[2026-06-08T07:45:11] Launching Arriba 2.4.0
[2026-06-08T07:45:11] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:45:28] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:45:34] Reading chimeric alignments from 'BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=4885527)
[2026-06-08T07:48:28] Marking multi-mapping alignments (marked=3255230)
[2026-06-08T07:48:30] Detecting strandedness (reverse)
[2026-06-08T07:48:30] Assigning strands to alignments 
[2026-06-08T07:48:31] Annotating alignments 
[2026-06-08T07:48:53] Filtering duplicates (remaining=1429403)
[2026-06-08T07:48:55] 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=1276962)
[2026-06-08T07:48:56] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1276962)
[2026-06-08T07:48:57] Filtering viral contigs with expression lower than the top 5 (remaining=1276962)
[2026-06-08T07:48:59] Filtering viral contigs with less than 5% coverage (remaining=1276962)
[2026-06-08T07:49:00] Estimating fragment length (mate gap mean=-81.9862, mate gap stddev=27.6828, read length mean=119.566)
[2026-06-08T07:49:01] Filtering read-through fragments with a distance <=10000bp (remaining=1218836)
[2026-06-08T07:49:02] Filtering inconsistently clipped mates (remaining=1191933)
[2026-06-08T07:49:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1145005)
[2026-06-08T07:49:04] Filtering fragments with small insert size (remaining=1144554)
[2026-06-08T07:49:05] Filtering alignments with long gaps (remaining=1144554)
[2026-06-08T07:49:06] Filtering fragments with both mates in the same gene (remaining=1144193)
[2026-06-08T07:49:07] Filtering fusions arising from hairpin structures (remaining=1098341)
[2026-06-08T07:49:09] Filtering reads with a mismatch p-value <=0.01 (remaining=462496)
[2026-06-08T07:49:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=135332)
[2026-06-08T07:49:17] Finding fusions and counting supporting reads (total=129993)
[2026-06-08T07:49:24] Merging adjacent fusion breakpoints (remaining=129341)
[2026-06-08T07:49:24] Filtering multi-mapping fusions by alignment score and read support (remaining=68380)
[2026-06-08T07:49:40] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:49:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=67957)
[2026-06-08T07:49:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=42696)
[2026-06-08T07:49:43] Filtering fusions with <2 supporting reads (remaining=2206)
[2026-06-08T07:49:43] Filtering fusions with an e-value >=0.3 (remaining=541)
[2026-06-08T07:49:43] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=553)
[2026-06-08T07:49:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=531)
[2026-06-08T07:49:45] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=532)
[2026-06-08T07:49:45] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=525)
[2026-06-08T07:49:48] Searching for fusions with spliced split reads (remaining=547)
[2026-06-08T07:49:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=453)
[2026-06-08T07:49:51] Filtering read-through fusions with breakpoints near the gene boundary (remaining=450)
[2026-06-08T07:49:51] Searching for fusions with >=4 spliced events (remaining=463)
[2026-06-08T07:49:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=155)
[2026-06-08T07:50:08] Filtering fusions with anchors <=23nt (remaining=132)
[2026-06-08T07:50:08] Filtering end-to-end fusions with low support (remaining=124)
[2026-06-08T07:50:08] Filtering fusions with no coverage around the breakpoints (remaining=115)
[2026-06-08T07:50:08] Indexing gene sequences 
[2026-06-08T07:50:10] Filtering genes with >=30% identity (remaining=50)
[2026-06-08T07:50:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=21)
[2026-06-08T07:50:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=21)
[2026-06-08T07:50:11] Searching for additional isoforms (remaining=22)
[2026-06-08T07:50:12] Assigning confidence scores to events 
[2026-06-08T07:50:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:50:13] Writing fusions to file 'BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T07:50:13] Writing discarded fusions to file 'BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T07:50:21] Freeing resources
[2026-06-08T07:50:33] Done (elapsed time=00:05:22, CPU time=00:05:21, peak memory=8.96gb)