[2026-06-04T20:20:23] Launching Arriba 2.4.0
[2026-06-04T20:20:23] Loading assembly from 'ref_genome.fa' 
[2026-06-04T20:20:34] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T20:20:37] Reading chimeric alignments from '659_R1-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=74589)
[2026-06-04T20:20:38] Marking multi-mapping alignments (marked=68555)
[2026-06-04T20:20:38] Detecting strandedness (no)
[2026-06-04T20:20:38] Annotating alignments 
[2026-06-04T20:20:38] Filtering duplicates (remaining=40235)
[2026-06-04T20:20:38] 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=33602)
[2026-06-04T20:20:38] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=33602)
[2026-06-04T20:20:38] Filtering viral contigs with expression lower than the top 5 (remaining=33602)
[2026-06-04T20:20:38] Filtering viral contigs with less than 5% coverage (remaining=33602)
[2026-06-04T20:20:38] Estimating fragment length (mate gap mean=-16.3583, mate gap stddev=2.89828, read length mean=52.4774)
[2026-06-04T20:20:38] Filtering read-through fragments with a distance <=10000bp (remaining=33590)
[2026-06-04T20:20:38] Filtering inconsistently clipped mates (remaining=32374)
[2026-06-04T20:20:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=30207)
[2026-06-04T20:20:38] Filtering fragments with small insert size (remaining=30176)
[2026-06-04T20:20:38] Filtering alignments with long gaps (remaining=30176)
[2026-06-04T20:20:38] Filtering fragments with both mates in the same gene (remaining=30046)
[2026-06-04T20:20:38] Filtering fusions arising from hairpin structures (remaining=29055)
[2026-06-04T20:20:38] Filtering reads with a mismatch p-value <=0.01 (remaining=581)
[2026-06-04T20:20:38] Filtering reads with low entropy (k-mer content >=60%) (remaining=72)
[2026-06-04T20:20:38] Finding fusions and counting supporting reads (total=79)
[2026-06-04T20:20:38] Merging adjacent fusion breakpoints (remaining=79)
[2026-06-04T20:20:38] Filtering multi-mapping fusions by alignment score and read support (remaining=78)
[2026-06-04T20:20:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T20:20:38] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=77)
[2026-06-04T20:20:38] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=76)
[2026-06-04T20:20:38] Filtering fusions with <2 supporting reads (remaining=1)
[2026-06-04T20:20:38] Filtering fusions with an e-value >=0.3 (remaining=1)
[2026-06-04T20:20:38] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1)
[2026-06-04T20:20:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=0)
[2026-06-04T20:20:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=0)
[2026-06-04T20:20:38] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=0)
[2026-06-04T20:20:38] Searching for fusions with spliced split reads (remaining=0)
[2026-06-04T20:20:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-04T20:20:38] Filtering read-through fusions with breakpoints near the gene boundary (remaining=0)
[2026-06-04T20:20:38] Searching for fusions with >=4 spliced events (remaining=0)
[2026-06-04T20:20:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=0)
[2026-06-04T20:20:47] Filtering fusions with anchors <=23nt (remaining=0)
[2026-06-04T20:20:47] Filtering end-to-end fusions with low support (remaining=0)
[2026-06-04T20:20:47] Filtering fusions with no coverage around the breakpoints (remaining=0)
[2026-06-04T20:20:47] Indexing gene sequences 
[2026-06-04T20:20:47] Filtering genes with >=30% identity (remaining=0)
[2026-06-04T20:20:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-04T20:20:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-04T20:20:47] Searching for additional isoforms (remaining=0)
[2026-06-04T20:20:47] Assigning confidence scores to events 
[2026-06-04T20:20:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T20:20:48] Writing fusions to file '659_R1-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T20:20:48] Writing discarded fusions to file '659_R1-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T20:20:48] Freeing resources
[2026-06-04T20:20:48] Done (elapsed time=00:00:25, CPU time=00:00:24, peak memory=4.15gb)