[2026-06-08T08:35:23] Launching Arriba 2.4.0
[2026-06-08T08:35:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:35:37] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:35:42] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=9888068)
[2026-06-08T08:41:18] Marking multi-mapping alignments (marked=6433150)
[2026-06-08T08:41:23] Detecting strandedness (reverse)
[2026-06-08T08:41:23] Assigning strands to alignments 
[2026-06-08T08:41:25] Annotating alignments 
[2026-06-08T08:41:56] Filtering duplicates (remaining=3191870)
[2026-06-08T08:42:01] 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=3002021)
[2026-06-08T08:42:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3002021)
[2026-06-08T08:42:04] Filtering viral contigs with expression lower than the top 5 (remaining=3002021)
[2026-06-08T08:42:10] Filtering viral contigs with less than 5% coverage (remaining=3002021)
[2026-06-08T08:42:12] Estimating fragment length (mate gap mean=-83.0235, mate gap stddev=26.4755, read length mean=119.344)
[2026-06-08T08:42:12] Filtering read-through fragments with a distance <=10000bp (remaining=2816236)
[2026-06-08T08:42:14] Filtering inconsistently clipped mates (remaining=2766334)
[2026-06-08T08:42:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2681025)
[2026-06-08T08:42:18] Filtering fragments with small insert size (remaining=2680170)
[2026-06-08T08:42:20] Filtering alignments with long gaps (remaining=2680170)
[2026-06-08T08:42:23] Filtering fragments with both mates in the same gene (remaining=2679619)
[2026-06-08T08:42:27] Filtering fusions arising from hairpin structures (remaining=2573089)
[2026-06-08T08:42:29] Filtering reads with a mismatch p-value <=0.01 (remaining=1082542)
[2026-06-08T08:42:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=381230)
[2026-06-08T08:42:50] Finding fusions and counting supporting reads (total=346765)
[2026-06-08T08:43:03] Merging adjacent fusion breakpoints (remaining=344124)
[2026-06-08T08:43:04] Filtering multi-mapping fusions by alignment score and read support (remaining=185208)
[2026-06-08T08:43:32] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:43:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=184444)
[2026-06-08T08:43:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=105237)
[2026-06-08T08:43:37] Filtering fusions with <2 supporting reads (remaining=8718)
[2026-06-08T08:43:37] Filtering fusions with an e-value >=0.3 (remaining=1948)
[2026-06-08T08:43:37] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1977)
[2026-06-08T08:43:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1915)
[2026-06-08T08:43:41] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1915)
[2026-06-08T08:43:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1906)
[2026-06-08T08:43:45] Searching for fusions with spliced split reads (remaining=2037)
[2026-06-08T08:43:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=1434)
[2026-06-08T08:43:50] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1423)
[2026-06-08T08:43:50] Searching for fusions with >=4 spliced events (remaining=1670)
[2026-06-08T08:43:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=727)
[2026-06-08T08:44:07] Filtering fusions with anchors <=23nt (remaining=646)
[2026-06-08T08:44:07] Filtering end-to-end fusions with low support (remaining=629)
[2026-06-08T08:44:07] Filtering fusions with no coverage around the breakpoints (remaining=613)
[2026-06-08T08:44:08] Indexing gene sequences 
[2026-06-08T08:44:11] Filtering genes with >=30% identity (remaining=172)
[2026-06-08T08:44:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=56)
[2026-06-08T08:44:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=53)
[2026-06-08T08:44:13] Searching for additional isoforms (remaining=72)
[2026-06-08T08:44:14] Assigning confidence scores to events 
[2026-06-08T08:44:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:44:16] Writing fusions to file 'BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:44:17] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:33] Freeing resources
[2026-06-08T08:44:50] Done (elapsed time=00:09:27, CPU time=00:09:26, peak memory=14.1gb)