[2026-06-08T07:38:45] Launching Arriba 2.4.0
[2026-06-08T07:38:45] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:39:04] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:39:11] Reading chimeric alignments from '659_dcz-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam' (total=2341118)
[2026-06-08T07:41:15] Marking multi-mapping alignments (marked=1641301)
[2026-06-08T07:41:16] Detecting strandedness (reverse)
[2026-06-08T07:41:16] Assigning strands to alignments 
[2026-06-08T07:41:17] Annotating alignments 
[2026-06-08T07:41:28] Filtering duplicates (remaining=559617)
[2026-06-08T07:41:30] 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=513679)
[2026-06-08T07:41:31] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=513679)
[2026-06-08T07:41:31] Filtering viral contigs with expression lower than the top 5 (remaining=513679)
[2026-06-08T07:41:32] Filtering viral contigs with less than 5% coverage (remaining=513679)
[2026-06-08T07:41:33] Estimating fragment length (mate gap mean=-81.5275, mate gap stddev=26.8896, read length mean=117.954)
[2026-06-08T07:41:33] Filtering read-through fragments with a distance <=10000bp (remaining=495097)
[2026-06-08T07:41:34] Filtering inconsistently clipped mates (remaining=481322)
[2026-06-08T07:41:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=441067)
[2026-06-08T07:41:35] Filtering fragments with small insert size (remaining=440880)
[2026-06-08T07:41:36] Filtering alignments with long gaps (remaining=440880)
[2026-06-08T07:41:36] Filtering fragments with both mates in the same gene (remaining=440714)
[2026-06-08T07:41:37] Filtering fusions arising from hairpin structures (remaining=418337)
[2026-06-08T07:41:38] Filtering reads with a mismatch p-value <=0.01 (remaining=138755)
[2026-06-08T07:41:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=58849)
[2026-06-08T07:41:41] Finding fusions and counting supporting reads (total=59923)
[2026-06-08T07:41:45] Merging adjacent fusion breakpoints (remaining=59710)
[2026-06-08T07:41:45] Filtering multi-mapping fusions by alignment score and read support (remaining=25909)
[2026-06-08T07:41:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:41:57] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=25644)
[2026-06-08T07:41:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=17574)
[2026-06-08T07:41:57] Filtering fusions with <2 supporting reads (remaining=776)
[2026-06-08T07:41:57] Filtering fusions with an e-value >=0.3 (remaining=252)
[2026-06-08T07:41:57] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=257)
[2026-06-08T07:41:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=230)
[2026-06-08T07:41:58] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=230)
[2026-06-08T07:41:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=223)
[2026-06-08T07:41:59] Searching for fusions with spliced split reads (remaining=236)
[2026-06-08T07:42:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=212)
[2026-06-08T07:42:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=209)
[2026-06-08T07:42:01] Searching for fusions with >=4 spliced events (remaining=211)
[2026-06-08T07:42:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=60)
[2026-06-08T07:42:26] Filtering fusions with anchors <=23nt (remaining=50)
[2026-06-08T07:42:26] Filtering end-to-end fusions with low support (remaining=44)
[2026-06-08T07:42:26] Filtering fusions with no coverage around the breakpoints (remaining=41)
[2026-06-08T07:42:26] Indexing gene sequences 
[2026-06-08T07:42:27] Filtering genes with >=30% identity (remaining=17)
[2026-06-08T07:42:27] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=8)
[2026-06-08T07:42:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=8)
[2026-06-08T07:42:28] Searching for additional isoforms (remaining=10)
[2026-06-08T07:42:28] Assigning confidence scores to events 
[2026-06-08T07:42:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:42:28] Writing fusions to file '659_dcz-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:42:29] Writing discarded fusions to file '659_dcz-T1-TRNA-1_B23WHTKLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:42:34] Freeing resources
[2026-06-08T07:42:41] Done (elapsed time=00:03:56, CPU time=00:03:54, peak memory=6.46gb)