[2026-06-08T08:11:31] Launching Arriba 2.4.0
[2026-06-08T08:11:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:11:41] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:11:45] Reading chimeric alignments from 'BVT_FFPE_TRNA_kid_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=8369081)
[2026-06-08T08:15:25] Marking multi-mapping alignments (marked=5601084)
[2026-06-08T08:15:29] Detecting strandedness (reverse)
[2026-06-08T08:15:29] Assigning strands to alignments 
[2026-06-08T08:15:30] Annotating alignments 
[2026-06-08T08:16:01] Filtering duplicates (remaining=2361820)
[2026-06-08T08:16:11] 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=2141949)
[2026-06-08T08:16:14] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2141949)
[2026-06-08T08:16:15] Filtering viral contigs with expression lower than the top 5 (remaining=2141949)
[2026-06-08T08:16:19] Filtering viral contigs with less than 5% coverage (remaining=2141949)
[2026-06-08T08:16:21] Estimating fragment length (mate gap mean=-85.4778, mate gap stddev=27.3642, read length mean=120.571)
[2026-06-08T08:16:21] Filtering read-through fragments with a distance <=10000bp (remaining=2050245)
[2026-06-08T08:16:23] Filtering inconsistently clipped mates (remaining=2009067)
[2026-06-08T08:16:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1953415)
[2026-06-08T08:16:27] Filtering fragments with small insert size (remaining=1952747)
[2026-06-08T08:16:29] Filtering alignments with long gaps (remaining=1952747)
[2026-06-08T08:16:31] Filtering fragments with both mates in the same gene (remaining=1952289)
[2026-06-08T08:16:33] Filtering fusions arising from hairpin structures (remaining=1870596)
[2026-06-08T08:16:34] Filtering reads with a mismatch p-value <=0.01 (remaining=728376)
[2026-06-08T08:16:41] Filtering reads with low entropy (k-mer content >=60%) (remaining=204767)
[2026-06-08T08:16:46] Finding fusions and counting supporting reads (total=185033)
[2026-06-08T08:16:56] Merging adjacent fusion breakpoints (remaining=183769)
[2026-06-08T08:16:57] Filtering multi-mapping fusions by alignment score and read support (remaining=105762)
[2026-06-08T08:17:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:17:26] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=105235)
[2026-06-08T08:17:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=63036)
[2026-06-08T08:17:27] Filtering fusions with <2 supporting reads (remaining=4300)
[2026-06-08T08:17:27] Filtering fusions with an e-value >=0.3 (remaining=1042)
[2026-06-08T08:17:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1064)
[2026-06-08T08:17:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1030)
[2026-06-08T08:17:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1030)
[2026-06-08T08:17:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1028)
[2026-06-08T08:17:34] Searching for fusions with spliced split reads (remaining=1103)
[2026-06-08T08:17:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=804)
[2026-06-08T08:17:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=798)
[2026-06-08T08:17:38] Searching for fusions with >=4 spliced events (remaining=865)
[2026-06-08T08:17:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=321)
[2026-06-08T08:17:49] Filtering fusions with anchors <=23nt (remaining=274)
[2026-06-08T08:17:49] Filtering end-to-end fusions with low support (remaining=258)
[2026-06-08T08:17:50] Filtering fusions with no coverage around the breakpoints (remaining=246)
[2026-06-08T08:17:50] Indexing gene sequences 
[2026-06-08T08:17:51] Filtering genes with >=30% identity (remaining=83)
[2026-06-08T08:17:52] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=41)
[2026-06-08T08:17:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=41)
[2026-06-08T08:17:53] Searching for additional isoforms (remaining=43)
[2026-06-08T08:17:54] Assigning confidence scores to events 
[2026-06-08T08:17:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:17:55] Writing fusions to file 'BVT_FFPE_TRNA_kid_01_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:17:56] Writing discarded fusions to file 'BVT_FFPE_TRNA_kid_01_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:08] Freeing resources
[2026-06-08T08:18:21] Done (elapsed time=00:06:50, CPU time=00:06:49, peak memory=12.5gb)