[2026-06-08T08:49:44] Launching Arriba 2.4.0
[2026-06-08T08:49:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:49:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:49:57] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_09_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=12811268)
[2026-06-08T08:56:44] Marking multi-mapping alignments (marked=8288013)
[2026-06-08T08:56:48] Detecting strandedness (reverse)
[2026-06-08T08:56:48] Assigning strands to alignments 
[2026-06-08T08:56:51] Annotating alignments 
[2026-06-08T08:57:33] Filtering duplicates (remaining=7052115)
[2026-06-08T08:57:41] 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=6716327)
[2026-06-08T08:57:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6716327)
[2026-06-08T08:57:46] Filtering viral contigs with expression lower than the top 5 (remaining=6716327)
[2026-06-08T08:57:51] Filtering viral contigs with less than 5% coverage (remaining=6716327)
[2026-06-08T08:57:54] Estimating fragment length (mate gap mean=-86.8585, mate gap stddev=27.513, read length mean=127.784)
[2026-06-08T08:57:54] Filtering read-through fragments with a distance <=10000bp (remaining=6287178)
[2026-06-08T08:57:57] Filtering inconsistently clipped mates (remaining=6159950)
[2026-06-08T08:57:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5950805)
[2026-06-08T08:58:04] Filtering fragments with small insert size (remaining=5949597)
[2026-06-08T08:58:06] Filtering alignments with long gaps (remaining=5949597)
[2026-06-08T08:58:09] Filtering fragments with both mates in the same gene (remaining=5948596)
[2026-06-08T08:58:11] Filtering fusions arising from hairpin structures (remaining=5587786)
[2026-06-08T08:58:14] Filtering reads with a mismatch p-value <=0.01 (remaining=2727450)
[2026-06-08T08:58:30] Filtering reads with low entropy (k-mer content >=60%) (remaining=1037505)
[2026-06-08T08:58:42] Finding fusions and counting supporting reads (total=868373)
[2026-06-08T08:59:02] Merging adjacent fusion breakpoints (remaining=858504)
[2026-06-08T08:59:04] Filtering multi-mapping fusions by alignment score and read support (remaining=502711)
[2026-06-08T08:59:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=501139)
[2026-06-08T08:59:50] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=297490)
[2026-06-08T08:59:51] Filtering fusions with <2 supporting reads (remaining=28030)
[2026-06-08T08:59:52] Filtering fusions with an e-value >=0.3 (remaining=6014)
[2026-06-08T08:59:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6066)
[2026-06-08T08:59:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5975)
[2026-06-08T08:59:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5975)
[2026-06-08T09:00:00] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5687)
[2026-06-08T09:00:05] Searching for fusions with spliced split reads (remaining=5801)
[2026-06-08T09:00:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=3833)
[2026-06-08T09:00:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3794)
[2026-06-08T09:00:13] Searching for fusions with >=4 spliced events (remaining=4823)
[2026-06-08T09:00:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2353)
[2026-06-08T09:00:28] Filtering fusions with anchors <=23nt (remaining=1989)
[2026-06-08T09:00:29] Filtering end-to-end fusions with low support (remaining=1929)
[2026-06-08T09:00:30] Filtering fusions with no coverage around the breakpoints (remaining=1889)
[2026-06-08T09:00:31] Indexing gene sequences 
[2026-06-08T09:00:36] Filtering genes with >=30% identity (remaining=564)
[2026-06-08T09:00:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=197)
[2026-06-08T09:00:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=160)
[2026-06-08T09:00:43] Searching for additional isoforms (remaining=210)
[2026-06-08T09:00:45] Assigning confidence scores to events 
[2026-06-08T09:00:48] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:48] Writing fusions to file 'BVT_FFPE_TRNA_utn_09_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:00:50] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_09_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:01:19] Freeing resources
[2026-06-08T09:01:39] Done (elapsed time=00:11:55, CPU time=00:11:53, peak memory=17.4gb)