[2026-06-08T08:18:24] Launching Arriba 2.4.0
[2026-06-08T08:18:24] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:18:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:18:42] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_07_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=10343043)
[2026-06-08T08:24:38] Marking multi-mapping alignments (marked=6777950)
[2026-06-08T08:24:43] Detecting strandedness (reverse)
[2026-06-08T08:24:43] Assigning strands to alignments 
[2026-06-08T08:24:45] Annotating alignments 
[2026-06-08T08:25:25] Filtering duplicates (remaining=2579656)
[2026-06-08T08:25:30] 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=2428347)
[2026-06-08T08:25:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2428347)
[2026-06-08T08:25:34] Filtering viral contigs with expression lower than the top 5 (remaining=2428347)
[2026-06-08T08:25:39] Filtering viral contigs with less than 5% coverage (remaining=2428347)
[2026-06-08T08:25:41] Estimating fragment length (mate gap mean=-85.6908, mate gap stddev=26.7743, read length mean=122.239)
[2026-06-08T08:25:41] Filtering read-through fragments with a distance <=10000bp (remaining=2302968)
[2026-06-08T08:25:44] Filtering inconsistently clipped mates (remaining=2261278)
[2026-06-08T08:25:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2165680)
[2026-06-08T08:25:49] Filtering fragments with small insert size (remaining=2165137)
[2026-06-08T08:25:51] Filtering alignments with long gaps (remaining=2165137)
[2026-06-08T08:25:53] Filtering fragments with both mates in the same gene (remaining=2164666)
[2026-06-08T08:25:56] Filtering fusions arising from hairpin structures (remaining=2091675)
[2026-06-08T08:25:58] Filtering reads with a mismatch p-value <=0.01 (remaining=856151)
[2026-06-08T08:26:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=254599)
[2026-06-08T08:26:11] Finding fusions and counting supporting reads (total=242420)
[2026-06-08T08:26:27] Merging adjacent fusion breakpoints (remaining=240353)
[2026-06-08T08:26:28] Filtering multi-mapping fusions by alignment score and read support (remaining=127076)
[2026-06-08T08:27:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=126438)
[2026-06-08T08:27:06] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=74618)
[2026-06-08T08:27:07] Filtering fusions with <2 supporting reads (remaining=6082)
[2026-06-08T08:27:07] Filtering fusions with an e-value >=0.3 (remaining=1529)
[2026-06-08T08:27:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1545)
[2026-06-08T08:27:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1477)
[2026-06-08T08:27:11] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1477)
[2026-06-08T08:27:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1469)
[2026-06-08T08:27:15] Searching for fusions with spliced split reads (remaining=1558)
[2026-06-08T08:27:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=1180)
[2026-06-08T08:27:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1161)
[2026-06-08T08:27:20] Searching for fusions with >=4 spliced events (remaining=1248)
[2026-06-08T08:27:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=467)
[2026-06-08T08:27:37] Filtering fusions with anchors <=23nt (remaining=406)
[2026-06-08T08:27:37] Filtering end-to-end fusions with low support (remaining=392)
[2026-06-08T08:27:38] Filtering fusions with no coverage around the breakpoints (remaining=380)
[2026-06-08T08:27:38] Indexing gene sequences 
[2026-06-08T08:27:40] Filtering genes with >=30% identity (remaining=113)
[2026-06-08T08:27:41] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=22)
[2026-06-08T08:27:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=22)
[2026-06-08T08:27:42] Searching for additional isoforms (remaining=28)
[2026-06-08T08:27:43] Assigning confidence scores to events 
[2026-06-08T08:27:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:27:45] Writing fusions to file 'BVT_FFPE_TRNA_utn_07_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:27:45] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_07_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:02] Freeing resources
[2026-06-08T08:28:21] Done (elapsed time=00:09:57, CPU time=00:09:56, peak memory=14.4gb)