[2026-06-08T08:30:44] Launching Arriba 2.4.0
[2026-06-08T08:30:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:57] Reading chimeric alignments from 'BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=12327698)
[2026-06-08T08:37:31] Marking multi-mapping alignments (marked=7951323)
[2026-06-08T08:37:36] Detecting strandedness (reverse)
[2026-06-08T08:37:36] Assigning strands to alignments 
[2026-06-08T08:37:38] Annotating alignments 
[2026-06-08T08:38:21] Filtering duplicates (remaining=6502680)
[2026-06-08T08:38:29] 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=6212270)
[2026-06-08T08:38:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6212270)
[2026-06-08T08:38:34] Filtering viral contigs with expression lower than the top 5 (remaining=6212270)
[2026-06-08T08:38:39] Filtering viral contigs with less than 5% coverage (remaining=6212270)
[2026-06-08T08:38:42] Estimating fragment length (mate gap mean=-85.4058, mate gap stddev=27.1794, read length mean=123.488)
[2026-06-08T08:38:42] Filtering read-through fragments with a distance <=10000bp (remaining=5763455)
[2026-06-08T08:38:45] Filtering inconsistently clipped mates (remaining=5670265)
[2026-06-08T08:38:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5535548)
[2026-06-08T08:38:53] Filtering fragments with small insert size (remaining=5534668)
[2026-06-08T08:38:55] Filtering alignments with long gaps (remaining=5534668)
[2026-06-08T08:38:58] Filtering fragments with both mates in the same gene (remaining=5533523)
[2026-06-08T08:39:01] Filtering fusions arising from hairpin structures (remaining=5285581)
[2026-06-08T08:39:04] Filtering reads with a mismatch p-value <=0.01 (remaining=2540893)
[2026-06-08T08:39:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=1070047)
[2026-06-08T08:39:29] Finding fusions and counting supporting reads (total=843676)
[2026-06-08T08:39:50] Merging adjacent fusion breakpoints (remaining=831489)
[2026-06-08T08:39:51] Filtering multi-mapping fusions by alignment score and read support (remaining=478230)
[2026-06-08T08:40:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:40:40] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=477028)
[2026-06-08T08:40:40] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=290598)
[2026-06-08T08:40:42] Filtering fusions with <2 supporting reads (remaining=31765)
[2026-06-08T08:40:42] Filtering fusions with an e-value >=0.3 (remaining=6668)
[2026-06-08T08:40:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6728)
[2026-06-08T08:40:47] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6631)
[2026-06-08T08:40:48] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6649)
[2026-06-08T08:40:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6507)
[2026-06-08T08:40:56] Searching for fusions with spliced split reads (remaining=6601)
[2026-06-08T08:41:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=4267)
[2026-06-08T08:41:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4243)
[2026-06-08T08:41:04] Searching for fusions with >=4 spliced events (remaining=5273)
[2026-06-08T08:41:05] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2377)
[2026-06-08T08:41:19] Filtering fusions with anchors <=23nt (remaining=2011)
[2026-06-08T08:41:19] Filtering end-to-end fusions with low support (remaining=1950)
[2026-06-08T08:41:20] Filtering fusions with no coverage around the breakpoints (remaining=1912)
[2026-06-08T08:41:21] Indexing gene sequences 
[2026-06-08T08:41:27] Filtering genes with >=30% identity (remaining=520)
[2026-06-08T08:41:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=107)
[2026-06-08T08:41:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=96)
[2026-06-08T08:41:33] Searching for additional isoforms (remaining=143)
[2026-06-08T08:41:34] Assigning confidence scores to events 
[2026-06-08T08:41:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:38] Writing fusions to file 'BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:40] Writing discarded fusions to file 'BVT_FFPE_TRNA_bld_02_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:14] Freeing resources
[2026-06-08T08:42:34] Done (elapsed time=00:11:50, CPU time=00:11:49, peak memory=16.9gb)