[2026-06-06T00:18:00] Launching Arriba 2.4.0
[2026-06-06T00:18:00] Loading assembly from 'ref_genome.fa' 
[2026-06-06T00:18:08] Loading annotation from 'ref_annot.gtf' 
[2026-06-06T00:18:11] Reading chimeric alignments from 'rna_s1200_S21.Aligned.sortedByCoord.out.bam' (total=280944)
[2026-06-06T00:18:24] Marking multi-mapping alignments (marked=187487)
[2026-06-06T00:18:24] Detecting strandedness (reverse)
[2026-06-06T00:18:24] Assigning strands to alignments 
[2026-06-06T00:18:24] Annotating alignments 
[2026-06-06T00:18:25] Filtering duplicates (remaining=241131)
[2026-06-06T00:18:25] 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=234070)
[2026-06-06T00:18:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=234070)
[2026-06-06T00:18:25] Filtering viral contigs with expression lower than the top 5 (remaining=234070)
[2026-06-06T00:18:25] Filtering viral contigs with less than 5% coverage (remaining=234070)
[2026-06-06T00:18:26] Estimating fragment length (mate gap mean=-83.0389, mate gap stddev=39.5422, read length mean=143.665)
[2026-06-06T00:18:26] Filtering read-through fragments with a distance <=10000bp (remaining=224343)
[2026-06-06T00:18:26] Filtering inconsistently clipped mates (remaining=219434)
[2026-06-06T00:18:26] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=207671)
[2026-06-06T00:18:26] Filtering fragments with small insert size (remaining=207640)
[2026-06-06T00:18:26] Filtering alignments with long gaps (remaining=207640)
[2026-06-06T00:18:26] Filtering fragments with both mates in the same gene (remaining=207597)
[2026-06-06T00:18:26] Filtering fusions arising from hairpin structures (remaining=189545)
[2026-06-06T00:18:26] Filtering reads with a mismatch p-value <=0.01 (remaining=97719)
[2026-06-06T00:18:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=38356)
[2026-06-06T00:18:27] Finding fusions and counting supporting reads (total=31062)
[2026-06-06T00:18:27] Merging adjacent fusion breakpoints (remaining=30985)
[2026-06-06T00:18:27] Filtering multi-mapping fusions by alignment score and read support (remaining=19639)
[2026-06-06T00:18:28] Estimating expected number of fusions by random chance (e-value) 
[2026-06-06T00:18:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=19447)
[2026-06-06T00:18:28] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=13413)
[2026-06-06T00:18:28] Filtering fusions with <2 supporting reads (remaining=1668)
[2026-06-06T00:18:28] Filtering fusions with an e-value >=0.3 (remaining=981)
[2026-06-06T00:18:28] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=995)
[2026-06-06T00:18:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=994)
[2026-06-06T00:18:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=995)
[2026-06-06T00:18:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=787)
[2026-06-06T00:18:28] Searching for fusions with spliced split reads (remaining=802)
[2026-06-06T00:18:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=541)
[2026-06-06T00:18:28] Filtering read-through fusions with breakpoints near the gene boundary (remaining=539)
[2026-06-06T00:18:28] Searching for fusions with >=4 spliced events (remaining=547)
[2026-06-06T00:18:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=124)
[2026-06-06T00:18:38] Filtering fusions with anchors <=23nt (remaining=73)
[2026-06-06T00:18:38] Filtering end-to-end fusions with low support (remaining=71)
[2026-06-06T00:18:38] Filtering fusions with no coverage around the breakpoints (remaining=61)
[2026-06-06T00:18:38] Indexing gene sequences 
[2026-06-06T00:18:39] Filtering genes with >=30% identity (remaining=36)
[2026-06-06T00:18:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=26)
[2026-06-06T00:18:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=26)
[2026-06-06T00:18:39] Searching for additional isoforms (remaining=29)
[2026-06-06T00:18:39] Assigning confidence scores to events 
[2026-06-06T00:18:39] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-06T00:18:39] Writing fusions to file 'rna_s1200_S21.arriba.fusions.tsv' 
[2026-06-06T00:18:39] Writing discarded fusions to file 'rna_s1200_S21.arriba.fusions.discarded.tsv'
[2026-06-06T00:18:41] Freeing resources
[2026-06-06T00:18:42] Done (elapsed time=00:00:42, CPU time=00:00:41, peak memory=4.39gb)