[2026-06-08T08:15:21] Launching Arriba 2.4.0
[2026-06-08T08:15:21] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:30] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:34] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_08_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=8027727)
[2026-06-08T08:19:41] Marking multi-mapping alignments (marked=5291327)
[2026-06-08T08:19:45] Detecting strandedness (reverse)
[2026-06-08T08:19:45] Assigning strands to alignments 
[2026-06-08T08:19:46] Annotating alignments 
[2026-06-08T08:20:13] Filtering duplicates (remaining=2029184)
[2026-06-08T08:20:17] 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=1850178)
[2026-06-08T08:20:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1850178)
[2026-06-08T08:20:20] Filtering viral contigs with expression lower than the top 5 (remaining=1850178)
[2026-06-08T08:20:23] Filtering viral contigs with less than 5% coverage (remaining=1850178)
[2026-06-08T08:20:25] Estimating fragment length (mate gap mean=-86.4112, mate gap stddev=28.6632, read length mean=126.89)
[2026-06-08T08:20:25] Filtering read-through fragments with a distance <=10000bp (remaining=1782891)
[2026-06-08T08:20:27] Filtering inconsistently clipped mates (remaining=1746809)
[2026-06-08T08:20:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1682239)
[2026-06-08T08:20:31] Filtering fragments with small insert size (remaining=1681703)
[2026-06-08T08:20:32] Filtering alignments with long gaps (remaining=1681703)
[2026-06-08T08:20:34] Filtering fragments with both mates in the same gene (remaining=1681376)
[2026-06-08T08:20:35] Filtering fusions arising from hairpin structures (remaining=1618741)
[2026-06-08T08:20:37] Filtering reads with a mismatch p-value <=0.01 (remaining=686619)
[2026-06-08T08:20:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=156858)
[2026-06-08T08:20:46] Finding fusions and counting supporting reads (total=141077)
[2026-06-08T08:20:56] Merging adjacent fusion breakpoints (remaining=140308)
[2026-06-08T08:20:57] Filtering multi-mapping fusions by alignment score and read support (remaining=75978)
[2026-06-08T08:21:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:21:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=75288)
[2026-06-08T08:21:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=44687)
[2026-06-08T08:21:26] Filtering fusions with <2 supporting reads (remaining=3290)
[2026-06-08T08:21:26] Filtering fusions with an e-value >=0.3 (remaining=905)
[2026-06-08T08:21:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=920)
[2026-06-08T08:21:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=888)
[2026-06-08T08:21:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=888)
[2026-06-08T08:21:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=843)
[2026-06-08T08:21:32] Searching for fusions with spliced split reads (remaining=946)
[2026-06-08T08:21:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=704)
[2026-06-08T08:21:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=687)
[2026-06-08T08:21:36] Searching for fusions with >=4 spliced events (remaining=755)
[2026-06-08T08:21:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=264)
[2026-06-08T08:21:48] Filtering fusions with anchors <=23nt (remaining=241)
[2026-06-08T08:21:48] Filtering end-to-end fusions with low support (remaining=231)
[2026-06-08T08:21:48] Filtering fusions with no coverage around the breakpoints (remaining=226)
[2026-06-08T08:21:48] Indexing gene sequences 
[2026-06-08T08:21:50] Filtering genes with >=30% identity (remaining=65)
[2026-06-08T08:21:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=38)
[2026-06-08T08:21:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=38)
[2026-06-08T08:21:51] Searching for additional isoforms (remaining=43)
[2026-06-08T08:21:52] Assigning confidence scores to events 
[2026-06-08T08:21:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:21:53] Writing fusions to file 'BVT_FFPE_TRNA_stm_08_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:21:53] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_08_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:22:04] Freeing resources
[2026-06-08T08:22:16] Done (elapsed time=00:06:55, CPU time=00:06:53, peak memory=12.1gb)