[2026-06-08T08:23:18] Launching Arriba 2.4.0
[2026-06-08T08:23:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:32] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:36] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=7766979)
[2026-06-08T08:27:35] Marking multi-mapping alignments (marked=4984640)
[2026-06-08T08:27:38] Detecting strandedness (reverse)
[2026-06-08T08:27:38] Assigning strands to alignments 
[2026-06-08T08:27:39] Annotating alignments 
[2026-06-08T08:28:01] Filtering duplicates (remaining=2555352)
[2026-06-08T08:28:05] 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=2437134)
[2026-06-08T08:28:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2437134)
[2026-06-08T08:28:07] Filtering viral contigs with expression lower than the top 5 (remaining=2437134)
[2026-06-08T08:28:10] Filtering viral contigs with less than 5% coverage (remaining=2437134)
[2026-06-08T08:28:11] Estimating fragment length (mate gap mean=-85.162, mate gap stddev=26.3175, read length mean=122.417)
[2026-06-08T08:28:11] Filtering read-through fragments with a distance <=10000bp (remaining=2293139)
[2026-06-08T08:28:13] Filtering inconsistently clipped mates (remaining=2257554)
[2026-06-08T08:28:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2196154)
[2026-06-08T08:28:16] Filtering fragments with small insert size (remaining=2195671)
[2026-06-08T08:28:17] Filtering alignments with long gaps (remaining=2195671)
[2026-06-08T08:28:18] Filtering fragments with both mates in the same gene (remaining=2195236)
[2026-06-08T08:28:20] Filtering fusions arising from hairpin structures (remaining=2120577)
[2026-06-08T08:28:21] Filtering reads with a mismatch p-value <=0.01 (remaining=901144)
[2026-06-08T08:28:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=304967)
[2026-06-08T08:28:31] Finding fusions and counting supporting reads (total=286600)
[2026-06-08T08:28:40] Merging adjacent fusion breakpoints (remaining=284697)
[2026-06-08T08:28:40] Filtering multi-mapping fusions by alignment score and read support (remaining=156686)
[2026-06-08T08:29:01] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:29:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=156013)
[2026-06-08T08:29:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=89364)
[2026-06-08T08:29:05] Filtering fusions with <2 supporting reads (remaining=6410)
[2026-06-08T08:29:05] Filtering fusions with an e-value >=0.3 (remaining=1406)
[2026-06-08T08:29:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1425)
[2026-06-08T08:29:07] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1392)
[2026-06-08T08:29:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1392)
[2026-06-08T08:29:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1375)
[2026-06-08T08:29:11] Searching for fusions with spliced split reads (remaining=1503)
[2026-06-08T08:29:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=1063)
[2026-06-08T08:29:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1056)
[2026-06-08T08:29:14] Searching for fusions with >=4 spliced events (remaining=1167)
[2026-06-08T08:29:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=511)
[2026-06-08T08:29:27] Filtering fusions with anchors <=23nt (remaining=469)
[2026-06-08T08:29:27] Filtering end-to-end fusions with low support (remaining=456)
[2026-06-08T08:29:27] Filtering fusions with no coverage around the breakpoints (remaining=443)
[2026-06-08T08:29:27] Indexing gene sequences 
[2026-06-08T08:29:30] Filtering genes with >=30% identity (remaining=150)
[2026-06-08T08:29:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=56)
[2026-06-08T08:29:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=56)
[2026-06-08T08:29:32] Searching for additional isoforms (remaining=66)
[2026-06-08T08:29:32] Assigning confidence scores to events 
[2026-06-08T08:29:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:34] Writing fusions to file 'BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:29:34] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:29:46] Freeing resources
[2026-06-08T08:29:57] Done (elapsed time=00:06:39, CPU time=00:06:39, peak memory=11.9gb)