[2026-06-08T07:18:08] Launching Arriba 2.4.0
[2026-06-08T07:18:08] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:18:23] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:18:28] Reading chimeric alignments from '659_Kh-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=172152)
[2026-06-08T07:18:36] Marking multi-mapping alignments (marked=119325)
[2026-06-08T07:18:36] Detecting strandedness (reverse)
[2026-06-08T07:18:36] Assigning strands to alignments 
[2026-06-08T07:18:36] Annotating alignments 
[2026-06-08T07:18:37] Filtering duplicates (remaining=67975)
[2026-06-08T07:18:37] 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=61580)
[2026-06-08T07:18:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=61580)
[2026-06-08T07:18:37] Filtering viral contigs with expression lower than the top 5 (remaining=61580)
[2026-06-08T07:18:37] Filtering viral contigs with less than 5% coverage (remaining=61580)
[2026-06-08T07:18:37] Estimating fragment length (mate gap mean=-46.3596, mate gap stddev=41.0168, read length mean=114.051)
[2026-06-08T07:18:38] Filtering read-through fragments with a distance <=10000bp (remaining=60477)
[2026-06-08T07:18:38] Filtering inconsistently clipped mates (remaining=58782)
[2026-06-08T07:18:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=55744)
[2026-06-08T07:18:38] Filtering fragments with small insert size (remaining=55725)
[2026-06-08T07:18:38] Filtering alignments with long gaps (remaining=55725)
[2026-06-08T07:18:38] Filtering fragments with both mates in the same gene (remaining=55594)
[2026-06-08T07:18:38] Filtering fusions arising from hairpin structures (remaining=53024)
[2026-06-08T07:18:38] Filtering reads with a mismatch p-value <=0.01 (remaining=15838)
[2026-06-08T07:18:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=3855)
[2026-06-08T07:18:38] Finding fusions and counting supporting reads (total=3796)
[2026-06-08T07:18:38] Merging adjacent fusion breakpoints (remaining=3795)
[2026-06-08T07:18:38] Filtering multi-mapping fusions by alignment score and read support (remaining=2413)
[2026-06-08T07:18:39] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:18:39] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=2373)
[2026-06-08T07:18:39] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=1413)
[2026-06-08T07:18:39] Filtering fusions with <2 supporting reads (remaining=70)
[2026-06-08T07:18:39] Filtering fusions with an e-value >=0.3 (remaining=51)
[2026-06-08T07:18:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=52)
[2026-06-08T07:18:39] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=50)
[2026-06-08T07:18:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=50)
[2026-06-08T07:18:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=47)
[2026-06-08T07:18:39] Searching for fusions with spliced split reads (remaining=48)
[2026-06-08T07:18:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=45)
[2026-06-08T07:18:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=45)
[2026-06-08T07:18:39] Searching for fusions with >=4 spliced events (remaining=45)
[2026-06-08T07:18:39] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7)
[2026-06-08T07:18:57] Filtering fusions with anchors <=23nt (remaining=7)
[2026-06-08T07:18:57] Filtering end-to-end fusions with low support (remaining=7)
[2026-06-08T07:18:57] Filtering fusions with no coverage around the breakpoints (remaining=7)
[2026-06-08T07:18:57] Indexing gene sequences 
[2026-06-08T07:18:57] Filtering genes with >=30% identity (remaining=7)
[2026-06-08T07:18:57] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=5)
[2026-06-08T07:18:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=5)
[2026-06-08T07:18:57] Searching for additional isoforms (remaining=6)
[2026-06-08T07:18:57] Assigning confidence scores to events 
[2026-06-08T07:18:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:18:58] Writing fusions to file '659_Kh-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-08T07:18:58] Writing discarded fusions to file '659_Kh-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:18:58] Freeing resources
[2026-06-08T07:18:59] Done (elapsed time=00:00:51, CPU time=00:00:50, peak memory=4.25gb)