[2026-06-08T08:39:43] Launching Arriba 2.4.0
[2026-06-08T08:39:43] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:39:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:39:55] Reading chimeric alignments from 'BVT_FFPE_TRNA_thy_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=13381113)
[2026-06-08T08:46:46] Marking multi-mapping alignments (marked=8601829)
[2026-06-08T08:46:52] Detecting strandedness (reverse)
[2026-06-08T08:46:52] Assigning strands to alignments 
[2026-06-08T08:46:55] Annotating alignments 
[2026-06-08T08:47:50] Filtering duplicates (remaining=6319785)
[2026-06-08T08:47:59] 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=6007526)
[2026-06-08T08:48:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6007526)
[2026-06-08T08:48:04] Filtering viral contigs with expression lower than the top 5 (remaining=6007526)
[2026-06-08T08:48:10] Filtering viral contigs with less than 5% coverage (remaining=6007526)
[2026-06-08T08:48:13] Estimating fragment length (mate gap mean=-85.5983, mate gap stddev=27.0413, read length mean=122.051)
[2026-06-08T08:48:13] Filtering read-through fragments with a distance <=10000bp (remaining=5553438)
[2026-06-08T08:48:16] Filtering inconsistently clipped mates (remaining=5460296)
[2026-06-08T08:48:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5320752)
[2026-06-08T08:48:24] Filtering fragments with small insert size (remaining=5319625)
[2026-06-08T08:48:27] Filtering alignments with long gaps (remaining=5319625)
[2026-06-08T08:48:30] Filtering fragments with both mates in the same gene (remaining=5318571)
[2026-06-08T08:48:33] Filtering fusions arising from hairpin structures (remaining=5083199)
[2026-06-08T08:48:36] Filtering reads with a mismatch p-value <=0.01 (remaining=2300651)
[2026-06-08T08:48:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=982405)
[2026-06-08T08:49:01] Finding fusions and counting supporting reads (total=788007)
[2026-06-08T08:49:22] Merging adjacent fusion breakpoints (remaining=775221)
[2026-06-08T08:49:24] Filtering multi-mapping fusions by alignment score and read support (remaining=454816)
[2026-06-08T08:50:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:50:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=453788)
[2026-06-08T08:50:17] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=271473)
[2026-06-08T08:50:18] Filtering fusions with <2 supporting reads (remaining=31742)
[2026-06-08T08:50:19] Filtering fusions with an e-value >=0.3 (remaining=7214)
[2026-06-08T08:50:19] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7264)
[2026-06-08T08:50:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7130)
[2026-06-08T08:50:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7130)
[2026-06-08T08:50:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7086)
[2026-06-08T08:50:32] Searching for fusions with spliced split reads (remaining=7165)
[2026-06-08T08:50:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=4679)
[2026-06-08T08:50:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4617)
[2026-06-08T08:50:40] Searching for fusions with >=4 spliced events (remaining=5409)
[2026-06-08T08:50:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2245)
[2026-06-08T08:51:01] Filtering fusions with anchors <=23nt (remaining=1699)
[2026-06-08T08:51:01] Filtering end-to-end fusions with low support (remaining=1668)
[2026-06-08T08:51:02] Filtering fusions with no coverage around the breakpoints (remaining=1636)
[2026-06-08T08:51:03] Indexing gene sequences 
[2026-06-08T08:51:08] Filtering genes with >=30% identity (remaining=440)
[2026-06-08T08:51:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=136)
[2026-06-08T08:51:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=133)
[2026-06-08T08:51:14] Searching for additional isoforms (remaining=151)
[2026-06-08T08:51:16] Assigning confidence scores to events 
[2026-06-08T08:51:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:51:19] Writing fusions to file 'BVT_FFPE_TRNA_thy_01_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:51:21] Writing discarded fusions to file 'BVT_FFPE_TRNA_thy_01_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:51:52] Freeing resources
[2026-06-08T08:52:13] Done (elapsed time=00:12:30, CPU time=00:12:30, peak memory=17.9gb)