[2026-06-08T08:47:18] Launching Arriba 2.4.0
[2026-06-08T08:47:18] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:47:33] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:47:38] Reading chimeric alignments from '659_dc8-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=10836442)
[2026-06-08T08:55:31] Marking multi-mapping alignments (marked=6806660)
[2026-06-08T08:55:36] Detecting strandedness (reverse)
[2026-06-08T08:55:36] Assigning strands to alignments 
[2026-06-08T08:55:38] Annotating alignments 
[2026-06-08T08:56:13] Filtering duplicates (remaining=3699982)
[2026-06-08T08:56:19] 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=3524499)
[2026-06-08T08:56:21] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3524499)
[2026-06-08T08:56:23] Filtering viral contigs with expression lower than the top 5 (remaining=3524499)
[2026-06-08T08:56:28] Filtering viral contigs with less than 5% coverage (remaining=3524499)
[2026-06-08T08:56:30] Estimating fragment length (mate gap mean=-86.2223, mate gap stddev=29.798, read length mean=134.441)
[2026-06-08T08:56:30] Filtering read-through fragments with a distance <=10000bp (remaining=3355476)
[2026-06-08T08:56:32] Filtering inconsistently clipped mates (remaining=3309789)
[2026-06-08T08:56:34] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3173140)
[2026-06-08T08:56:38] Filtering fragments with small insert size (remaining=3172699)
[2026-06-08T08:56:40] Filtering alignments with long gaps (remaining=3172699)
[2026-06-08T08:56:42] Filtering fragments with both mates in the same gene (remaining=3172071)
[2026-06-08T08:56:44] Filtering fusions arising from hairpin structures (remaining=3050278)
[2026-06-08T08:56:47] Filtering reads with a mismatch p-value <=0.01 (remaining=1264020)
[2026-06-08T08:56:56] Filtering reads with low entropy (k-mer content >=60%) (remaining=435625)
[2026-06-08T08:57:04] Finding fusions and counting supporting reads (total=384392)
[2026-06-08T08:57:19] Merging adjacent fusion breakpoints (remaining=380709)
[2026-06-08T08:57:20] Filtering multi-mapping fusions by alignment score and read support (remaining=219945)
[2026-06-08T08:57:53] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:57:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=217713)
[2026-06-08T08:57:58] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=118821)
[2026-06-08T08:57:59] Filtering fusions with <2 supporting reads (remaining=14549)
[2026-06-08T08:57:59] Filtering fusions with an e-value >=0.3 (remaining=4624)
[2026-06-08T08:58:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4653)
[2026-06-08T08:58:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4565)
[2026-06-08T08:58:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4568)
[2026-06-08T08:58:04] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3366)
[2026-06-08T08:58:09] Searching for fusions with spliced split reads (remaining=3415)
[2026-06-08T08:58:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=2321)
[2026-06-08T08:58:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2297)
[2026-06-08T08:58:14] Searching for fusions with >=4 spliced events (remaining=2512)
[2026-06-08T08:58:15] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=717)
[2026-06-08T08:58:32] Filtering fusions with anchors <=23nt (remaining=538)
[2026-06-08T08:58:33] Filtering end-to-end fusions with low support (remaining=518)
[2026-06-08T08:58:33] Filtering fusions with no coverage around the breakpoints (remaining=498)
[2026-06-08T08:58:33] Indexing gene sequences 
[2026-06-08T08:58:37] Filtering genes with >=30% identity (remaining=178)
[2026-06-08T08:58:38] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=96)
[2026-06-08T08:58:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=76)
[2026-06-08T08:58:41] Searching for additional isoforms (remaining=103)
[2026-06-08T08:58:41] Assigning confidence scores to events 
[2026-06-08T08:58:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:58:44] Writing fusions to file '659_dc8-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:58:45] Writing discarded fusions to file '659_dc8-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:59:05] Freeing resources
[2026-06-08T08:59:23] Done (elapsed time=00:12:05, CPU time=00:12:03, peak memory=15.2gb)