[2026-06-08T08:44:46] Launching Arriba 2.4.0
[2026-06-08T08:44:46] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:45:00] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:45:05] Reading chimeric alignments from 'BVT_FFPE_TRNA_thy_02_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam' (total=11603910)
[2026-06-08T08:53:13] Marking multi-mapping alignments (marked=6967851)
[2026-06-08T08:53:18] Detecting strandedness (reverse)
[2026-06-08T08:53:18] Assigning strands to alignments 
[2026-06-08T08:53:20] Annotating alignments 
[2026-06-08T08:54:00] Filtering duplicates (remaining=6674746)
[2026-06-08T08:54:09] 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=6485138)
[2026-06-08T08:54:11] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6485138)
[2026-06-08T08:54:13] Filtering viral contigs with expression lower than the top 5 (remaining=6485138)
[2026-06-08T08:54:18] Filtering viral contigs with less than 5% coverage (remaining=6485138)
[2026-06-08T08:54:21] Estimating fragment length (mate gap mean=-89.5529, mate gap stddev=27.8037, read length mean=132.73)
[2026-06-08T08:54:21] Filtering read-through fragments with a distance <=10000bp (remaining=6034223)
[2026-06-08T08:54:23] Filtering inconsistently clipped mates (remaining=5938825)
[2026-06-08T08:54:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5748316)
[2026-06-08T08:54:31] Filtering fragments with small insert size (remaining=5747540)
[2026-06-08T08:54:33] Filtering alignments with long gaps (remaining=5747539)
[2026-06-08T08:54:35] Filtering fragments with both mates in the same gene (remaining=5746569)
[2026-06-08T08:54:38] Filtering fusions arising from hairpin structures (remaining=5449443)
[2026-06-08T08:54:40] Filtering reads with a mismatch p-value <=0.01 (remaining=2708097)
[2026-06-08T08:54:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=1069092)
[2026-06-08T08:55:09] Finding fusions and counting supporting reads (total=855111)
[2026-06-08T08:55:28] Merging adjacent fusion breakpoints (remaining=845759)
[2026-06-08T08:55:29] Filtering multi-mapping fusions by alignment score and read support (remaining=537068)
[2026-06-08T08:56:06] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:56:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=535340)
[2026-06-08T08:56:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=301136)
[2026-06-08T08:56:16] Filtering fusions with <2 supporting reads (remaining=36288)
[2026-06-08T08:56:17] Filtering fusions with an e-value >=0.3 (remaining=8972)
[2026-06-08T08:56:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9028)
[2026-06-08T08:56:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8946)
[2026-06-08T08:56:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8946)
[2026-06-08T08:56:24] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7387)
[2026-06-08T08:56:29] Searching for fusions with spliced split reads (remaining=7514)
[2026-06-08T08:56:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=4826)
[2026-06-08T08:56:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4775)
[2026-06-08T08:56:37] Searching for fusions with >=4 spliced events (remaining=5832)
[2026-06-08T08:56:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2282)
[2026-06-08T08:56:58] Filtering fusions with anchors <=23nt (remaining=1813)
[2026-06-08T08:56:59] Filtering end-to-end fusions with low support (remaining=1768)
[2026-06-08T08:56:59] Filtering fusions with no coverage around the breakpoints (remaining=1712)
[2026-06-08T08:57:00] Indexing gene sequences 
[2026-06-08T08:57:07] Filtering genes with >=30% identity (remaining=464)
[2026-06-08T08:57:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=171)
[2026-06-08T08:57:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=158)
[2026-06-08T08:57:15] Searching for additional isoforms (remaining=186)
[2026-06-08T08:57:17] Assigning confidence scores to events 
[2026-06-08T08:57:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:57:21] Writing fusions to file 'BVT_FFPE_TRNA_thy_02_A23WKFTLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:57:22] Writing discarded fusions to file 'BVT_FFPE_TRNA_thy_02_A23WKFTLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:57:58] Freeing resources
[2026-06-08T08:58:19] Done (elapsed time=00:13:33, CPU time=00:13:32, peak memory=16.3gb)