[2026-06-08T08:40:49] Launching Arriba 2.4.0
[2026-06-08T08:40:49] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:41:05] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:41:12] Reading chimeric alignments from 'BVT_FFPE_TRNA_utn_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=13169764)
[2026-06-08T08:50:41] Marking multi-mapping alignments (marked=8514510)
[2026-06-08T08:50:47] Detecting strandedness (reverse)
[2026-06-08T08:50:47] Assigning strands to alignments 
[2026-06-08T08:50:49] Annotating alignments 
[2026-06-08T08:51:31] Filtering duplicates (remaining=8045735)
[2026-06-08T08:51:40] 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=7713182)
[2026-06-08T08:51:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7713182)
[2026-06-08T08:51:45] Filtering viral contigs with expression lower than the top 5 (remaining=7713182)
[2026-06-08T08:51:51] Filtering viral contigs with less than 5% coverage (remaining=7713182)
[2026-06-08T08:51:53] Estimating fragment length (mate gap mean=-88.2064, mate gap stddev=27.2795, read length mean=130.623)
[2026-06-08T08:51:54] Filtering read-through fragments with a distance <=10000bp (remaining=7062418)
[2026-06-08T08:51:56] Filtering inconsistently clipped mates (remaining=6928229)
[2026-06-08T08:51:59] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6773465)
[2026-06-08T08:52:05] Filtering fragments with small insert size (remaining=6772504)
[2026-06-08T08:52:08] Filtering alignments with long gaps (remaining=6772504)
[2026-06-08T08:52:11] Filtering fragments with both mates in the same gene (remaining=6771532)
[2026-06-08T08:52:14] Filtering fusions arising from hairpin structures (remaining=6342025)
[2026-06-08T08:52:17] Filtering reads with a mismatch p-value <=0.01 (remaining=3137167)
[2026-06-08T08:52:36] Filtering reads with low entropy (k-mer content >=60%) (remaining=1384480)
[2026-06-08T08:52:53] Finding fusions and counting supporting reads (total=1044581)
[2026-06-08T08:53:20] Merging adjacent fusion breakpoints (remaining=1030271)
[2026-06-08T08:53:22] Filtering multi-mapping fusions by alignment score and read support (remaining=616723)
[2026-06-08T08:54:09] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:54:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=615191)
[2026-06-08T08:54:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=359439)
[2026-06-08T08:54:20] Filtering fusions with <2 supporting reads (remaining=38005)
[2026-06-08T08:54:21] Filtering fusions with an e-value >=0.3 (remaining=8008)
[2026-06-08T08:54:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8096)
[2026-06-08T08:54:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7945)
[2026-06-08T08:54:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7947)
[2026-06-08T08:54:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7682)
[2026-06-08T08:54:36] Searching for fusions with spliced split reads (remaining=7809)
[2026-06-08T08:54:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=4892)
[2026-06-08T08:54:44] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4850)
[2026-06-08T08:54:44] Searching for fusions with >=4 spliced events (remaining=6277)
[2026-06-08T08:54:46] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2910)
[2026-06-08T08:55:09] Filtering fusions with anchors <=23nt (remaining=2397)
[2026-06-08T08:55:10] Filtering end-to-end fusions with low support (remaining=2356)
[2026-06-08T08:55:11] Filtering fusions with no coverage around the breakpoints (remaining=2318)
[2026-06-08T08:55:12] Indexing gene sequences 
[2026-06-08T08:55:20] Filtering genes with >=30% identity (remaining=577)
[2026-06-08T08:55:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=156)
[2026-06-08T08:55:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=153)
[2026-06-08T08:55:27] Searching for additional isoforms (remaining=192)
[2026-06-08T08:55:29] Assigning confidence scores to events 
[2026-06-08T08:55:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:55:33] Writing fusions to file 'BVT_FFPE_TRNA_utn_02_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:55:35] Writing discarded fusions to file 'BVT_FFPE_TRNA_utn_02_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:56:15] Freeing resources
[2026-06-08T08:56:41] Done (elapsed time=00:15:52, CPU time=00:15:51, peak memory=18.1gb)