[2026-06-08T08:30:43] Launching Arriba 2.4.0
[2026-06-08T08:30:43] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:57] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:31:02] Reading chimeric alignments from 'BVT_FFPE_TRNA_thy_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam' (total=11914897)
[2026-06-08T08:39:45] Marking multi-mapping alignments (marked=7253074)
[2026-06-08T08:39:50] Detecting strandedness (reverse)
[2026-06-08T08:39:50] Assigning strands to alignments 
[2026-06-08T08:39:52] Annotating alignments 
[2026-06-08T08:40:33] Filtering duplicates (remaining=5462828)
[2026-06-08T08:40:40] 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=5311815)
[2026-06-08T08:40:43] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5311815)
[2026-06-08T08:40:45] Filtering viral contigs with expression lower than the top 5 (remaining=5311815)
[2026-06-08T08:40:50] Filtering viral contigs with less than 5% coverage (remaining=5311815)
[2026-06-08T08:40:53] Estimating fragment length (mate gap mean=-87.5649, mate gap stddev=27.891, read length mean=130.117)
[2026-06-08T08:40:53] Filtering read-through fragments with a distance <=10000bp (remaining=5011415)
[2026-06-08T08:40:55] Filtering inconsistently clipped mates (remaining=4945029)
[2026-06-08T08:40:57] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4791691)
[2026-06-08T08:41:01] Filtering fragments with small insert size (remaining=4790993)
[2026-06-08T08:41:04] Filtering alignments with long gaps (remaining=4790992)
[2026-06-08T08:41:06] Filtering fragments with both mates in the same gene (remaining=4790149)
[2026-06-08T08:41:08] Filtering fusions arising from hairpin structures (remaining=4611005)
[2026-06-08T08:41:11] Filtering reads with a mismatch p-value <=0.01 (remaining=2195389)
[2026-06-08T08:41:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=701058)
[2026-06-08T08:41:34] Finding fusions and counting supporting reads (total=584822)
[2026-06-08T08:41:51] Merging adjacent fusion breakpoints (remaining=579381)
[2026-06-08T08:41:53] Filtering multi-mapping fusions by alignment score and read support (remaining=364109)
[2026-06-08T08:42:30] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:42:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=362766)
[2026-06-08T08:42:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=196861)
[2026-06-08T08:42:37] Filtering fusions with <2 supporting reads (remaining=24269)
[2026-06-08T08:42:38] Filtering fusions with an e-value >=0.3 (remaining=6202)
[2026-06-08T08:42:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6248)
[2026-06-08T08:42:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6167)
[2026-06-08T08:42:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6170)
[2026-06-08T08:42:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5325)
[2026-06-08T08:42:49] Searching for fusions with spliced split reads (remaining=5414)
[2026-06-08T08:42:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=3715)
[2026-06-08T08:42:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3674)
[2026-06-08T08:42:56] Searching for fusions with >=4 spliced events (remaining=4238)
[2026-06-08T08:42:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1466)
[2026-06-08T08:43:17] Filtering fusions with anchors <=23nt (remaining=1170)
[2026-06-08T08:43:17] Filtering end-to-end fusions with low support (remaining=1144)
[2026-06-08T08:43:18] Filtering fusions with no coverage around the breakpoints (remaining=1106)
[2026-06-08T08:43:19] Indexing gene sequences 
[2026-06-08T08:43:24] Filtering genes with >=30% identity (remaining=334)
[2026-06-08T08:43:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=157)
[2026-06-08T08:43:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=157)
[2026-06-08T08:43:29] Searching for additional isoforms (remaining=182)
[2026-06-08T08:43:30] Assigning confidence scores to events 
[2026-06-08T08:43:33] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:33] Writing fusions to file 'BVT_FFPE_TRNA_thy_02_A23WKFTLT4_2.arriba.fusions.tsv' 
[2026-06-08T08:43:35] Writing discarded fusions to file 'BVT_FFPE_TRNA_thy_02_A23WKFTLT4_2.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:02] Freeing resources
[2026-06-08T08:44:22] Done (elapsed time=00:13:39, CPU time=00:13:38, peak memory=16.2gb)