[2026-06-08T08:46:45] Launching Arriba 2.4.0
[2026-06-08T08:46:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:46:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:05] Reading chimeric alignments from 'BVT_FFPE_TRNA_crv_04_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=15186164)
[2026-06-08T08:55:16] Marking multi-mapping alignments (marked=9845361)
[2026-06-08T08:55:23] Detecting strandedness (reverse)
[2026-06-08T08:55:23] Assigning strands to alignments 
[2026-06-08T08:55:27] Annotating alignments 
[2026-06-08T08:56:21] Filtering duplicates (remaining=6022973)
[2026-06-08T08:56:31] 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=5811043)
[2026-06-08T08:56:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5811043)
[2026-06-08T08:56:37] Filtering viral contigs with expression lower than the top 5 (remaining=5811043)
[2026-06-08T08:56:44] Filtering viral contigs with less than 5% coverage (remaining=5811043)
[2026-06-08T08:56:48] Estimating fragment length (mate gap mean=-85.4428, mate gap stddev=26.3795, read length mean=123.019)
[2026-06-08T08:56:48] Filtering read-through fragments with a distance <=10000bp (remaining=5351570)
[2026-06-08T08:56:51] Filtering inconsistently clipped mates (remaining=5249676)
[2026-06-08T08:56:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5108804)
[2026-06-08T08:57:00] Filtering fragments with small insert size (remaining=5107725)
[2026-06-08T08:57:03] Filtering alignments with long gaps (remaining=5107725)
[2026-06-08T08:57:06] Filtering fragments with both mates in the same gene (remaining=5106823)
[2026-06-08T08:57:09] Filtering fusions arising from hairpin structures (remaining=4874135)
[2026-06-08T08:57:13] Filtering reads with a mismatch p-value <=0.01 (remaining=2167432)
[2026-06-08T08:57:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=919673)
[2026-06-08T08:57:38] Finding fusions and counting supporting reads (total=763473)
[2026-06-08T08:58:01] Merging adjacent fusion breakpoints (remaining=751161)
[2026-06-08T08:58:03] Filtering multi-mapping fusions by alignment score and read support (remaining=418279)
[2026-06-08T08:58:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:59:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=417154)
[2026-06-08T08:59:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=241039)
[2026-06-08T08:59:04] Filtering fusions with <2 supporting reads (remaining=27969)
[2026-06-08T08:59:05] Filtering fusions with an e-value >=0.3 (remaining=5472)
[2026-06-08T08:59:06] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5507)
[2026-06-08T08:59:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5391)
[2026-06-08T08:59:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5396)
[2026-06-08T08:59:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5380)
[2026-06-08T08:59:20] Searching for fusions with spliced split reads (remaining=5455)
[2026-06-08T08:59:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=3463)
[2026-06-08T08:59:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3441)
[2026-06-08T08:59:29] Searching for fusions with >=4 spliced events (remaining=4396)
[2026-06-08T08:59:30] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2099)
[2026-06-08T08:59:44] Filtering fusions with anchors <=23nt (remaining=1819)
[2026-06-08T08:59:45] Filtering end-to-end fusions with low support (remaining=1771)
[2026-06-08T08:59:46] Filtering fusions with no coverage around the breakpoints (remaining=1730)
[2026-06-08T08:59:46] Indexing gene sequences 
[2026-06-08T08:59:51] Filtering genes with >=30% identity (remaining=429)
[2026-06-08T08:59:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=69)
[2026-06-08T08:59:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=66)
[2026-06-08T08:59:57] Searching for additional isoforms (remaining=83)
[2026-06-08T08:59:58] Assigning confidence scores to events 
[2026-06-08T09:00:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:00:02] Writing fusions to file 'BVT_FFPE_TRNA_crv_04_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:00:03] Writing discarded fusions to file 'BVT_FFPE_TRNA_crv_04_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:00:35] Freeing resources
[2026-06-08T09:01:02] Done (elapsed time=00:14:17, CPU time=00:14:15, peak memory=19.6gb)