[2026-06-08T08:36:41] Launching Arriba 2.4.0
[2026-06-08T08:36:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:58] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_09_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=12369107)
[2026-06-08T08:44:02] Marking multi-mapping alignments (marked=8048925)
[2026-06-08T08:44:07] Detecting strandedness (reverse)
[2026-06-08T08:44:07] Assigning strands to alignments 
[2026-06-08T08:44:09] Annotating alignments 
[2026-06-08T08:44:43] Filtering duplicates (remaining=5203997)
[2026-06-08T08:44:49] 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=4918951)
[2026-06-08T08:44:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4918951)
[2026-06-08T08:44:54] Filtering viral contigs with expression lower than the top 5 (remaining=4918951)
[2026-06-08T08:44:58] Filtering viral contigs with less than 5% coverage (remaining=4918951)
[2026-06-08T08:45:00] Estimating fragment length (mate gap mean=-87.6244, mate gap stddev=27.2897, read length mean=128.104)
[2026-06-08T08:45:01] Filtering read-through fragments with a distance <=10000bp (remaining=4648100)
[2026-06-08T08:45:03] Filtering inconsistently clipped mates (remaining=4563813)
[2026-06-08T08:45:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4406340)
[2026-06-08T08:45:09] Filtering fragments with small insert size (remaining=4405405)
[2026-06-08T08:45:11] Filtering alignments with long gaps (remaining=4405403)
[2026-06-08T08:45:13] Filtering fragments with both mates in the same gene (remaining=4404611)
[2026-06-08T08:45:15] Filtering fusions arising from hairpin structures (remaining=4191614)
[2026-06-08T08:45:18] Filtering reads with a mismatch p-value <=0.01 (remaining=1974773)
[2026-06-08T08:45:28] Filtering reads with low entropy (k-mer content >=60%) (remaining=640489)
[2026-06-08T08:45:38] Finding fusions and counting supporting reads (total=544212)
[2026-06-08T08:45:53] Merging adjacent fusion breakpoints (remaining=539063)
[2026-06-08T08:45:54] Filtering multi-mapping fusions by alignment score and read support (remaining=312635)
[2026-06-08T08:46:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:32] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=311453)
[2026-06-08T08:46:32] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=176080)
[2026-06-08T08:46:33] Filtering fusions with <2 supporting reads (remaining=17625)
[2026-06-08T08:46:34] Filtering fusions with an e-value >=0.3 (remaining=4034)
[2026-06-08T08:46:34] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4074)
[2026-06-08T08:46:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3998)
[2026-06-08T08:46:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3998)
[2026-06-08T08:46:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3830)
[2026-06-08T08:46:44] Searching for fusions with spliced split reads (remaining=3899)
[2026-06-08T08:46:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=2700)
[2026-06-08T08:46:49] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2669)
[2026-06-08T08:46:50] Searching for fusions with >=4 spliced events (remaining=3209)
[2026-06-08T08:46:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1382)
[2026-06-08T08:47:04] Filtering fusions with anchors <=23nt (remaining=1166)
[2026-06-08T08:47:05] Filtering end-to-end fusions with low support (remaining=1137)
[2026-06-08T08:47:05] Filtering fusions with no coverage around the breakpoints (remaining=1106)
[2026-06-08T08:47:06] Indexing gene sequences 
[2026-06-08T08:47:10] Filtering genes with >=30% identity (remaining=355)
[2026-06-08T08:47:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=134)
[2026-06-08T08:47:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=115)
[2026-06-08T08:47:14] Searching for additional isoforms (remaining=146)
[2026-06-08T08:47:15] Assigning confidence scores to events 
[2026-06-08T08:47:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:47:18] Writing fusions to file 'BVT_FFPE_TRNA_utn_09_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:47:19] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_09_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:41] Freeing resources
[2026-06-08T08:47:59] Done (elapsed time=00:11:18, CPU time=00:11:18, peak memory=16.7gb)