[2026-06-08T08:35:41] Launching Arriba 2.4.0
[2026-06-08T08:35:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:54] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_04_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=14315841)
[2026-06-08T08:42:57] Marking multi-mapping alignments (marked=9175464)
[2026-06-08T08:43:03] Detecting strandedness (reverse)
[2026-06-08T08:43:03] Assigning strands to alignments 
[2026-06-08T08:43:06] Annotating alignments 
[2026-06-08T08:43:53] Filtering duplicates (remaining=4477703)
[2026-06-08T08:43:59] 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=4276223)
[2026-06-08T08:44:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4276223)
[2026-06-08T08:44:05] Filtering viral contigs with expression lower than the top 5 (remaining=4276223)
[2026-06-08T08:44:11] Filtering viral contigs with less than 5% coverage (remaining=4276223)
[2026-06-08T08:44:14] Estimating fragment length (mate gap mean=-87.636, mate gap stddev=26.9234, read length mean=126.977)
[2026-06-08T08:44:14] Filtering read-through fragments with a distance <=10000bp (remaining=4031789)
[2026-06-08T08:44:17] Filtering inconsistently clipped mates (remaining=3958397)
[2026-06-08T08:44:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3819607)
[2026-06-08T08:44:24] Filtering fragments with small insert size (remaining=3818750)
[2026-06-08T08:44:27] Filtering alignments with long gaps (remaining=3818749)
[2026-06-08T08:44:30] Filtering fragments with both mates in the same gene (remaining=3818035)
[2026-06-08T08:44:32] Filtering fusions arising from hairpin structures (remaining=3655900)
[2026-06-08T08:44:35] Filtering reads with a mismatch p-value <=0.01 (remaining=1615566)
[2026-06-08T08:44:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=546097)
[2026-06-08T08:44:56] Finding fusions and counting supporting reads (total=482674)
[2026-06-08T08:45:15] Merging adjacent fusion breakpoints (remaining=477094)
[2026-06-08T08:45:16] Filtering multi-mapping fusions by alignment score and read support (remaining=263586)
[2026-06-08T08:46:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=262531)
[2026-06-08T08:46:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=152835)
[2026-06-08T08:46:17] Filtering fusions with <2 supporting reads (remaining=13953)
[2026-06-08T08:46:18] Filtering fusions with an e-value >=0.3 (remaining=2863)
[2026-06-08T08:46:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2891)
[2026-06-08T08:46:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2820)
[2026-06-08T08:46:25] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2820)
[2026-06-08T08:46:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2774)
[2026-06-08T08:46:35] Searching for fusions with spliced split reads (remaining=2822)
[2026-06-08T08:46:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=2006)
[2026-06-08T08:46:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1998)
[2026-06-08T08:46:43] Searching for fusions with >=4 spliced events (remaining=2276)
[2026-06-08T08:46:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=933)
[2026-06-08T08:46:56] Filtering fusions with anchors <=23nt (remaining=808)
[2026-06-08T08:46:57] Filtering end-to-end fusions with low support (remaining=781)
[2026-06-08T08:46:57] Filtering fusions with no coverage around the breakpoints (remaining=742)
[2026-06-08T08:46:58] Indexing gene sequences 
[2026-06-08T08:47:02] Filtering genes with >=30% identity (remaining=238)
[2026-06-08T08:47:03] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=82)
[2026-06-08T08:47:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=68)
[2026-06-08T08:47:06] Searching for additional isoforms (remaining=86)
[2026-06-08T08:47:08] Assigning confidence scores to events 
[2026-06-08T08:47:10] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:10] Writing fusions to file 'BVT_FFPE_TRNA_stm_04_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:47:11] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_04_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:35] Freeing resources
[2026-06-08T08:48:00] Done (elapsed time=00:12:19, CPU time=00:12:17, peak memory=18.6gb)