting reads (total=372010)
[2026-06-08T08:57:07] Merging adjacent fusion breakpoints (remaining=368964)
[2026-06-08T08:57:08] Filtering multi-mapping fusions by alignment score and read support (remaining=200538)
[2026-06-08T08:57:51] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=199669)
[2026-06-08T08:57:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=116251)
[2026-06-08T08:57:58] Filtering fusions with <2 supporting reads (remaining=8884)
[2026-06-08T08:57:58] Filtering fusions with an e-value >=0.3 (remaining=1833)
[2026-06-08T08:57:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1856)
[2026-06-08T08:58:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1786)
[2026-06-08T08:58:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1786)
[2026-06-08T08:58:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1760)
[2026-06-08T08:58:09] Searching for fusions with spliced split reads (remaining=1806)
[2026-06-08T08:58:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=1324)
[2026-06-08T08:58:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1314)
[2026-06-08T08:58:15] Searching for fusions with >=4 spliced events (remaining=1528)
[2026-06-08T08:58:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=704)
[2026-06-08T08:58:27] Filtering fusions with anchors <=23nt (remaining=629)
[2026-06-08T08:58:28] Filtering end-to-end fusions with low support (remaining=616)
[2026-06-08T08:58:28] Filtering fusions with no coverage around the breakpoints (remaining=602)
[2026-06-08T08:58:29] Indexing gene sequences 
[2026-06-08T08:58:31] Filtering genes with >=30% identity (remaining=207)
[2026-06-08T08:58:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=85)
[2026-06-08T08:58:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=55)
[2026-06-08T08:58:34] Searching for additional isoforms (remaining=70)
[2026-06-08T08:58:35] Assigning confidence scores to events 
[2026-06-08T08:58:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:37] Writing fusions to file 'BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:58:38] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:58:58] Freeing resources
[2026-06-08T08:59:20] Done (elapsed time=00:11:45, CPU time=00:11:43, peak memory=17.3gb)