[2026-06-08T08:28:38] Launching Arriba 2.4.0
[2026-06-08T08:28:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:28:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:28:50] Reading chimeric alignments from 'BVT_FFPE_TRNA_thy_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam' (total=12752472)
[2026-06-08T08:35:04] Marking multi-mapping alignments (marked=8154283)
[2026-06-08T08:35:09] Detecting strandedness (reverse)
[2026-06-08T08:35:09] Assigning strands to alignments 
[2026-06-08T08:35:12] Annotating alignments 
[2026-06-08T08:35:56] Filtering duplicates (remaining=3747853)
[2026-06-08T08:36:02] 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=3559000)
[2026-06-08T08:36:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3559000)
[2026-06-08T08:36:07] Filtering viral contigs with expression lower than the top 5 (remaining=3559000)
[2026-06-08T08:36:13] Filtering viral contigs with less than 5% coverage (remaining=3559000)
[2026-06-08T08:36:15] Estimating fragment length (mate gap mean=-87.0329, mate gap stddev=26.7266, read length mean=123.325)
[2026-06-08T08:36:16] Filtering read-through fragments with a distance <=10000bp (remaining=3331909)
[2026-06-08T08:36:18] Filtering inconsistently clipped mates (remaining=3276662)
[2026-06-08T08:36:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3178685)
[2026-06-08T08:36:25] Filtering fragments with small insert size (remaining=3177966)
[2026-06-08T08:36:27] Filtering alignments with long gaps (remaining=3177966)
[2026-06-08T08:36:30] Filtering fragments with both mates in the same gene (remaining=3177318)
[2026-06-08T08:36:32] Filtering fusions arising from hairpin structures (remaining=3064123)
[2026-06-08T08:36:35] Filtering reads with a mismatch p-value <=0.01 (remaining=1281587)
[2026-06-08T08:36:44] Filtering reads with low entropy (k-mer content >=60%) (remaining=461286)
[2026-06-08T08:36:53] Finding fusions and counting supporting reads (total=408090)
[2026-06-08T08:37:10] Merging adjacent fusion breakpoints (remaining=401889)
[2026-06-08T08:37:11] Filtering multi-mapping fusions by alignment score and read support (remaining=226470)
[2026-06-08T08:37:54] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:37:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=225702)
[2026-06-08T08:37:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=126846)
[2026-06-08T08:38:00] Filtering fusions with <2 supporting reads (remaining=14123)
[2026-06-08T08:38:01] Filtering fusions with an e-value >=0.3 (remaining=3600)
[2026-06-08T08:38:01] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3629)
[2026-06-08T08:38:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3527)
[2026-06-08T08:38:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3529)
[2026-06-08T08:38:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3487)
[2026-06-08T08:38:11] Searching for fusions with spliced split reads (remaining=3522)
[2026-06-08T08:38:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=2535)
[2026-06-08T08:38:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2507)
[2026-06-08T08:38:18] Searching for fusions with >=4 spliced events (remaining=2708)
[2026-06-08T08:38:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=921)
[2026-06-08T08:38:34] Filtering fusions with anchors <=23nt (remaining=650)
[2026-06-08T08:38:35] Filtering end-to-end fusions with low support (remaining=629)
[2026-06-08T08:38:35] Filtering fusions with no coverage around the breakpoints (remaining=602)
[2026-06-08T08:38:36] Indexing gene sequences 
[2026-06-08T08:38:39] Filtering genes with >=30% identity (remaining=185)
[2026-06-08T08:38:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=50)
[2026-06-08T08:38:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=50)
[2026-06-08T08:38:42] Searching for additional isoforms (remaining=54)
[2026-06-08T08:38:43] Assigning confidence scores to events 
[2026-06-08T08:38:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:38:45] Writing fusions to file 'BVT_FFPE_TRNA_thy_01_A23WKFTLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:38:46] Writing discarded fusions to file 'BVT_FFPE_TRNA_thy_01_A23WKFTLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:39:07] Freeing resources
[2026-06-08T08:39:27] Done (elapsed time=00:10:49, CPU time=00:10:47, peak memory=17gb)