[2026-06-08T08:30:35] Launching Arriba 2.4.0
[2026-06-08T08:30:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:48] Reading chimeric alignments from 'BVT_FFPE_TRNA_thy_02_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=9595897)
[2026-06-08T08:36:14] Marking multi-mapping alignments (marked=5790287)
[2026-06-08T08:36:17] Detecting strandedness (reverse)
[2026-06-08T08:36:18] Assigning strands to alignments 
[2026-06-08T08:36:19] Annotating alignments 
[2026-06-08T08:36:53] Filtering duplicates (remaining=3869083)
[2026-06-08T08:37:00] 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=3759287)
[2026-06-08T08:37:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3759287)
[2026-06-08T08:37:03] Filtering viral contigs with expression lower than the top 5 (remaining=3759287)
[2026-06-08T08:37:08] Filtering viral contigs with less than 5% coverage (remaining=3759287)
[2026-06-08T08:37:10] Estimating fragment length (mate gap mean=-89.4134, mate gap stddev=28.1925, read length mean=133.147)
[2026-06-08T08:37:11] Filtering read-through fragments with a distance <=10000bp (remaining=3563541)
[2026-06-08T08:37:13] Filtering inconsistently clipped mates (remaining=3518743)
[2026-06-08T08:37:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3409039)
[2026-06-08T08:37:19] Filtering fragments with small insert size (remaining=3408625)
[2026-06-08T08:37:21] Filtering alignments with long gaps (remaining=3408625)
[2026-06-08T08:37:23] Filtering fragments with both mates in the same gene (remaining=3408081)
[2026-06-08T08:37:25] Filtering fusions arising from hairpin structures (remaining=3295719)
[2026-06-08T08:37:27] Filtering reads with a mismatch p-value <=0.01 (remaining=1547745)
[2026-06-08T08:37:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=452396)
[2026-06-08T08:37:42] Finding fusions and counting supporting reads (total=386143)
[2026-06-08T08:37:55] Merging adjacent fusion breakpoints (remaining=383322)
[2026-06-08T08:37:56] Filtering multi-mapping fusions by alignment score and read support (remaining=240171)
[2026-06-08T08:38:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:38:37] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=239142)
[2026-06-08T08:38:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=132822)
[2026-06-08T08:38:39] Filtering fusions with <2 supporting reads (remaining=15698)
[2026-06-08T08:38:40] Filtering fusions with an e-value >=0.3 (remaining=4289)
[2026-06-08T08:38:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4324)
[2026-06-08T08:38:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4258)
[2026-06-08T08:38:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4258)
[2026-06-08T08:38:47] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3734)
[2026-06-08T08:38:52] Searching for fusions with spliced split reads (remaining=3781)
[2026-06-08T08:38:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=2724)
[2026-06-08T08:38:57] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2691)
[2026-06-08T08:38:57] Searching for fusions with >=4 spliced events (remaining=3031)
[2026-06-08T08:38:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=950)
[2026-06-08T08:39:12] Filtering fusions with anchors <=23nt (remaining=709)
[2026-06-08T08:39:13] Filtering end-to-end fusions with low support (remaining=694)
[2026-06-08T08:39:13] Filtering fusions with no coverage around the breakpoints (remaining=669)
[2026-06-08T08:39:14] Indexing gene sequences 
[2026-06-08T08:39:17] Filtering genes with >=30% identity (remaining=199)
[2026-06-08T08:39:18] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=110)
[2026-06-08T08:39:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=110)
[2026-06-08T08:39:20] Searching for additional isoforms (remaining=126)
[2026-06-08T08:39:21] Assigning confidence scores to events 
[2026-06-08T08:39:23] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:39:24] Writing fusions to file 'BVT_FFPE_TRNA_thy_02_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:39:25] Writing discarded fusions to file 'BVT_FFPE_TRNA_thy_02_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:39:43] Freeing resources
[2026-06-08T08:40:00] Done (elapsed time=00:09:25, CPU time=00:09:23, peak memory=13.7gb)