[2026-06-08T08:52:46] Launching Arriba 2.4.0
[2026-06-08T08:52:46] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:53:02] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:53:07] Reading chimeric alignments from 'BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=11712708)
[2026-06-08T09:03:40] Marking multi-mapping alignments (marked=7315612)
[2026-06-08T09:03:46] Detecting strandedness (reverse)
[2026-06-08T09:03:46] Assigning strands to alignments 
[2026-06-08T09:03:49] Annotating alignments 
[2026-06-08T09:04:34] Filtering duplicates (remaining=5947007)
[2026-06-08T09:04:43] 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=5761661)
[2026-06-08T09:04:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5761661)
[2026-06-08T09:04:47] Filtering viral contigs with expression lower than the top 5 (remaining=5761661)
[2026-06-08T09:04:53] Filtering viral contigs with less than 5% coverage (remaining=5761661)
[2026-06-08T09:04:55] Estimating fragment length (mate gap mean=-85.9698, mate gap stddev=30.1691, read length mean=136.69)
[2026-06-08T09:04:55] Filtering read-through fragments with a distance <=10000bp (remaining=5492745)
[2026-06-08T09:04:58] Filtering inconsistently clipped mates (remaining=5419825)
[2026-06-08T09:05:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5248020)
[2026-06-08T09:05:04] Filtering fragments with small insert size (remaining=5247420)
[2026-06-08T09:05:07] Filtering alignments with long gaps (remaining=5247420)
[2026-06-08T09:05:09] Filtering fragments with both mates in the same gene (remaining=5246388)
[2026-06-08T09:05:12] Filtering fusions arising from hairpin structures (remaining=4995312)
[2026-06-08T09:05:15] Filtering reads with a mismatch p-value <=0.01 (remaining=2663436)
[2026-06-08T09:05:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=855197)
[2026-06-08T09:05:41] Finding fusions and counting supporting reads (total=621287)
[2026-06-08T09:05:59] Merging adjacent fusion breakpoints (remaining=617057)
[2026-06-08T09:06:01] Filtering multi-mapping fusions by alignment score and read support (remaining=371003)
[2026-06-08T09:06:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:06:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=364858)
[2026-06-08T09:06:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=208027)
[2026-06-08T09:06:48] Filtering fusions with <2 supporting reads (remaining=30486)
[2026-06-08T09:06:48] Filtering fusions with an e-value >=0.3 (remaining=10917)
[2026-06-08T09:06:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=10955)
[2026-06-08T09:06:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10838)
[2026-06-08T09:06:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10897)
[2026-06-08T09:06:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6259)
[2026-06-08T09:07:00] Searching for fusions with spliced split reads (remaining=6319)
[2026-06-08T09:07:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=3862)
[2026-06-08T09:07:06] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3815)
[2026-06-08T09:07:07] Searching for fusions with >=4 spliced events (remaining=4568)
[2026-06-08T09:07:08] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1604)
[2026-06-08T09:07:25] Filtering fusions with anchors <=23nt (remaining=1355)
[2026-06-08T09:07:25] Filtering end-to-end fusions with low support (remaining=1312)
[2026-06-08T09:07:26] Filtering fusions with no coverage around the breakpoints (remaining=1268)
[2026-06-08T09:07:27] Indexing gene sequences 
[2026-06-08T09:07:32] Filtering genes with >=30% identity (remaining=441)
[2026-06-08T09:07:46] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=238)
[2026-06-08T09:07:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=143)
[2026-06-08T09:07:57] Searching for additional isoforms (remaining=297)
[2026-06-08T09:07:59] Assigning confidence scores to events 
[2026-06-08T09:08:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:08:02] Writing fusions to file 'BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T09:08:08] Writing discarded fusions to file 'BVT_FFPE_TRNA_crv_01_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T09:08:45] Freeing resources
[2026-06-08T09:09:08] Done (elapsed time=00:16:22, CPU time=00:16:20, peak memory=16.1gb)