[2026-06-02T16:20:43] Launching Arriba 2.4.0
[2026-06-02T16:20:43] Loading assembly from 'ref_genome.fa' 
[2026-06-02T16:20:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-02T16:21:00] Reading chimeric alignments from 'rna_s1221_S42.Aligned.sortedByCoord.out.bam' (total=641586)
[2026-06-02T16:21:21] Marking multi-mapping alignments (marked=528121)
[2026-06-02T16:21:22] Detecting strandedness (reverse)
[2026-06-02T16:21:22] Assigning strands to alignments 
[2026-06-02T16:21:22] Annotating alignments 
[2026-06-02T16:21:24] Filtering duplicates (remaining=451162)
[2026-06-02T16:21:24] 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=300486)
[2026-06-02T16:21:24] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=300486)
[2026-06-02T16:21:24] Filtering viral contigs with expression lower than the top 5 (remaining=300486)
[2026-06-02T16:21:24] Filtering viral contigs with less than 5% coverage (remaining=300486)
[2026-06-02T16:21:25] Estimating fragment length (mate gap mean=-75.3836, mate gap stddev=35.9642, read length mean=142.703)
[2026-06-02T16:21:25] Filtering read-through fragments with a distance <=10000bp (remaining=287815)
[2026-06-02T16:21:25] Filtering inconsistently clipped mates (remaining=278243)
[2026-06-02T16:21:25] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=265896)
[2026-06-02T16:21:25] Filtering fragments with small insert size (remaining=265860)
[2026-06-02T16:21:25] Filtering alignments with long gaps (remaining=265860)
[2026-06-02T16:21:25] Filtering fragments with both mates in the same gene (remaining=265817)
[2026-06-02T16:21:25] Filtering fusions arising from hairpin structures (remaining=242483)
[2026-06-02T16:21:26] Filtering reads with a mismatch p-value <=0.01 (remaining=161410)
[2026-06-02T16:21:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=98982)
[2026-06-02T16:21:27] Finding fusions and counting supporting reads (total=78969)
[2026-06-02T16:21:28] Merging adjacent fusion breakpoints (remaining=78844)
[2026-06-02T16:21:28] Filtering multi-mapping fusions by alignment score and read support (remaining=32035)
[2026-06-02T16:21:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-02T16:21:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=31724)
[2026-06-02T16:21:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=25969)
[2026-06-02T16:21:30] Filtering fusions with <2 supporting reads (remaining=2505)
[2026-06-02T16:21:30] Filtering fusions with an e-value >=0.3 (remaining=1067)
[2026-06-02T16:21:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1083)
[2026-06-02T16:21:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1070)
[2026-06-02T16:21:30] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1071)
[2026-06-02T16:21:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=954)
[2026-06-02T16:21:30] Searching for fusions with spliced split reads (remaining=965)
[2026-06-02T16:21:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=569)
[2026-06-02T16:21:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=566)
[2026-06-02T16:21:30] Searching for fusions with >=4 spliced events (remaining=570)
[2026-06-02T16:21:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=128)
[2026-06-02T16:21:44] Filtering fusions with anchors <=23nt (remaining=81)
[2026-06-02T16:21:44] Filtering end-to-end fusions with low support (remaining=76)
[2026-06-02T16:21:44] Filtering fusions with no coverage around the breakpoints (remaining=72)
[2026-06-02T16:21:44] Indexing gene sequences 
[2026-06-02T16:21:45] Filtering genes with >=30% identity (remaining=31)
[2026-06-02T16:21:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=24)
[2026-06-02T16:21:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=24)
[2026-06-02T16:21:45] Searching for additional isoforms (remaining=25)
[2026-06-02T16:21:45] Assigning confidence scores to events 
[2026-06-02T16:21:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-02T16:21:45] Writing fusions to file 'rna_s1221_S42.arriba.fusions.tsv' 
[2026-06-02T16:21:45] Writing discarded fusions to file 'rna_s1221_S42.arriba.fusions.discarded.tsv'
[2026-06-02T16:21:47] Freeing resources
[2026-06-02T16:21:49] Done (elapsed time=00:01:06, CPU time=00:01:05, peak memory=4.81gb)