[2026-06-08T08:53:45] Launching Arriba 2.4.0
[2026-06-08T08:53:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:57] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_08_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=13880310)
[2026-06-08T09:00:55] Marking multi-mapping alignments (marked=9086762)
[2026-06-08T09:01:01] Detecting strandedness (reverse)
[2026-06-08T09:01:01] Assigning strands to alignments 
[2026-06-08T09:01:04] Annotating alignments 
[2026-06-08T09:01:53] Filtering duplicates (remaining=5207904)
[2026-06-08T09:02:03] 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=4867844)
[2026-06-08T09:02:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4867844)
[2026-06-08T09:02:10] Filtering viral contigs with expression lower than the top 5 (remaining=4867844)
[2026-06-08T09:02:18] Filtering viral contigs with less than 5% coverage (remaining=4867844)
[2026-06-08T09:02:21] Estimating fragment length (mate gap mean=-87.2338, mate gap stddev=28.0794, read length mean=127.799)
[2026-06-08T09:02:21] Filtering read-through fragments with a distance <=10000bp (remaining=4611522)
[2026-06-08T09:02:25] Filtering inconsistently clipped mates (remaining=4505324)
[2026-06-08T09:02:27] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4365676)
[2026-06-08T09:02:32] Filtering fragments with small insert size (remaining=4364605)
[2026-06-08T09:02:35] Filtering alignments with long gaps (remaining=4364604)
[2026-06-08T09:02:39] Filtering fragments with both mates in the same gene (remaining=4363830)
[2026-06-08T09:02:42] Filtering fusions arising from hairpin structures (remaining=4109436)
[2026-06-08T09:02:45] Filtering reads with a mismatch p-value <=0.01 (remaining=1859987)
[2026-06-08T09:02:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=600094)
[2026-06-08T09:03:08] Finding fusions and counting supporting reads (total=502200)
[2026-06-08T09:03:28] Merging adjacent fusion breakpoints (remaining=496740)
[2026-06-08T09:03:30] Filtering multi-mapping fusions by alignment score and read support (remaining=277420)
[2026-06-08T09:04:18] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:04:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=275634)
[2026-06-08T09:04:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=156220)
[2026-06-08T09:04:26] Filtering fusions with <2 supporting reads (remaining=14850)
[2026-06-08T09:04:27] Filtering fusions with an e-value >=0.3 (remaining=3635)
[2026-06-08T09:04:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3676)
[2026-06-08T09:04:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3587)
[2026-06-08T09:04:33] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3587)
[2026-06-08T09:04:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3363)
[2026-06-08T09:04:40] Searching for fusions with spliced split reads (remaining=3430)
[2026-06-08T09:04:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=2420)
[2026-06-08T09:04:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2394)
[2026-06-08T09:04:48] Searching for fusions with >=4 spliced events (remaining=2776)
[2026-06-08T09:04:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1058)
[2026-06-08T09:05:03] Filtering fusions with anchors <=23nt (remaining=875)
[2026-06-08T09:05:04] Filtering end-to-end fusions with low support (remaining=853)
[2026-06-08T09:05:05] Filtering fusions with no coverage around the breakpoints (remaining=830)
[2026-06-08T09:05:05] Indexing gene sequences 
[2026-06-08T09:05:09] Filtering genes with >=30% identity (remaining=274)
[2026-06-08T09:05:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=124)
[2026-06-08T09:05:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=124)
[2026-06-08T09:05:14] Searching for additional isoforms (remaining=145)
[2026-06-08T09:05:15] Assigning confidence scores to events 
[2026-06-08T09:05:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:05:18] Writing fusions to file 'BVT_FFPE_TRNA_stm_08_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:05:19] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_08_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:05:45] Freeing resources
[2026-06-08T09:06:08] Done (elapsed time=00:12:23, CPU time=00:12:21, peak memory=18.3gb)