[2026-06-08T08:47:27] Launching Arriba 2.4.0
[2026-06-08T08:47:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:44] Reading chimeric alignments from '659_cVw-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10209995)
[2026-06-08T08:55:40] Marking multi-mapping alignments (marked=6615867)
[2026-06-08T08:55:45] Detecting strandedness (reverse)
[2026-06-08T08:55:45] Assigning strands to alignments 
[2026-06-08T08:55:47] Annotating alignments 
[2026-06-08T08:56:23] Filtering duplicates (remaining=4596529)
[2026-06-08T08:56:29] 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=4345722)
[2026-06-08T08:56:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4345722)
[2026-06-08T08:56:33] Filtering viral contigs with expression lower than the top 5 (remaining=4345722)
[2026-06-08T08:56:38] Filtering viral contigs with less than 5% coverage (remaining=4345722)
[2026-06-08T08:56:40] Estimating fragment length (mate gap mean=-85.4499, mate gap stddev=32.1637, read length mean=137.902)
[2026-06-08T08:56:41] Filtering read-through fragments with a distance <=10000bp (remaining=4110289)
[2026-06-08T08:56:43] Filtering inconsistently clipped mates (remaining=4050732)
[2026-06-08T08:56:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3890765)
[2026-06-08T08:56:49] Filtering fragments with small insert size (remaining=3890421)
[2026-06-08T08:56:52] Filtering alignments with long gaps (remaining=3890421)
[2026-06-08T08:56:54] Filtering fragments with both mates in the same gene (remaining=3889754)
[2026-06-08T08:56:56] Filtering fusions arising from hairpin structures (remaining=3702337)
[2026-06-08T08:56:58] Filtering reads with a mismatch p-value <=0.01 (remaining=1576975)
[2026-06-08T08:57:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=538371)
[2026-06-08T08:57:17] Finding fusions and counting supporting reads (total=434420)
[2026-06-08T08:57:32] Merging adjacent fusion breakpoints (remaining=430548)
[2026-06-08T08:57:34] Filtering multi-mapping fusions by alignment score and read support (remaining=270817)
[2026-06-08T08:58:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:58:13] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=267989)
[2026-06-08T08:58:13] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=140983)
[2026-06-08T08:58:14] Filtering fusions with <2 supporting reads (remaining=20323)
[2026-06-08T08:58:15] Filtering fusions with an e-value >=0.3 (remaining=7939)
[2026-06-08T08:58:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7974)
[2026-06-08T08:58:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7854)
[2026-06-08T08:58:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7859)
[2026-06-08T08:58:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5289)
[2026-06-08T08:58:27] Searching for fusions with spliced split reads (remaining=5369)
[2026-06-08T08:58:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=3221)
[2026-06-08T08:58:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3183)
[2026-06-08T08:58:34] Searching for fusions with >=4 spliced events (remaining=3532)
[2026-06-08T08:58:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1051)
[2026-06-08T08:58:50] Filtering fusions with anchors <=23nt (remaining=710)
[2026-06-08T08:58:50] Filtering end-to-end fusions with low support (remaining=683)
[2026-06-08T08:58:51] Filtering fusions with no coverage around the breakpoints (remaining=663)
[2026-06-08T08:58:51] Indexing gene sequences 
[2026-06-08T08:58:55] Filtering genes with >=30% identity (remaining=235)
[2026-06-08T08:58:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=96)
[2026-06-08T08:58:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=94)
[2026-06-08T08:58:59] Searching for additional isoforms (remaining=123)
[2026-06-08T08:59:00] Assigning confidence scores to events 
[2026-06-08T08:59:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:59:02] Writing fusions to file '659_cVw-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:59:04] Writing discarded fusions to file '659_cVw-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:28] Freeing resources
[2026-06-08T08:59:44] Done (elapsed time=00:12:17, CPU time=00:12:16, peak memory=14.6gb)