[2026-06-08T08:16:41] Launching Arriba 2.4.0
[2026-06-08T08:16:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:16:56] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_06_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=8891546)
[2026-06-08T08:21:01] Marking multi-mapping alignments (marked=5915409)
[2026-06-08T08:21:04] Detecting strandedness (reverse)
[2026-06-08T08:21:04] Assigning strands to alignments 
[2026-06-08T08:21:06] Annotating alignments 
[2026-06-08T08:21:34] Filtering duplicates (remaining=2192148)
[2026-06-08T08:21:37] 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=1997097)
[2026-06-08T08:21:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1997097)
[2026-06-08T08:21:41] Filtering viral contigs with expression lower than the top 5 (remaining=1997097)
[2026-06-08T08:21:44] Filtering viral contigs with less than 5% coverage (remaining=1997097)
[2026-06-08T08:21:46] Estimating fragment length (mate gap mean=-85.1954, mate gap stddev=27.9619, read length mean=125.648)
[2026-06-08T08:21:46] Filtering read-through fragments with a distance <=10000bp (remaining=1913142)
[2026-06-08T08:21:48] Filtering inconsistently clipped mates (remaining=1878104)
[2026-06-08T08:21:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1800743)
[2026-06-08T08:21:51] Filtering fragments with small insert size (remaining=1800231)
[2026-06-08T08:21:53] Filtering alignments with long gaps (remaining=1800231)
[2026-06-08T08:21:55] Filtering fragments with both mates in the same gene (remaining=1799840)
[2026-06-08T08:21:56] Filtering fusions arising from hairpin structures (remaining=1743926)
[2026-06-08T08:21:58] Filtering reads with a mismatch p-value <=0.01 (remaining=730373)
[2026-06-08T08:22:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=170599)
[2026-06-08T08:22:08] Finding fusions and counting supporting reads (total=158170)
[2026-06-08T08:22:18] Merging adjacent fusion breakpoints (remaining=157279)
[2026-06-08T08:22:19] Filtering multi-mapping fusions by alignment score and read support (remaining=82578)
[2026-06-08T08:22:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:22:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=81858)
[2026-06-08T08:22:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=49829)
[2026-06-08T08:22:48] Filtering fusions with <2 supporting reads (remaining=2938)
[2026-06-08T08:22:48] Filtering fusions with an e-value >=0.3 (remaining=787)
[2026-06-08T08:22:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=803)
[2026-06-08T08:22:51] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=771)
[2026-06-08T08:22:51] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=771)
[2026-06-08T08:22:51] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=760)
[2026-06-08T08:22:54] Searching for fusions with spliced split reads (remaining=827)
[2026-06-08T08:22:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=658)
[2026-06-08T08:22:58] Filtering read-through fusions with breakpoints near the gene boundary (remaining=650)
[2026-06-08T08:22:58] Searching for fusions with >=4 spliced events (remaining=676)
[2026-06-08T08:22:59] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=219)
[2026-06-08T08:23:10] Filtering fusions with anchors <=23nt (remaining=182)
[2026-06-08T08:23:10] Filtering end-to-end fusions with low support (remaining=171)
[2026-06-08T08:23:11] Filtering fusions with no coverage around the breakpoints (remaining=155)
[2026-06-08T08:23:11] Indexing gene sequences 
[2026-06-08T08:23:13] Filtering genes with >=30% identity (remaining=52)
[2026-06-08T08:23:13] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=17)
[2026-06-08T08:23:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=17)
[2026-06-08T08:23:14] Searching for additional isoforms (remaining=20)
[2026-06-08T08:23:15] Assigning confidence scores to events 
[2026-06-08T08:23:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:23:16] Writing fusions to file 'BVT_FFPE_TRNA_stm_06_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:23:16] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_06_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:23:25] Freeing resources
[2026-06-08T08:23:37] Done (elapsed time=00:06:56, CPU time=00:06:55, peak memory=12.9gb)