[2026-06-08T08:42:44] Launching Arriba 2.4.0
[2026-06-08T08:42:44] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:42:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:42:56] Reading chimeric alignments from 'BVT_FFPE_TRNA_stm_04_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=14608630)
[2026-06-08T08:49:45] Marking multi-mapping alignments (marked=9520077)
[2026-06-08T08:49:50] Detecting strandedness (reverse)
[2026-06-08T08:49:50] Assigning strands to alignments 
[2026-06-08T08:49:53] Annotating alignments 
[2026-06-08T08:50:37] Filtering duplicates (remaining=6350437)
[2026-06-08T08:50:45] 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=6029905)
[2026-06-08T08:50:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6029905)
[2026-06-08T08:50:50] Filtering viral contigs with expression lower than the top 5 (remaining=6029905)
[2026-06-08T08:50:56] Filtering viral contigs with less than 5% coverage (remaining=6029905)
[2026-06-08T08:50:59] Estimating fragment length (mate gap mean=-86.2714, mate gap stddev=26.67, read length mean=124.802)
[2026-06-08T08:51:00] Filtering read-through fragments with a distance <=10000bp (remaining=5604930)
[2026-06-08T08:51:02] Filtering inconsistently clipped mates (remaining=5484632)
[2026-06-08T08:51:05] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5332817)
[2026-06-08T08:51:10] Filtering fragments with small insert size (remaining=5331438)
[2026-06-08T08:51:12] Filtering alignments with long gaps (remaining=5331438)
[2026-06-08T08:51:15] Filtering fragments with both mates in the same gene (remaining=5330433)
[2026-06-08T08:51:18] Filtering fusions arising from hairpin structures (remaining=5010838)
[2026-06-08T08:51:21] Filtering reads with a mismatch p-value <=0.01 (remaining=2287099)
[2026-06-08T08:51:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=943664)
[2026-06-08T08:51:45] Finding fusions and counting supporting reads (total=781922)
[2026-06-08T08:52:05] Merging adjacent fusion breakpoints (remaining=771235)
[2026-06-08T08:52:06] Filtering multi-mapping fusions by alignment score and read support (remaining=433283)
[2026-06-08T08:52:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:52:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=431993)
[2026-06-08T08:52:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=248165)
[2026-06-08T08:53:00] Filtering fusions with <2 supporting reads (remaining=25461)
[2026-06-08T08:53:01] Filtering fusions with an e-value >=0.3 (remaining=5501)
[2026-06-08T08:53:02] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5554)
[2026-06-08T08:53:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5432)
[2026-06-08T08:53:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5434)
[2026-06-08T08:53:09] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5310)
[2026-06-08T08:53:14] Searching for fusions with spliced split reads (remaining=5386)
[2026-06-08T08:53:20] Selecting best breakpoints from genes with multiple breakpoints (remaining=3497)
[2026-06-08T08:53:22] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3477)
[2026-06-08T08:53:22] Searching for fusions with >=4 spliced events (remaining=4254)
[2026-06-08T08:53:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1964)
[2026-06-08T08:53:37] Filtering fusions with anchors <=23nt (remaining=1684)
[2026-06-08T08:53:38] Filtering end-to-end fusions with low support (remaining=1642)
[2026-06-08T08:53:39] Filtering fusions with no coverage around the breakpoints (remaining=1601)
[2026-06-08T08:53:39] Indexing gene sequences 
[2026-06-08T08:53:45] Filtering genes with >=30% identity (remaining=536)
[2026-06-08T08:53:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=196)
[2026-06-08T08:53:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=176)
[2026-06-08T08:53:50] Searching for additional isoforms (remaining=205)
[2026-06-08T08:53:52] Assigning confidence scores to events 
[2026-06-08T08:53:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:53:55] Writing fusions to file 'BVT_FFPE_TRNA_stm_04_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:53:57] Writing discarded fusions to file 'BVT_FFPE_TRNA_stm_04_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:54:25] Freeing resources
[2026-06-08T08:54:48] Done (elapsed time=00:12:04, CPU time=00:12:04, peak memory=19.2gb)