[2026-06-08T08:29:51] Launching Arriba 2.4.0
[2026-06-08T08:29:51] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:05] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:10] Reading chimeric alignments from '659_bR4-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12282097)
[2026-06-08T08:38:27] Marking multi-mapping alignments (marked=7614416)
[2026-06-08T08:38:32] Detecting strandedness (reverse)
[2026-06-08T08:38:32] Assigning strands to alignments 
[2026-06-08T08:38:34] Annotating alignments 
[2026-06-08T08:39:14] Filtering duplicates (remaining=8811767)
[2026-06-08T08:39:23] 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)
[2026-06-08T08:39:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8424185)
[2026-06-08T08:39:27] Filtering viral contigs with expression lower than the top 5 (remaining=8424185)
[2026-06-08T08:39:33] Filtering viral contigs with less than 5% coverage (remaining=8424185)
[2026-06-08T08:39:35] Estimating fragment length (mate gap mean=-85.5738, mate gap stddev=28.9493, read length mean=130.778)
[2026-06-08T08:39:36] Filtering read-through fragments with a distance <=10000bp (remaining=7948156)
[2026-06-08T08:39:38] Filtering inconsistently clipped mates (remaining=7792843)
[2026-06-08T08:39:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7517644)
[2026-06-08T08:39:46] Filtering fragments with small insert size (remaining=7516365)
[2026-06-08T08:39:48] Filtering alignments with long gaps (remaining=7516365)
[2026-06-08T08:39:50] Filtering fragments with both mates in the same gene (remaining=7515098)
[2026-06-08T08:39:53] Filtering fusions arising from hairpin structures (remaining=6978174)
[2026-06-08T08:39:55] Filtering reads with a mismatch p-value <=0.01 (remaining=3794357)
[2026-06-08T08:40:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=1660452)
[2026-06-08T08:40:30] Finding fusions and counting supporting reads (total=1206898)
[2026-06-08T08:41:04] Merging adjacent fusion breakpoints (remaining=1194445)
[2026-06-08T08:41:06] Filtering multi-mapping fusions by alignment score and read support (remaining=713337)
[2026-06-08T08:41:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=709193)
[2026-06-08T08:42:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=453618)
[2026-06-08T08:42:01] Filtering fusions with <2 supporting reads (remaining=50487)
[2026-06-08T08:42:02] Filtering fusions with an e-value >=0.3 (remaining=11035)
[2026-06-08T08:42:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11106)
[2026-06-08T08:42:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=10933)
[2026-06-08T08:42:09] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=10933)
[2026-06-08T08:42:11] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9486)
[2026-06-08T08:42:17] Searching for fusions with spliced split reads (remaining=9541)
[2026-06-08T08:42:24] Selecting best breakpoints from genes with multiple breakpoints (remaining=5768)
[2026-06-08T08:42:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=5703)
[2026-06-08T08:42:27] Searching for fusions with >=4 spliced events (remaining=7243)
[2026-06-08T08:42:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2719)
[2026-06-08T08:42:46] Filtering fusions with anchors <=23nt (remaining=2251)
[2026-06-08T08:42:47] Filtering end-to-end fusions with low support (remaining=2195)
[2026-06-08T08:42:48] Filtering fusions with no coverage around the breakpoints (remaining=2146)
[2026-06-08T08:42:49] Indexing gene sequences 
[2026-06-08T08:42:58] Filtering genes with >=30% identity (remaining=688)
[2026-06-08T08:43:04] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=323)
[2026-06-08T08:43:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=241)
[2026-06-08T08:43:12] Searching for additional isoforms (remaining=331)
[2026-06-08T08:43:14] Assigning confidence scores to events 
[2026-06-08T08:43:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:43:19] Writing fusions to file '659_bR4-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:43:23] Writing discarded fusions to file '659_bR4-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:44:05] Freeing resources
[2026-06-08T08:44:29] Done (elapsed time=00:14:38, CPU time=00:14:36, peak memory=17.1gb)