[2026-06-08T09:03:16] Launching Arriba 2.4.0
[2026-06-08T09:03:16] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:03:25] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:03:29] Reading chimeric alignments from '659_bQZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10358544)
[2026-06-08T09:09:44] Marking multi-mapping alignments (marked=6756943)
[2026-06-08T09:09:48] Detecting strandedness (reverse)
[2026-06-08T09:09:48] Assigning strands to alignments 
[2026-06-08T09:09:50] Annotating alignments 
[2026-06-08T09:10:25] Filtering duplicates (remaining=3285271)
[2026-06-08T09:10:30] 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=3050770)
[2026-06-08T09:10:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3050770)
[2026-06-08T09:10:34] Filtering viral contigs with expression lower than the top 5 (remaining=3050770)
[2026-06-08T09:10:38] Filtering viral contigs with less than 5% coverage (remaining=3050770)
[2026-06-08T09:10:40] Estimating fragment length (mate gap mean=-87.6525, mate gap stddev=28.4005, read length mean=130.89)
[2026-06-08T09:10:40] Filtering read-through fragments with a distance <=10000bp (remaining=2889666)
[2026-06-08T09:10:42] Filtering inconsistently clipped mates (remaining=2845381)
[2026-06-08T09:10:44] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2701309)
[2026-06-08T09:10:48] Filtering fragments with small insert size (remaining=2700899)
[2026-06-08T09:10:50] Filtering alignments with long gaps (remaining=2700899)
[2026-06-08T09:10:52] Filtering fragments with both mates in the same gene (remaining=2700313)
[2026-06-08T09:10:54] Filtering fusions arising from hairpin structures (remaining=2586563)
[2026-06-08T09:10:56] Filtering reads with a mismatch p-value <=0.01 (remaining=1049044)
[2026-06-08T09:11:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=382932)
[2026-06-08T09:11:11] Finding fusions and counting supporting reads (total=329309)
[2026-06-08T09:11:24] Merging adjacent fusion breakpoints (remaining=325933)
[2026-06-08T09:11:25] Filtering multi-mapping fusions by alignment score and read support (remaining=189976)
[2026-06-08T09:11:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:12:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=188759)
[2026-06-08T09:12:02] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=104969)
[2026-06-08T09:12:03] Filtering fusions with <2 supporting reads (remaining=12223)
[2026-06-08T09:12:03] Filtering fusions with an e-value >=0.3 (remaining=3527)
[2026-06-08T09:12:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3557)
[2026-06-08T09:12:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3500)
[2026-06-08T09:12:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3500)
[2026-06-08T09:12:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2640)
[2026-06-08T09:12:11] Searching for fusions with spliced split reads (remaining=2682)
[2026-06-08T09:12:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=1991)
[2026-06-08T09:12:16] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1969)
[2026-06-08T09:12:16] Searching for fusions with >=4 spliced events (remaining=2112)
[2026-06-08T09:12:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=605)
[2026-06-08T09:12:29] Filtering fusions with anchors <=23nt (remaining=455)
[2026-06-08T09:12:30] Filtering end-to-end fusions with low support (remaining=425)
[2026-06-08T09:12:30] Filtering fusions with no coverage around the breakpoints (remaining=401)
[2026-06-08T09:12:31] Indexing gene sequences 
[2026-06-08T09:12:33] Filtering genes with >=30% identity (remaining=155)
[2026-06-08T09:12:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=69)
[2026-06-08T09:12:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=66)
[2026-06-08T09:12:35] Searching for additional isoforms (remaining=78)
[2026-06-08T09:12:36] Assigning confidence scores to events 
[2026-06-08T09:12:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:12:38] Writing fusions to file '659_bQZ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:12:39] Writing discarded fusions to file '659_bQZ-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:12:54] Freeing resources
[2026-06-08T09:13:09] Done (elapsed time=00:09:53, CPU time=00:09:52, peak memory=14.8gb)