[2026-06-08T07:31:10] Launching Arriba 2.4.0
[2026-06-08T07:31:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:31:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:31:29] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=943832)
[2026-06-08T07:32:00] Marking multi-mapping alignments (marked=664325)
[2026-06-08T07:32:01] Detecting strandedness (reverse)
[2026-06-08T07:32:01] Assigning strands to alignments 
[2026-06-08T07:32:01] Annotating alignments 
[2026-06-08T07:32:06] Filtering duplicates (remaining=263091)
[2026-06-08T07:32:07] 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=246190)
[2026-06-08T07:32:07] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=246190)
[2026-06-08T07:32:07] Filtering viral contigs with expression lower than the top 5 (remaining=246190)
[2026-06-08T07:32:07] Filtering viral contigs with less than 5% coverage (remaining=246190)
[2026-06-08T07:32:08] Estimating fragment length (mate gap mean=-74.9675, mate gap stddev=27.78, read length mean=112.308)
[2026-06-08T07:32:08] Filtering read-through fragments with a distance <=10000bp (remaining=234328)
[2026-06-08T07:32:08] Filtering inconsistently clipped mates (remaining=226213)
[2026-06-08T07:32:09] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=217844)
[2026-06-08T07:32:09] Filtering fragments with small insert size (remaining=217547)
[2026-06-08T07:32:09] Filtering alignments with long gaps (remaining=217547)
[2026-06-08T07:32:09] Filtering fragments with both mates in the same gene (remaining=217461)
[2026-06-08T07:32:09] Filtering fusions arising from hairpin structures (remaining=205627)
[2026-06-08T07:32:10] Filtering reads with a mismatch p-value <=0.01 (remaining=71879)
[2026-06-08T07:32:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=23517)
[2026-06-08T07:32:11] Finding fusions and counting supporting reads (total=24798)
[2026-06-08T07:32:13] Merging adjacent fusion breakpoints (remaining=24785)
[2026-06-08T07:32:13] Filtering multi-mapping fusions by alignment score and read support (remaining=11435)
[2026-06-08T07:32:17] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:32:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=11359)
[2026-06-08T07:32:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=7343)
[2026-06-08T07:32:17] Filtering fusions with <2 supporting reads (remaining=302)
[2026-06-08T07:32:17] Filtering fusions with an e-value >=0.3 (remaining=133)
[2026-06-08T07:32:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=135)
[2026-06-08T07:32:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=131)
[2026-06-08T07:32:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=131)
[2026-06-08T07:32:18] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=123)
[2026-06-08T07:32:18] Searching for fusions with spliced split reads (remaining=127)
[2026-06-08T07:32:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=115)
[2026-06-08T07:32:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=115)
[2026-06-08T07:32:19] Searching for fusions with >=4 spliced events (remaining=117)
[2026-06-08T07:32:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=41)
[2026-06-08T07:32:36] Filtering fusions with anchors <=23nt (remaining=36)
[2026-06-08T07:32:36] Filtering end-to-end fusions with low support (remaining=26)
[2026-06-08T07:32:36] Filtering fusions with no coverage around the breakpoints (remaining=22)
[2026-06-08T07:32:36] Indexing gene sequences 
[2026-06-08T07:32:37] Filtering genes with >=30% identity (remaining=13)
[2026-06-08T07:32:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=6)
[2026-06-08T07:32:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=6)
[2026-06-08T07:32:37] Searching for additional isoforms (remaining=6)
[2026-06-08T07:32:37] Assigning confidence scores to events 
[2026-06-08T07:32:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:32:37] Writing fusions to file 'BVT_FFPE_TRNA_utn_01_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T07:32:37] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_01_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T07:32:40] Freeing resources
[2026-06-08T07:32:43] Done (elapsed time=00:01:33, CPU time=00:01:32, peak memory=5.01gb)