[2026-06-08T08:54:45] Launching Arriba 2.4.0
[2026-06-08T08:54:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:54:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:55:00] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=13132219)
[2026-06-08T09:03:17] Marking multi-mapping alignments (marked=8389121)
[2026-06-08T09:03:23] Detecting strandedness (reverse)
[2026-06-08T09:03:23] Assigning strands to alignments 
[2026-06-08T09:03:26] Annotating alignments 
[2026-06-08T09:04:08] Filtering duplicates (remaining=6906096)
[2026-06-08T09:04:16] 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=6675455)
[2026-06-08T09:04:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6675455)
[2026-06-08T09:04:22] Filtering viral contigs with expression lower than the top 5 (remaining=6675455)
[2026-06-08T09:04:28] Filtering viral contigs with less than 5% coverage (remaining=6675455)
[2026-06-08T09:04:31] Estimating fragment length (mate gap mean=-89.2073, mate gap stddev=27.4527, read length mean=131.808)
[2026-06-08T09:04:31] Filtering read-through fragments with a distance <=10000bp (remaining=6168397)
[2026-06-08T09:04:33] Filtering inconsistently clipped mates (remaining=6067476)
[2026-06-08T09:04:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5919382)
[2026-06-08T09:04:41] Filtering fragments with small insert size (remaining=5918588)
[2026-06-08T09:04:44] Filtering alignments with long gaps (remaining=5918588)
[2026-06-08T09:04:47] Filtering fragments with both mates in the same gene (remaining=5917678)
[2026-06-08T09:04:50] Filtering fusions arising from hairpin structures (remaining=5610322)
[2026-06-08T09:04:53] Filtering reads with a mismatch p-value <=0.01 (remaining=2710286)
[2026-06-08T09:05:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=1055415)
[2026-06-08T09:05:21] Finding fusions and counting supporting reads (total=827610)
[2026-06-08T09:05:41] Merging adjacent fusion breakpoints (remaining=817578)
[2026-06-08T09:05:43] Filtering multi-mapping fusions by alignment score and read support (remaining=498740)
[2026-06-08T09:06:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:06:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=497148)
[2026-06-08T09:06:31] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=279730)
[2026-06-08T09:06:32] Filtering fusions with <2 supporting reads (remaining=30647)
[2026-06-08T09:06:33] Filtering fusions with an e-value >=0.3 (remaining=6813)
[2026-06-08T09:06:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6871)
[2026-06-08T09:06:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6781)
[2026-06-08T09:06:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6781)
[2026-06-08T09:06:40] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6483)
[2026-06-08T09:06:46] Searching for fusions with spliced split reads (remaining=6626)
[2026-06-08T09:06:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=4245)
[2026-06-08T09:06:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4203)
[2026-06-08T09:06:54] Searching for fusions with >=4 spliced events (remaining=5313)
[2026-06-08T09:06:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2350)
[2026-06-08T09:07:11] Filtering fusions with anchors <=23nt (remaining=1955)
[2026-06-08T09:07:12] Filtering end-to-end fusions with low support (remaining=1917)
[2026-06-08T09:07:12] Filtering fusions with no coverage around the breakpoints (remaining=1879)
[2026-06-08T09:07:13] Indexing gene sequences 
[2026-06-08T09:07:19] Filtering genes with >=30% identity (remaining=490)
[2026-06-08T09:07:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=127)
[2026-06-08T09:07:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=122)
[2026-06-08T09:07:25] Searching for additional isoforms (remaining=156)
[2026-06-08T09:07:26] Assigning confidence scores to events 
[2026-06-08T09:07:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:07:30] Writing fusions to file 'BVT_FFPE_TRNA_utn_02_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:07:31] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_02_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:04] Freeing resources
[2026-06-08T09:08:26] Done (elapsed time=00:13:41, CPU time=00:13:41, peak memory=17.7gb)