[2026-06-04T21:09:45] Launching Arriba 2.4.0
[2026-06-04T21:09:45] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:09:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:09:56] Reading chimeric alignments from '659_bR4-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12282097)
[2026-06-04T21:16:31] Marking multi-mapping alignments (marked=7614416)
[2026-06-04T21:16:36] Detecting strandedness (reverse)
[2026-06-04T21:16:36] Assigning strands to alignments 
[2026-06-04T21:16:38] Annotating alignments 
[2026-06-04T21:17:15] Filtering duplicates (remaining=8811767)
[2026-06-04T21:17:23] 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=8424185)
[2026-06-04T21:17:26] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8424185)
[2026-06-04T21:17:28] Filtering viral contigs with expression lower than the top 5 (remaining=8424185)
[2026-06-04T21:17:34] Filtering viral contigs with less than 5% coverage (remaining=8424185)
[2026-06-04T21:17:37] Estimating fragment length (mate gap mean=-85.5738, mate gap stddev=28.9493, read length mean=130.778)
[2026-06-04T21:17:37] Filtering read-through fragments with a distance <=10000bp (remaining=7948156)
[2026-06-04T21:17:39] Filtering inconsistently clipped mates (remaining=7792843)
[2026-06-04T21:17:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7517644)
[2026-06-04T21:17:47] Filtering fragments with small insert size (remaining=7516365)
[2026-06-04T21:17:49] Filtering alignments with long gaps (remaining=7516365)
[2026-06-04T21:17:51] Filtering fragments with both mates in the same gene (remaining=7515098)
[2026-06-04T21:17:54] Filtering fusions arising from hairpin structures (remaining=6978174)
[2026-06-04T21:17:57] Filtering reads with a mismatch p-value <=0.01 (remaining=3794357)
[2026-06-04T21:18:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=1660452)
[2026-06-04T21:18:27] Finding fusions and counting supporting reads (total=1206898)
[2026-06-04T21:18:47] Merging adjacent fusion breakpoints (remaining=1194445)
[2026-06-04T21:18:49] Filtering multi-mapping fusions by alignment score and read support (remaining=713337)
[2026-06-04T21:19:26] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:19:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=709193)
[2026-06-04T21:19:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=453618)
[2026-06-04T21:19:38] Filtering fusions with <2 supporting reads (remaining=50487)
[2026-06-04T21:19:39] Filtering fusions with an e-value >=0.3 (remaining=11035)
[2026-06-04T21:19:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11106)
[2026-06-04T21:19:45] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10933)
[2026-06-04T21:19:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10933)
[2026-06-04T21:19:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9486)
[2026-06-04T21:19:55] Searching for fusions with spliced split reads (remaining=9541)
[2026-06-04T21:20:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=5768)
[2026-06-04T21:20:03] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5703)
[2026-06-04T21:20:04] Searching for fusions with >=4 spliced events (remaining=7243)
[2026-06-04T21:20:06] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2719)
[2026-06-04T21:20:21] Filtering fusions with anchors <=23nt (remaining=2251)
[2026-06-04T21:20:22] Filtering end-to-end fusions with low support (remaining=2195)
[2026-06-04T21:20:23] Filtering fusions with no coverage around the breakpoints (remaining=2146)
[2026-06-04T21:20:24] Indexing gene sequences 
[2026-06-04T21:20:32] Filtering genes with >=30% identity (remaining=688)
[2026-06-04T21:20:36] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=323)
[2026-06-04T21:20:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=241)
[2026-06-04T21:20:44] Searching for additional isoforms (remaining=331)
[2026-06-04T21:20:46] Assigning confidence scores to events 
[2026-06-04T21:20:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:20:51] Writing fusions to file '659_bR4-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:20:54] Writing discarded fusions to file '659_bR4-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:21:29] Freeing resources
[2026-06-04T21:21:50] Done (elapsed time=00:12:05, CPU time=00:12:04, peak memory=17.2gb)