[2026-06-08T08:19:32] Launching Arriba 2.4.0
[2026-06-08T08:19:32] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:19:46] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=10370192)
[2026-06-08T08:25:18] Marking multi-mapping alignments (marked=6717658)
[2026-06-08T08:25:24] Detecting strandedness (reverse)
[2026-06-08T08:25:24] Assigning strands to alignments 
[2026-06-08T08:25:27] Annotating alignments 
[2026-06-08T08:26:20] Filtering duplicates (remaining=4905861)
[2026-06-08T08:26:28] 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=4663027)
[2026-06-08T08:26:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4663027)
[2026-06-08T08:26:34] Filtering viral contigs with expression lower than the top 5 (remaining=4663027)
[2026-06-08T08:26:41] Filtering viral contigs with less than 5% coverage (remaining=4663027)
[2026-06-08T08:26:44] Estimating fragment length (mate gap mean=-84.7136, mate gap stddev=26.6729, read length mean=120.767)
[2026-06-08T08:26:45] Filtering read-through fragments with a distance <=10000bp (remaining=4307350)
[2026-06-08T08:26:48] Filtering inconsistently clipped mates (remaining=4223259)
[2026-06-08T08:26:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4115458)
[2026-06-08T08:26:56] Filtering fragments with small insert size (remaining=4114441)
[2026-06-08T08:26:59] Filtering alignments with long gaps (remaining=4114441)
[2026-06-08T08:27:02] Filtering fragments with both mates in the same gene (remaining=4113589)
[2026-06-08T08:27:05] Filtering fusions arising from hairpin structures (remaining=3902051)
[2026-06-08T08:27:09] Filtering reads with a mismatch p-value <=0.01 (remaining=1733797)
[2026-06-08T08:27:22] Filtering reads with low entropy (k-mer content >=60%) (remaining=718028)
[2026-06-08T08:27:32] Finding fusions and counting supporting reads (total=612439)
[2026-06-08T08:27:57] Merging adjacent fusion breakpoints (remaining=605439)
[2026-06-08T08:27:59] Filtering multi-mapping fusions by alignment score and read support (remaining=340564)
[2026-06-08T08:28:45] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=339482)
[2026-06-08T08:28:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=197840)
[2026-06-08T08:28:57] Filtering fusions with <2 supporting reads (remaining=18961)
[2026-06-08T08:28:58] Filtering fusions with an e-value >=0.3 (remaining=4029)
[2026-06-08T08:28:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4076)
[2026-06-08T08:29:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4000)
[2026-06-08T08:29:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4000)
[2026-06-08T08:29:07] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3965)
[2026-06-08T08:29:14] Searching for fusions with spliced split reads (remaining=4017)
[2026-06-08T08:29:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=2684)
[2026-06-08T08:29:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2673)
[2026-06-08T08:29:24] Searching for fusions with >=4 spliced events (remaining=3191)
[2026-06-08T08:29:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1523)
[2026-06-08T08:29:44] Filtering fusions with anchors <=23nt (remaining=1347)
[2026-06-08T08:29:45] Filtering end-to-end fusions with low support (remaining=1311)
[2026-06-08T08:29:46] Filtering fusions with no coverage around the breakpoints (remaining=1280)
[2026-06-08T08:29:47] Indexing gene sequences 
[2026-06-08T08:29:54] Filtering genes with >=30% identity (remaining=379)
[2026-06-08T08:29:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=102)
[2026-06-08T08:29:59] Selecting best breakpoints from genes with multiple breakpoints (remaining=101)
[2026-06-08T08:30:01] Searching for additional isoforms (remaining=131)
[2026-06-08T08:30:03] Assigning confidence scores to events 
[2026-06-08T08:30:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:30:07] Writing fusions to file 'BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:30:08] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:30:51] Freeing resources
[2026-06-08T08:31:18] Done (elapsed time=00:11:46, CPU time=00:11:45, peak memory=14.8gb)