[2026-06-08T08:56:45] Launching Arriba 2.4.0
[2026-06-08T08:56:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:57:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:57:04] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_07_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=12428043)
[2026-06-08T09:05:43] Marking multi-mapping alignments (marked=7993795)
[2026-06-08T09:05:48] Detecting strandedness (reverse)
[2026-06-08T09:05:48] Assigning strands to alignments 
[2026-06-08T09:05:51] Annotating alignments 
[2026-06-08T09:06:31] Filtering duplicates (remaining=6783089)
[2026-06-08T09:06:40] 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=6538548)
[2026-06-08T09:06:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6538548)
[2026-06-08T09:06:45] Filtering viral contigs with expression lower than the top 5 (remaining=6538548)
[2026-06-08T09:06:50] Filtering viral contigs with less than 5% coverage (remaining=6538548)
[2026-06-08T09:06:53] Estimating fragment length (mate gap mean=-88.7583, mate gap stddev=27.7538, read length mean=131.911)
[2026-06-08T09:06:53] Filtering read-through fragments with a distance <=10000bp (remaining=6100321)
[2026-06-08T09:06:56] Filtering inconsistently clipped mates (remaining=5986656)
[2026-06-08T09:06:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5845395)
[2026-06-08T09:07:03] Filtering fragments with small insert size (remaining=5844385)
[2026-06-08T09:07:06] Filtering alignments with long gaps (remaining=5844385)
[2026-06-08T09:07:09] Filtering fragments with both mates in the same gene (remaining=5843489)
[2026-06-08T09:07:12] Filtering fusions arising from hairpin structures (remaining=5488707)
[2026-06-08T09:07:15] Filtering reads with a mismatch p-value <=0.01 (remaining=2686909)
[2026-06-08T09:07:31] Filtering reads with low entropy (k-mer content >=60%) (remaining=1014166)
[2026-06-08T09:07:44] Finding fusions and counting supporting reads (total=787406)
[2026-06-08T09:08:05] Merging adjacent fusion breakpoints (remaining=775958)
[2026-06-08T09:08:06] Filtering multi-mapping fusions by alignment score and read support (remaining=464685)
[2026-06-08T09:08:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:08:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=462251)
[2026-06-08T09:08:56] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=250875)
[2026-06-08T09:08:57] Filtering fusions with <2 supporting reads (remaining=31825)
[2026-06-08T09:08:58] Filtering fusions with an e-value >=0.3 (remaining=8248)
[2026-06-08T09:08:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8302)
[2026-06-08T09:09:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8176)
[2026-06-08T09:09:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8178)
[2026-06-08T09:09:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7034)
[2026-06-08T09:09:11] Searching for fusions with spliced split reads (remaining=7146)
[2026-06-08T09:09:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=4557)
[2026-06-08T09:09:18] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4505)
[2026-06-08T09:09:19] Searching for fusions with >=4 spliced events (remaining=5448)
[2026-06-08T09:09:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2245)
[2026-06-08T09:09:41] Filtering fusions with anchors <=23nt (remaining=1768)
[2026-06-08T09:09:42] Filtering end-to-end fusions with low support (remaining=1726)
[2026-06-08T09:09:43] Filtering fusions with no coverage around the breakpoints (remaining=1683)
[2026-06-08T09:09:43] Indexing gene sequences 
[2026-06-08T09:09:50] Filtering genes with >=30% identity (remaining=487)
[2026-06-08T09:09:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=193)
[2026-06-08T09:09:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=177)
[2026-06-08T09:10:00] Searching for additional isoforms (remaining=235)
[2026-06-08T09:10:01] Assigning confidence scores to events 
[2026-06-08T09:10:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:10:05] Writing fusions to file 'BVT_FFPE_TRNA_stm_07_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T09:10:07] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_07_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T09:10:41] Freeing resources
[2026-06-08T09:11:04] Done (elapsed time=00:14:19, CPU time=00:14:18, peak memory=17gb)