[2026-06-08T09:01:48] Launching Arriba 2.4.0
[2026-06-08T09:01:48] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:02:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:02:07] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_07_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=12458610)
[2026-06-08T09:10:49] Marking multi-mapping alignments (marked=8017288)
[2026-06-08T09:10:55] Detecting strandedness (reverse)
[2026-06-08T09:10:55] Assigning strands to alignments 
[2026-06-08T09:10:58] Annotating alignments 
[2026-06-08T09:11:39] Filtering duplicates (remaining=5331826)
[2026-06-08T09:11:46] 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=5124152)
[2026-06-08T09:11:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5124152)
[2026-06-08T09:11:51] Filtering viral contigs with expression lower than the top 5 (remaining=5124152)
[2026-06-08T09:11:56] Filtering viral contigs with less than 5% coverage (remaining=5124152)
[2026-06-08T09:11:59] Estimating fragment length (mate gap mean=-89.0852, mate gap stddev=28.1061, read length mean=132.567)
[2026-06-08T09:11:59] Filtering read-through fragments with a distance <=10000bp (remaining=4827220)
[2026-06-08T09:12:02] Filtering inconsistently clipped mates (remaining=4749436)
[2026-06-08T09:12:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4623453)
[2026-06-08T09:12:09] Filtering fragments with small insert size (remaining=4622625)
[2026-06-08T09:12:12] Filtering alignments with long gaps (remaining=4622624)
[2026-06-08T09:12:14] Filtering fragments with both mates in the same gene (remaining=4621871)
[2026-06-08T09:12:17] Filtering fusions arising from hairpin structures (remaining=4397933)
[2026-06-08T09:12:20] Filtering reads with a mismatch p-value <=0.01 (remaining=2091562)
[2026-06-08T09:12:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=692398)
[2026-06-08T09:12:44] Finding fusions and counting supporting reads (total=561973)
[2026-06-08T09:13:02] Merging adjacent fusion breakpoints (remaining=555579)
[2026-06-08T09:13:04] Filtering multi-mapping fusions by alignment score and read support (remaining=331926)
[2026-06-08T09:13:43] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:13:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=329945)
[2026-06-08T09:13:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=181820)
[2026-06-08T09:13:51] Filtering fusions with <2 supporting reads (remaining=21923)
[2026-06-08T09:13:51] Filtering fusions with an e-value >=0.3 (remaining=5883)
[2026-06-08T09:13:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5925)
[2026-06-08T09:13:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5842)
[2026-06-08T09:13:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5843)
[2026-06-08T09:13:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4926)
[2026-06-08T09:14:03] Searching for fusions with spliced split reads (remaining=5011)
[2026-06-08T09:14:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=3370)
[2026-06-08T09:14:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3333)
[2026-06-08T09:14:09] Searching for fusions with >=4 spliced events (remaining=3835)
[2026-06-08T09:14:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1481)
[2026-06-08T09:14:29] Filtering fusions with anchors <=23nt (remaining=1162)
[2026-06-08T09:14:30] Filtering end-to-end fusions with low support (remaining=1130)
[2026-06-08T09:14:30] Filtering fusions with no coverage around the breakpoints (remaining=1094)
[2026-06-08T09:14:31] Indexing gene sequences 
[2026-06-08T09:14:36] Filtering genes with >=30% identity (remaining=357)
[2026-06-08T09:14:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=152)
[2026-06-08T09:14:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=142)
[2026-06-08T09:14:42] Searching for additional isoforms (remaining=177)
[2026-06-08T09:14:43] Assigning confidence scores to events 
[2026-06-08T09:14:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:14:46] Writing fusions to file 'BVT_FFPE_TRNA_stm_07_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T09:14:47] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_07_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T09:15:13] Freeing resources
[2026-06-08T09:15:33] Done (elapsed time=00:13:45, CPU time=00:13:44, peak memory=16.8gb)