[2026-06-08T08:44:36] Launching Arriba 2.4.0
[2026-06-08T08:44:36] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:44:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:44:54] Reading chimeric alignments from 'BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=14773613)
[2026-06-08T08:53:00] Marking multi-mapping alignments (marked=10033707)
[2026-06-08T08:53:06] Detecting strandedness (reverse)
[2026-06-08T08:53:06] Assigning strands to alignments 
[2026-06-08T08:53:09] Annotating alignments 
[2026-06-08T08:53:58] Filtering duplicates (remaining=3941622)
[2026-06-08T08:54:06] 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=3470299)
[2026-06-08T08:54:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3470299)
[2026-06-08T08:54:12] Filtering viral contigs with expression lower than the top 5 (remaining=3470299)
[2026-06-08T08:54:18] Filtering viral contigs with less than 5% coverage (remaining=3470299)
[2026-06-08T08:54:21] Estimating fragment length (mate gap mean=-85.6932, mate gap stddev=29.7277, read length mean=128.337)
[2026-06-08T08:54:21] Filtering read-through fragments with a distance <=10000bp (remaining=3356544)
[2026-06-08T08:54:26] Filtering inconsistently clipped mates (remaining=3288898)
[2026-06-08T08:54:30] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3166876)
[2026-06-08T08:54:37] Filtering fragments with small insert size (remaining=3165908)
[2026-06-08T08:54:48] Filtering alignments with long gaps (remaining=3165908)
[2026-06-08T08:54:53] Filtering fragments with both mates in the same gene (remaining=3165315)
[2026-06-08T08:54:57] Filtering fusions arising from hairpin structures (remaining=3027834)
[2026-06-08T08:55:01] Filtering reads with a mismatch p-value <=0.01 (remaining=1348484)
[2026-06-08T08:55:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=287114)
[2026-06-08T08:55:24] Finding fusions and counting supporting reads (total=248434)
[2026-06-08T08:55:43] Merging adjacent fusion breakpoints (remaining=246752)
[2026-06-08T08:55:44] Filtering multi-mapping fusions by alignment score and read support (remaining=133542)
[2026-06-08T08:56:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=132249)
[2026-06-08T08:56:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=83102)
[2026-06-08T08:56:35] Filtering fusions with <2 supporting reads (remaining=6396)
[2026-06-08T08:56:35] Filtering fusions with an e-value >=0.3 (remaining=1848)
[2026-06-08T08:56:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1867)
[2026-06-08T08:56:40] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1776)
[2026-06-08T08:56:40] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1776)
[2026-06-08T08:56:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1627)
[2026-06-08T08:56:47] Searching for fusions with spliced split reads (remaining=1663)
[2026-06-08T08:56:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=1227)
[2026-06-08T08:56:54] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1200)
[2026-06-08T08:56:54] Searching for fusions with >=4 spliced events (remaining=1333)
[2026-06-08T08:56:55] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=498)
[2026-06-08T08:57:10] Filtering fusions with anchors <=23nt (remaining=434)
[2026-06-08T08:57:11] Filtering end-to-end fusions with low support (remaining=412)
[2026-06-08T08:57:11] Filtering fusions with no coverage around the breakpoints (remaining=395)
[2026-06-08T08:57:12] Indexing gene sequences 
[2026-06-08T08:57:14] Filtering genes with >=30% identity (remaining=152)
[2026-06-08T08:57:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=76)
[2026-06-08T08:57:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=73)
[2026-06-08T08:57:17] Searching for additional isoforms (remaining=79)
[2026-06-08T08:57:18] Assigning confidence scores to events 
[2026-06-08T08:57:20] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:21] Writing fusions to file 'BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:57:21] Writing discarded fusions to file 'BVT_FFPE_TRNA_liv_03_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:40] Freeing resources
[2026-06-08T08:58:07] Done (elapsed time=00:13:31, CPU time=00:13:30, peak memory=18.9gb)