[2026-06-08T08:32:31] Launching Arriba 2.4.0
[2026-06-08T08:32:31] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:43] Reading chimeric alignments from '659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=8951982)
[2026-06-08T08:38:42] Marking multi-mapping alignments (marked=5635383)
[2026-06-08T08:38:46] Detecting strandedness (reverse)
[2026-06-08T08:38:46] Assigning strands to alignments 
[2026-06-08T08:38:47] Annotating alignments 
[2026-06-08T08:39:21] Filtering duplicates (remaining=3172298)
[2026-06-08T08:39:31] 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=3001647)
[2026-06-08T08:39:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3001647)
[2026-06-08T08:39:36] Filtering viral contigs with expression lower than the top 5 (remaining=3001647)
[2026-06-08T08:39:40] Filtering viral contigs with less than 5% coverage (remaining=3001647)
[2026-06-08T08:39:42] Estimating fragment length (mate gap mean=-88.8363, mate gap stddev=28.1108, read length mean=133.44)
[2026-06-08T08:39:42] Filtering read-through fragments with a distance <=10000bp (remaining=2859099)
[2026-06-08T08:39:44] Filtering inconsistently clipped mates (remaining=2807996)
[2026-06-08T08:39:46] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2678284)
[2026-06-08T08:39:49] Filtering fragments with small insert size (remaining=2677851)
[2026-06-08T08:39:51] Filtering alignments with long gaps (remaining=2677851)
[2026-06-08T08:39:52] Filtering fragments with both mates in the same gene (remaining=2677223)
[2026-06-08T08:39:54] Filtering fusions arising from hairpin structures (remaining=2549781)
[2026-06-08T08:39:56] Filtering reads with a mismatch p-value <=0.01 (remaining=1014116)
[2026-06-08T08:40:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=381613)
[2026-06-08T08:40:12] Finding fusions and counting supporting reads (total=323075)
[2026-06-08T08:40:29] Merging adjacent fusion breakpoints (remaining=320404)
[2026-06-08T08:40:30] Filtering multi-mapping fusions by alignment score and read support (remaining=198613)
[2026-06-08T08:41:04] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:08] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=197317)
[2026-06-08T08:41:08] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=108150)
[2026-06-08T08:41:09] Filtering fusions with <2 supporting reads (remaining=12645)
[2026-06-08T08:41:09] Filtering fusions with an e-value >=0.3 (remaining=3683)
[2026-06-08T08:41:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3707)
[2026-06-08T08:41:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3645)
[2026-06-08T08:41:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3647)
[2026-06-08T08:41:15] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2598)
[2026-06-08T08:41:20] Searching for fusions with spliced split reads (remaining=2646)
[2026-06-08T08:41:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=1872)
[2026-06-08T08:41:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1855)
[2026-06-08T08:41:26] Searching for fusions with >=4 spliced events (remaining=2073)
[2026-06-08T08:41:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=653)
[2026-06-08T08:41:40] Filtering fusions with anchors <=23nt (remaining=530)
[2026-06-08T08:41:41] Filtering end-to-end fusions with low support (remaining=512)
[2026-06-08T08:41:41] Filtering fusions with no coverage around the breakpoints (remaining=502)
[2026-06-08T08:41:42] Indexing gene sequences 
[2026-06-08T08:41:45] Filtering genes with >=30% identity (remaining=150)
[2026-06-08T08:41:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=58)
[2026-06-08T08:41:48] Selecting best breakpoints from genes with multiple breakpoints (remaining=51)
[2026-06-08T08:41:48] Searching for additional isoforms (remaining=67)
[2026-06-08T08:41:49] Assigning confidence scores to events 
[2026-06-08T08:41:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:41:51] Writing fusions to file '659_bua-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:41:52] Writing discarded fusions to file '659_bua-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:42:12] Freeing resources
[2026-06-08T08:42:27] Done (elapsed time=00:09:56, CPU time=00:09:55, peak memory=13.3gb)