[2026-06-08T08:31:50] Launching Arriba 2.4.0
[2026-06-08T08:31:50] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:31:58] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:02] Reading chimeric alignments from '659_bua-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=9047293)
[2026-06-08T08:38:44] Marking multi-mapping alignments (marked=5512704)
[2026-06-08T08:38:48] Detecting strandedness (reverse)
[2026-06-08T08:38:48] Assigning strands to alignments 
[2026-06-08T08:38:53] Annotating alignments 
[2026-06-08T08:39:26] Filtering duplicates (remaining=5972758)
[2026-06-08T08:39:34] 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=5691966)
[2026-06-08T08:39:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5691966)
[2026-06-08T08:39:37] Filtering viral contigs with expression lower than the top 5 (remaining=5691966)
[2026-06-08T08:39:41] Filtering viral contigs with less than 5% coverage (remaining=5691966)
[2026-06-08T08:39:44] Estimating fragment length (mate gap mean=-86.7072, mate gap stddev=28.2655, read length mean=129.633)
[2026-06-08T08:39:44] Filtering read-through fragments with a distance <=10000bp (remaining=5347957)
[2026-06-08T08:39:45] Filtering inconsistently clipped mates (remaining=5240694)
[2026-06-08T08:39:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5093550)
[2026-06-08T08:39:52] Filtering fragments with small insert size (remaining=5092554)
[2026-06-08T08:39:54] Filtering alignments with long gaps (remaining=5092553)
[2026-06-08T08:39:56] Filtering fragments with both mates in the same gene (remaining=5091447)
[2026-06-08T08:39:58] Filtering fusions arising from hairpin structures (remaining=4751124)
[2026-06-08T08:40:00] Filtering reads with a mismatch p-value <=0.01 (remaining=2437570)
[2026-06-08T08:40:13] Filtering reads with low entropy (k-mer content >=60%) (remaining=1042855)
[2026-06-08T08:40:24] Finding fusions and counting supporting reads (total=741622)
[2026-06-08T08:40:42] Merging adjacent fusion breakpoints (remaining=735450)
[2026-06-08T08:40:44] Filtering multi-mapping fusions by alignment score and read support (remaining=485657)
[2026-06-08T08:41:16] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:23] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=483701)
[2026-06-08T08:41:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=280053)
[2026-06-08T08:41:25] Filtering fusions with <2 supporting reads (remaining=36704)
[2026-06-08T08:41:25] Filtering fusions with an e-value >=0.3 (remaining=9404)
[2026-06-08T08:41:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9466)
[2026-06-08T08:41:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9406)
[2026-06-08T08:41:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9412)
[2026-06-08T08:41:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6749)
[2026-06-08T08:41:36] Searching for fusions with spliced split reads (remaining=6770)
[2026-06-08T08:41:41] Selecting best breakpoints from genes with multiple breakpoints (remaining=4361)
[2026-06-08T08:41:42] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4329)
[2026-06-08T08:41:43] Searching for fusions with >=4 spliced events (remaining=5331)
[2026-06-08T08:41:44] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2032)
[2026-06-08T08:41:57] Filtering fusions with anchors <=23nt (remaining=1690)
[2026-06-08T08:41:58] Filtering end-to-end fusions with low support (remaining=1651)
[2026-06-08T08:41:58] Filtering fusions with no coverage around the breakpoints (remaining=1614)
[2026-06-08T08:41:59] Indexing gene sequences 
[2026-06-08T08:42:05] Filtering genes with >=30% identity (remaining=504)
[2026-06-08T08:42:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=203)
[2026-06-08T08:42:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=161)
[2026-06-08T08:42:11] Searching for additional isoforms (remaining=240)
[2026-06-08T08:42:13] Assigning confidence scores to events 
[2026-06-08T08:42:16] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:16] Writing fusions to file '659_bua-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:18] Writing discarded fusions to file '659_bua-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:47] Freeing resources
[2026-06-08T08:43:02] Done (elapsed time=00:11:12, CPU time=00:11:12, peak memory=13.6gb)