[2026-06-08T08:16:40] Launching Arriba 2.4.0
[2026-06-08T08:16:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:16:57] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s21.Aligned.sortedByCoord.out.bam' (total=14382262)
[2026-06-08T08:24:20] Marking multi-mapping alignments (marked=10621724)
[2026-06-08T08:24:26] Detecting strandedness (reverse)
[2026-06-08T08:24:26] Assigning strands to alignments 
[2026-06-08T08:24:28] Annotating alignments 
[2026-06-08T08:25:11] Filtering duplicates (remaining=7163890)
[2026-06-08T08:25:20] 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=6165054)
[2026-06-08T08:25:23] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6165054)
[2026-06-08T08:25:25] Filtering viral contigs with expression lower than the top 5 (remaining=6165054)
[2026-06-08T08:25:30] Filtering viral contigs with less than 5% coverage (remaining=6165054)
[2026-06-08T08:25:33] Estimating fragment length (mate gap mean=-83.3359, mate gap stddev=31.9702, read length mean=124.686)
[2026-06-08T08:25:33] Filtering read-through fragments with a distance <=10000bp (remaining=5916619)
[2026-06-08T08:25:36] Filtering inconsistently clipped mates (remaining=5800013)
[2026-06-08T08:25:38] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5176147)
[2026-06-08T08:25:44] Filtering fragments with small insert size (remaining=5174488)
[2026-06-08T08:25:46] Filtering alignments with long gaps (remaining=5174488)
[2026-06-08T08:25:49] Filtering fragments with both mates in the same gene (remaining=5172302)
[2026-06-08T08:25:51] Filtering fusions arising from hairpin structures (remaining=4808107)
[2026-06-08T08:25:54] Filtering reads with a mismatch p-value <=0.01 (remaining=1767733)
[2026-06-08T08:26:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=972629)
[2026-06-08T08:26:16] Finding fusions and counting supporting reads (total=858156)
[2026-06-08T08:26:35] Merging adjacent fusion breakpoints (remaining=851285)
[2026-06-08T08:26:37] Filtering multi-mapping fusions by alignment score and read support (remaining=424667)
[2026-06-08T08:27:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=421492)
[2026-06-08T08:27:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=294143)
[2026-06-08T08:27:24] Filtering fusions with <2 supporting reads (remaining=20770)
[2026-06-08T08:27:25] Filtering fusions with an e-value >=0.3 (remaining=4579)
[2026-06-08T08:27:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4615)
[2026-06-08T08:27:30] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4257)
[2026-06-08T08:27:31] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4257)
[2026-06-08T08:27:33] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3931)
[2026-06-08T08:27:38] Searching for fusions with spliced split reads (remaining=4011)
[2026-06-08T08:27:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=2698)
[2026-06-08T08:27:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2661)
[2026-06-08T08:27:47] Searching for fusions with >=4 spliced events (remaining=3124)
[2026-06-08T08:27:48] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1100)
[2026-06-08T08:28:02] Filtering fusions with anchors <=23nt (remaining=821)
[2026-06-08T08:28:02] Filtering end-to-end fusions with low support (remaining=785)
[2026-06-08T08:28:03] Filtering fusions with no coverage around the breakpoints (remaining=772)
[2026-06-08T08:28:04] Indexing gene sequences 
[2026-06-08T08:28:08] Filtering genes with >=30% identity (remaining=204)
[2026-06-08T08:28:09] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=64)
[2026-06-08T08:28:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=64)
[2026-06-08T08:28:13] Searching for additional isoforms (remaining=79)
[2026-06-08T08:28:14] Assigning confidence scores to events 
[2026-06-08T08:28:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:28:18] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s21.arriba.fusions.tsv' 
[2026-06-08T08:28:19] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s21.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:48] Freeing resources
[2026-06-08T08:29:09] Done (elapsed time=00:12:29, CPU time=00:12:27, peak memory=19.8gb)