[2026-06-08T08:47:38] Launching Arriba 2.4.0
[2026-06-08T08:47:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:55] Reading chimeric alignments from 'BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=12429775)
[2026-06-08T08:54:42] Marking multi-mapping alignments (marked=7939086)
[2026-06-08T08:54:47] Detecting strandedness (reverse)
[2026-06-08T08:54:47] Assigning strands to alignments 
[2026-06-08T08:54:49] Annotating alignments 
[2026-06-08T08:55:34] Filtering duplicates (remaining=4720275)
[2026-06-08T08:55:40] 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=4514259)
[2026-06-08T08:55:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4514259)
[2026-06-08T08:55:46] Filtering viral contigs with expression lower than the top 5 (remaining=4514259)
[2026-06-08T08:55:51] Filtering viral contigs with less than 5% coverage (remaining=4514259)
[2026-06-08T08:55:54] Estimating fragment length (mate gap mean=-86.1007, mate gap stddev=26.4788, read length mean=123.706)
[2026-06-08T08:55:54] Filtering read-through fragments with a distance <=10000bp (remaining=4199537)
[2026-06-08T08:55:57] Filtering inconsistently clipped mates (remaining=4120028)
[2026-06-08T08:56:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3993436)
[2026-06-08T08:56:04] Filtering fragments with small insert size (remaining=3992554)
[2026-06-08T08:56:07] Filtering alignments with long gaps (remaining=3992554)
[2026-06-08T08:56:10] Filtering fragments with both mates in the same gene (remaining=3991854)
[2026-06-08T08:56:12] Filtering fusions arising from hairpin structures (remaining=3807589)
[2026-06-08T08:56:15] Filtering reads with a mismatch p-value <=0.01 (remaining=1670077)
[2026-06-08T08:56:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=648687)
[2026-06-08T08:56:36] Finding fusions and counting supporting reads (total=567014)
[2026-06-08T08:56:55] Merging adjacent fusion breakpoints (remaining=560264)
[2026-06-08T08:56:57] Filtering multi-mapping fusions by alignment score and read support (remaining=312396)
[2026-06-08T08:57:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=311281)
[2026-06-08T08:57:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=180402)
[2026-06-08T08:57:46] Filtering fusions with <2 supporting reads (remaining=16894)
[2026-06-08T08:57:47] Filtering fusions with an e-value >=0.3 (remaining=3562)
[2026-06-08T08:57:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3599)
[2026-06-08T08:57:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3482)
[2026-06-08T08:57:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3482)
[2026-06-08T08:57:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3446)
[2026-06-08T08:57:59] Searching for fusions with spliced split reads (remaining=3506)
[2026-06-08T08:58:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=2360)
[2026-06-08T08:58:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2347)
[2026-06-08T08:58:06] Searching for fusions with >=4 spliced events (remaining=2809)
[2026-06-08T08:58:07] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1332)
[2026-06-08T08:58:19] Filtering fusions with anchors <=23nt (remaining=1177)
[2026-06-08T08:58:20] Filtering end-to-end fusions with low support (remaining=1143)
[2026-06-08T08:58:20] Filtering fusions with no coverage around the breakpoints (remaining=1114)
[2026-06-08T08:58:21] Indexing gene sequences 
[2026-06-08T08:58:25] Filtering genes with >=30% identity (remaining=323)
[2026-06-08T08:58:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=95)
[2026-06-08T08:58:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=83)
[2026-06-08T08:58:29] Searching for additional isoforms (remaining=113)
[2026-06-08T08:58:30] Assigning confidence scores to events 
[2026-06-08T08:58:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:33] Writing fusions to file 'BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:58:34] Writing discarded fusions to file 'BVT_FFPE_TRNA_bst_01_03_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:01] Freeing resources
[2026-06-08T08:59:22] Done (elapsed time=00:11:44, CPU time=00:11:42, peak memory=16.8gb)