[2026-06-08T08:24:31] Launching Arriba 2.4.0
[2026-06-08T08:24:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:45] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:24:49] Reading chimeric alignments from 'BVT_FFPE_TRNA_kid_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=11382672)
[2026-06-08T08:31:01] Marking multi-mapping alignments (marked=7593546)
[2026-06-08T08:31:05] Detecting strandedness (reverse)
[2026-06-08T08:31:05] Assigning strands to alignments 
[2026-06-08T08:31:08] Annotating alignments 
[2026-06-08T08:31:49] Filtering duplicates (remaining=3715246)
[2026-06-08T08:31:56] 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=3441849)
[2026-06-08T08:31:58] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3441849)
[2026-06-08T08:32:00] Filtering viral contigs with expression lower than the top 5 (remaining=3441849)
[2026-06-08T08:32:05] Filtering viral contigs with less than 5% coverage (remaining=3441849)
[2026-06-08T08:32:08] Estimating fragment length (mate gap mean=-84.3295, mate gap stddev=27.5192, read length mean=119.808)
[2026-06-08T08:32:08] Filtering read-through fragments with a distance <=10000bp (remaining=3289730)
[2026-06-08T08:32:10] Filtering inconsistently clipped mates (remaining=3225665)
[2026-06-08T08:32:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3138225)
[2026-06-08T08:32:16] Filtering fragments with small insert size (remaining=3137329)
[2026-06-08T08:32:19] Filtering alignments with long gaps (remaining=3137329)
[2026-06-08T08:32:21] Filtering fragments with both mates in the same gene (remaining=3136634)
[2026-06-08T08:32:23] Filtering fusions arising from hairpin structures (remaining=3002344)
[2026-06-08T08:32:26] Filtering reads with a mismatch p-value <=0.01 (remaining=1195645)
[2026-06-08T08:32:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=342650)
[2026-06-08T08:32:43] Finding fusions and counting supporting reads (total=302364)
[2026-06-08T08:33:00] Merging adjacent fusion breakpoints (remaining=299868)
[2026-06-08T08:33:01] Filtering multi-mapping fusions by alignment score and read support (remaining=172772)
[2026-06-08T08:33:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=172070)
[2026-06-08T08:33:44] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=102871)
[2026-06-08T08:33:45] Filtering fusions with <2 supporting reads (remaining=8127)
[2026-06-08T08:33:45] Filtering fusions with an e-value >=0.3 (remaining=1941)
[2026-06-08T08:33:45] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1971)
[2026-06-08T08:33:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1927)
[2026-06-08T08:33:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1927)
[2026-06-08T08:33:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1911)
[2026-06-08T08:33:55] Searching for fusions with spliced split reads (remaining=2054)
[2026-06-08T08:34:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=1495)
[2026-06-08T08:34:00] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1482)
[2026-06-08T08:34:01] Searching for fusions with >=4 spliced events (remaining=1691)
[2026-06-08T08:34:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=716)
[2026-06-08T08:34:17] Filtering fusions with anchors <=23nt (remaining=601)
[2026-06-08T08:34:17] Filtering end-to-end fusions with low support (remaining=570)
[2026-06-08T08:34:18] Filtering fusions with no coverage around the breakpoints (remaining=547)
[2026-06-08T08:34:18] Indexing gene sequences 
[2026-06-08T08:34:21] Filtering genes with >=30% identity (remaining=170)
[2026-06-08T08:34:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=66)
[2026-06-08T08:34:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=66)
[2026-06-08T08:34:25] Searching for additional isoforms (remaining=69)
[2026-06-08T08:34:26] Assigning confidence scores to events 
[2026-06-08T08:34:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:29] Writing fusions to file 'BVT_FFPE_TRNA_kid_01_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:34:29] Writing discarded fusions to file 'BVT_FFPE_TRNA_kid_01_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:53] Freeing resources
[2026-06-08T08:35:13] Done (elapsed time=00:10:42, CPU time=00:10:41, peak memory=15.5gb)