[2026-06-04T21:13:45] Launching Arriba 2.4.0
[2026-06-04T21:13:45] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:13:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:13:57] Reading chimeric alignments from '659_bua-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9047293)
[2026-06-04T21:20:12] Marking multi-mapping alignments (marked=5512704)
[2026-06-04T21:20:15] Detecting strandedness (reverse)
[2026-06-04T21:20:15] Assigning strands to alignments 
[2026-06-04T21:20:17] Annotating alignments 
[2026-06-04T21:20:43] Filtering duplicates (remaining=5972758)
[2026-06-04T21:20:49] 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=5691966)
[2026-06-04T21:20:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5691966)
[2026-06-04T21:20:52] Filtering viral contigs with expression lower than the top 5 (remaining=5691966)
[2026-06-04T21:20:56] Filtering viral contigs with less than 5% coverage (remaining=5691966)
[2026-06-04T21:20:58] Estimating fragment length (mate gap mean=-86.7072, mate gap stddev=28.2655, read length mean=129.633)
[2026-06-04T21:20:58] Filtering read-through fragments with a distance <=10000bp (remaining=5347957)
[2026-06-04T21:21:00] Filtering inconsistently clipped mates (remaining=5240694)
[2026-06-04T21:21:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5093550)
[2026-06-04T21:21:06] Filtering fragments with small insert size (remaining=5092554)
[2026-06-04T21:21:07] Filtering alignments with long gaps (remaining=5092553)
[2026-06-04T21:21:09] Filtering fragments with both mates in the same gene (remaining=5091447)
[2026-06-04T21:21:11] Filtering fusions arising from hairpin structures (remaining=4751124)
[2026-06-04T21:21:13] Filtering reads with a mismatch p-value <=0.01 (remaining=2437570)
[2026-06-04T21:21:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=1042855)
[2026-06-04T21:21:33] Finding fusions and counting supporting reads (total=741622)
[2026-06-04T21:21:46] Merging adjacent fusion breakpoints (remaining=735450)
[2026-06-04T21:21:48] Filtering multi-mapping fusions by alignment score and read support (remaining=485657)
[2026-06-04T21:22:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:22:19] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=483701)
[2026-06-04T21:22:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=280053)
[2026-06-04T21:22:21] Filtering fusions with <2 supporting reads (remaining=36704)
[2026-06-04T21:22:21] Filtering fusions with an e-value >=0.3 (remaining=9404)
[2026-06-04T21:22:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9466)
[2026-06-04T21:22:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9406)
[2026-06-04T21:22:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9412)
[2026-06-04T21:22:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6749)
[2026-06-04T21:22:32] Searching for fusions with spliced split reads (remaining=6770)
[2026-06-04T21:22:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=4361)
[2026-06-04T21:22:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4329)
[2026-06-04T21:22:38] Searching for fusions with >=4 spliced events (remaining=5331)
[2026-06-04T21:22:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2032)
[2026-06-04T21:22:52] Filtering fusions with anchors <=23nt (remaining=1690)
[2026-06-04T21:22:52] Filtering end-to-end fusions with low support (remaining=1651)
[2026-06-04T21:22:53] Filtering fusions with no coverage around the breakpoints (remaining=1614)
[2026-06-04T21:22:53] Indexing gene sequences 
[2026-06-04T21:22:59] Filtering genes with >=30% identity (remaining=504)
[2026-06-04T21:23:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=203)
[2026-06-04T21:23:04] Selecting best breakpoints from genes with multiple breakpoints (remaining=161)
[2026-06-04T21:23:05] Searching for additional isoforms (remaining=240)
[2026-06-04T21:23:06] Assigning confidence scores to events 
[2026-06-04T21:23:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:23:09] Writing fusions to file '659_bua-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:23:11] Writing discarded fusions to file '659_bua-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:23:34] Freeing resources
[2026-06-04T21:23:49] Done (elapsed time=00:10:04, CPU time=00:10:03, peak memory=13.6gb)