[2026-06-08T08:17:05] Launching Arriba 2.4.0
[2026-06-08T08:17:05] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:18] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:22] Reading chimeric alignments from '659_gK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=6302621)
[2026-06-08T08:21:38] Marking multi-mapping alignments (marked=4071611)
[2026-06-08T08:21:40] Detecting strandedness (reverse)
[2026-06-08T08:21:40] Assigning strands to alignments 
[2026-06-08T08:21:41] Annotating alignments 
[2026-06-08T08:21:58] Filtering duplicates (remaining=2639945)
[2026-06-08T08:22:00] 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=2555334)
[2026-06-08T08:22:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2555334)
[2026-06-08T08:22:03] Filtering viral contigs with expression lower than the top 5 (remaining=2555334)
[2026-06-08T08:22:05] Filtering viral contigs with less than 5% coverage (remaining=2555334)
[2026-06-08T08:22:06] Estimating fragment length (mate gap mean=-85.3643, mate gap stddev=30.2125, read length mean=136.103)
[2026-06-08T08:22:06] Filtering read-through fragments with a distance <=10000bp (remaining=2428464)
[2026-06-08T08:22:07] Filtering inconsistently clipped mates (remaining=2396717)
[2026-06-08T08:22:08] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2305204)
[2026-06-08T08:22:10] Filtering fragments with small insert size (remaining=2304952)
[2026-06-08T08:22:11] Filtering alignments with long gaps (remaining=2304951)
[2026-06-08T08:22:12] Filtering fragments with both mates in the same gene (remaining=2304476)
[2026-06-08T08:22:13] Filtering fusions arising from hairpin structures (remaining=2211687)
[2026-06-08T08:22:14] Filtering reads with a mismatch p-value <=0.01 (remaining=965741)
[2026-06-08T08:22:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=315808)
[2026-06-08T08:22:24] Finding fusions and counting supporting reads (total=265272)
[2026-06-08T08:22:32] Merging adjacent fusion breakpoints (remaining=263282)
[2026-06-08T08:22:33] Filtering multi-mapping fusions by alignment score and read support (remaining=155588)
[2026-06-08T08:22:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:22:52] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=154330)
[2026-06-08T08:22:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=82045)
[2026-06-08T08:22:53] Filtering fusions with <2 supporting reads (remaining=9714)
[2026-06-08T08:22:53] Filtering fusions with an e-value >=0.3 (remaining=3466)
[2026-06-08T08:22:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3491)
[2026-06-08T08:22:55] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3432)
[2026-06-08T08:22:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3436)
[2026-06-08T08:22:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2458)
[2026-06-08T08:22:59] Searching for fusions with spliced split reads (remaining=2512)
[2026-06-08T08:23:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=1795)
[2026-06-08T08:23:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1771)
[2026-06-08T08:23:02] Searching for fusions with >=4 spliced events (remaining=1887)
[2026-06-08T08:23:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=500)
[2026-06-08T08:23:14] Filtering fusions with anchors <=23nt (remaining=383)
[2026-06-08T08:23:14] Filtering end-to-end fusions with low support (remaining=374)
[2026-06-08T08:23:14] Filtering fusions with no coverage around the breakpoints (remaining=359)
[2026-06-08T08:23:15] Indexing gene sequences 
[2026-06-08T08:23:17] Filtering genes with >=30% identity (remaining=126)
[2026-06-08T08:23:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=51)
[2026-06-08T08:23:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=45)
[2026-06-08T08:23:19] Searching for additional isoforms (remaining=60)
[2026-06-08T08:23:20] Assigning confidence scores to events 
[2026-06-08T08:23:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:23:21] Writing fusions to file '659_gK-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:23:21] Writing discarded fusions to file '659_gK-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:23:32] Freeing resources
[2026-06-08T08:23:42] Done (elapsed time=00:06:37, CPU time=00:06:36, peak memory=10.5gb)