[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_s1221_S42.Aligned.sortedByCoord.out.bam' (total=648799)
[2026-06-06T00:18:27] Marking multi-mapping alignments (marked=534747)
[2026-06-06T00:18:27] Detecting strandedness (reverse)
[2026-06-06T00:18:27] Assigning strands to alignments 
[2026-06-06T00:18:28] Annotating alignments 
[2026-06-06T00:18:30] Filtering duplicates (remaining=458713)
[2026-06-06T00:18:30] 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=303220)
[2026-06-06T00:18:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=303220)
[2026-06-06T00:18:30] Filtering viral contigs with expression lower than the top 5 (remaining=303220)
[2026-06-06T00:18:30] Filtering viral contigs with less than 5% coverage (remaining=303220)
[2026-06-06T00:18:31] Estimating fragment length (mate gap mean=-74.9889, mate gap stddev=37.351, read length mean=142.995)
[2026-06-06T00:18:31] Filtering read-through fragments with a distance <=10000bp (remaining=290314)
[2026-06-06T00:18:31] Filtering inconsistently clipped mates (remaining=281240)
[2026-06-06T00:18:31] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=269625)
[2026-06-06T00:18:31] Filtering fragments with small insert size (remaining=269584)
[2026-06-06T00:18:31] Filtering alignments with long gaps (remaining=269584)
[2026-06-06T00:18:32] Filtering fragments with both mates in the same gene (remaining=269541)
[2026-06-06T00:18:32] Filtering fusions arising from hairpin structures (remaining=246085)
[2026-06-06T00:18:32] Filtering reads with a mismatch p-value <=0.01 (remaining=162339)
[2026-06-06T00:18:33] Filtering reads with low entropy (k-mer content >=60%) (remaining=99583)
[2026-06-06T00:18:33] Finding fusions and counting supporting reads (total=79947)
[2026-06-06T00:18:34] Merging adjacent fusion breakpoints (remaining=79866)
[2026-06-06T00:18:34] Filtering multi-mapping fusions by alignment score and read support (remaining=32678)
[2026-06-06T00:18:36] Estimating expected number of fusions by random chance (e-value) 
[2026-06-06T00:18:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=32360)
[2026-06-06T00:18:36] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=26606)
[2026-06-06T00:18:36] Filtering fusions with <2 supporting reads (remaining=2705)
[2026-06-06T00:18:36] Filtering fusions with an e-value >=0.3 (remaining=1064)
[2026-06-06T00:18:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1080)
[2026-06-06T00:18:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1070)
[2026-06-06T00:18:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1071)
[2026-06-06T00:18:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=945)
[2026-06-06T00:18:36] Searching for fusions with spliced split reads (remaining=950)
[2026-06-06T00:18:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=552)
[2026-06-06T00:18:37] Filtering read-through fusions with breakpoints near the gene boundary (remaining=549)
[2026-06-06T00:18:37] Searching for fusions with >=4 spliced events (remaining=549)
[2026-06-06T00:18:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=123)
[2026-06-06T00:18:46] Filtering fusions with anchors <=23nt (remaining=88)
[2026-06-06T00:18:46] Filtering end-to-end fusions with low support (remaining=86)
[2026-06-06T00:18:46] Filtering fusions with no coverage around the breakpoints (remaining=81)
[2026-06-06T00:18:46] Indexing gene sequences 
[2026-06-06T00:18:47] Filtering genes with >=30% identity (remaining=39)
[2026-06-06T00:18:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=26)
[2026-06-06T00:18:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=26)
[2026-06-06T00:18:47] Searching for additional isoforms (remaining=29)
[2026-06-06T00:18:47] Assigning confidence scores to events 
[2026-06-06T00:18:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-06T00:18:47] Writing fusions to file 'rna_s1221_S42.arriba.fusions.tsv' 
[2026-06-06T00:18:47] Writing discarded fusions to file 'rna_s1221_S42.arriba.fusions.discarded.tsv'
[2026-06-06T00:18:49] Freeing resources
[2026-06-06T00:18:50] Done (elapsed time=00:00:50, CPU time=00:00:49, peak memory=4.81gb)