[2026-06-08T08:26:41] Launching Arriba 2.4.0
[2026-06-08T08:26:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:54] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_05_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=12748595)
[2026-06-08T08:34:36] Marking multi-mapping alignments (marked=8317196)
[2026-06-08T08:34:44] Detecting strandedness (reverse)
[2026-06-08T08:34:44] Assigning strands to alignments 
[2026-06-08T08:34:48] Annotating alignments 
[2026-06-08T08:36:09] Filtering duplicates (remaining=5586361)
[2026-06-08T08:36:22] 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=5369675)
[2026-06-08T08:36:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5369675)
[2026-06-08T08:36:31] Filtering viral contigs with expression lower than the top 5 (remaining=5369675)
[2026-06-08T08:36:40] Filtering viral contigs with less than 5% coverage (remaining=5369675)
[2026-06-08T08:36:45] Estimating fragment length (mate gap mean=-85.94, mate gap stddev=25.8234, read length mean=124.259)
[2026-06-08T08:36:45] Filtering read-through fragments with a distance <=10000bp (remaining=5004102)
[2026-06-08T08:36:49] Filtering inconsistently clipped mates (remaining=4903934)
[2026-06-08T08:36:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4756081)
[2026-06-08T08:37:00] Filtering fragments with small insert size (remaining=4754957)
[2026-06-08T08:37:05] Filtering alignments with long gaps (remaining=4754957)
[2026-06-08T08:37:09] Filtering fragments with both mates in the same gene (remaining=4754033)
[2026-06-08T08:37:13] Filtering fusions arising from hairpin structures (remaining=4494027)
[2026-06-08T08:37:17] Filtering reads with a mismatch p-value <=0.01 (remaining=2092545)
[2026-06-08T08:37:34] Filtering reads with low entropy (k-mer content >=60%) (remaining=924355)
[2026-06-08T08:37:48] Finding fusions and counting supporting reads (total=737846)
[2026-06-08T08:38:18] Merging adjacent fusion breakpoints (remaining=725759)
[2026-06-08T08:38:20] Filtering multi-mapping fusions by alignment score and read support (remaining=385893)
[2026-06-08T08:39:21] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:33] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=384896)
[2026-06-08T08:39:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=228899)
[2026-06-08T08:39:36] Filtering fusions with <2 supporting reads (remaining=26270)
[2026-06-08T08:39:37] Filtering fusions with an e-value >=0.3 (remaining=5639)
[2026-06-08T08:39:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5691)
[2026-06-08T08:39:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5573)
[2026-06-08T08:39:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5573)
[2026-06-08T08:39:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5564)
[2026-06-08T08:39:56] Searching for fusions with spliced split reads (remaining=5611)
[2026-06-08T08:40:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=3508)
[2026-06-08T08:40:07] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3476)
[2026-06-08T08:40:08] Searching for fusions with >=4 spliced events (remaining=4255)
[2026-06-08T08:40:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1956)
[2026-06-08T08:40:28] Filtering fusions with anchors <=23nt (remaining=1715)
[2026-06-08T08:40:29] Filtering end-to-end fusions with low support (remaining=1663)
[2026-06-08T08:40:30] Filtering fusions with no coverage around the breakpoints (remaining=1630)
[2026-06-08T08:40:31] Indexing gene sequences 
[2026-06-08T08:40:38] Filtering genes with >=30% identity (remaining=407)
[2026-06-08T08:40:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=82)
[2026-06-08T08:40:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=78)
[2026-06-08T08:40:46] Searching for additional isoforms (remaining=94)
[2026-06-08T08:40:48] Assigning confidence scores to events 
[2026-06-08T08:40:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:52] Writing fusions to file 'BVT_FFPE_TRNA_utn_05_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:40:53] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_05_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:39] Freeing resources
[2026-06-08T08:42:13] Done (elapsed time=00:15:32, CPU time=00:15:31, peak memory=17.3gb)