[2026-06-08T07:36:08] Launching Arriba 2.4.0
[2026-06-08T07:36:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:36:27] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:36:33] Reading chimeric alignments from 'BVT_FFPE_TRNA_bld_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=1999616)
[2026-06-08T07:37:59] Marking multi-mapping alignments (marked=1328046)
[2026-06-08T07:38:00] Detecting strandedness (reverse)
[2026-06-08T07:38:00] Assigning strands to alignments 
[2026-06-08T07:38:00] Annotating alignments 
[2026-06-08T07:38:08] Filtering duplicates (remaining=632957)
[2026-06-08T07:38:10] 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=556700)
[2026-06-08T07:38:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=556700)
[2026-06-08T07:38:10] Filtering viral contigs with expression lower than the top 5 (remaining=556700)
[2026-06-08T07:38:11] Filtering viral contigs with less than 5% coverage (remaining=556700)
[2026-06-08T07:38:12] Estimating fragment length (mate gap mean=-80.4392, mate gap stddev=27.6288, read length mean=117.921)
[2026-06-08T07:38:12] Filtering read-through fragments with a distance <=10000bp (remaining=528341)
[2026-06-08T07:38:13] Filtering inconsistently clipped mates (remaining=514579)
[2026-06-08T07:38:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=497481)
[2026-06-08T07:38:14] Filtering fragments with small insert size (remaining=497259)
[2026-06-08T07:38:14] Filtering alignments with long gaps (remaining=497259)
[2026-06-08T07:38:14] Filtering fragments with both mates in the same gene (remaining=497144)
[2026-06-08T07:38:15] Filtering fusions arising from hairpin structures (remaining=474134)
[2026-06-08T07:38:15] Filtering reads with a mismatch p-value <=0.01 (remaining=209417)
[2026-06-08T07:38:17] Filtering reads with low entropy (k-mer content >=60%) (remaining=66916)
[2026-06-08T07:38:18] Finding fusions and counting supporting reads (total=64632)
[2026-06-08T07:38:22] Merging adjacent fusion breakpoints (remaining=64350)
[2026-06-08T07:38:22] Filtering multi-mapping fusions by alignment score and read support (remaining=34120)
[2026-06-08T07:38:30] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:38:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=33864)
[2026-06-08T07:38:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=19772)
[2026-06-08T07:38:30] Filtering fusions with <2 supporting reads (remaining=1137)
[2026-06-08T07:38:31] Filtering fusions with an e-value >=0.3 (remaining=444)
[2026-06-08T07:38:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=453)
[2026-06-08T07:38:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=438)
[2026-06-08T07:38:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=439)
[2026-06-08T07:38:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=419)
[2026-06-08T07:38:32] Searching for fusions with spliced split reads (remaining=431)
[2026-06-08T07:38:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=370)
[2026-06-08T07:38:34] Filtering read-through fusions with breakpoints near the gene boundary (remaining=358)
[2026-06-08T07:38:34] Searching for fusions with >=4 spliced events (remaining=367)
[2026-06-08T07:38:34] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=123)
[2026-06-08T07:38:54] Filtering fusions with anchors <=23nt (remaining=100)
[2026-06-08T07:38:54] Filtering end-to-end fusions with low support (remaining=94)
[2026-06-08T07:38:54] Filtering fusions with no coverage around the breakpoints (remaining=91)
[2026-06-08T07:38:54] Indexing gene sequences 
[2026-06-08T07:38:55] Filtering genes with >=30% identity (remaining=53)
[2026-06-08T07:38:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=38)
[2026-06-08T07:38:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=38)
[2026-06-08T07:38:56] Searching for additional isoforms (remaining=42)
[2026-06-08T07:38:56] Assigning confidence scores to events 
[2026-06-08T07:38:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:38:57] Writing fusions to file 'BVT_FFPE_TRNA_bld_01_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T07:38:57] Writing discarded fusions to file 'BVT_FFPE_TRNA_bld_01_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T07:39:02] Freeing resources
[2026-06-08T07:39:07] Done (elapsed time=00:02:59, CPU time=00:02:58, peak memory=6.11gb)