[2026-06-08T08:15:35] Launching Arriba 2.4.0
[2026-06-08T08:15:35] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:15:44] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:15:49] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s43.Aligned.sortedByCoord.out.bam' (total=11918236)
[2026-06-08T08:23:27] Marking multi-mapping alignments (marked=8487630)
[2026-06-08T08:23:34] Detecting strandedness (reverse)
[2026-06-08T08:23:34] Assigning strands to alignments 
[2026-06-08T08:23:38] Annotating alignments 
[2026-06-08T08:24:40] Filtering duplicates (remaining=5444814)
[2026-06-08T08:24:49] 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=4798156)
[2026-06-08T08:24:52] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4798156)
[2026-06-08T08:24:56] Filtering viral contigs with expression lower than the top 5 (remaining=4798156)
[2026-06-08T08:25:03] Filtering viral contigs with less than 5% coverage (remaining=4798156)
[2026-06-08T08:25:07] Estimating fragment length (mate gap mean=-81.9003, mate gap stddev=30.5719, read length mean=126.555)
[2026-06-08T08:25:07] Filtering read-through fragments with a distance <=10000bp (remaining=4610062)
[2026-06-08T08:25:11] Filtering inconsistently clipped mates (remaining=4526376)
[2026-06-08T08:25:14] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3989381)
[2026-06-08T08:25:21] Filtering fragments with small insert size (remaining=3988231)
[2026-06-08T08:25:24] Filtering alignments with long gaps (remaining=3988231)
[2026-06-08T08:25:28] Filtering fragments with both mates in the same gene (remaining=3986459)
[2026-06-08T08:25:31] Filtering fusions arising from hairpin structures (remaining=3762777)
[2026-06-08T08:25:35] Filtering reads with a mismatch p-value <=0.01 (remaining=1487611)
[2026-06-08T08:25:47] Filtering reads with low entropy (k-mer content >=60%) (remaining=712057)
[2026-06-08T08:25:58] Finding fusions and counting supporting reads (total=632654)
[2026-06-08T08:26:20] Merging adjacent fusion breakpoints (remaining=629117)
[2026-06-08T08:26:22] Filtering multi-mapping fusions by alignment score and read support (remaining=308612)
[2026-06-08T08:27:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:17] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=305985)
[2026-06-08T08:27:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=209326)
[2026-06-08T08:27:20] Filtering fusions with <2 supporting reads (remaining=15428)
[2026-06-08T08:27:21] Filtering fusions with an e-value >=0.3 (remaining=3874)
[2026-06-08T08:27:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3894)
[2026-06-08T08:27:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3579)
[2026-06-08T08:27:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3586)
[2026-06-08T08:27:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3003)
[2026-06-08T08:27:37] Searching for fusions with spliced split reads (remaining=3046)
[2026-06-08T08:27:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=2093)
[2026-06-08T08:27:46] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2060)
[2026-06-08T08:27:47] Searching for fusions with >=4 spliced events (remaining=2346)
[2026-06-08T08:27:49] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=814)
[2026-06-08T08:28:07] Filtering fusions with anchors <=23nt (remaining=606)
[2026-06-08T08:28:08] Filtering end-to-end fusions with low support (remaining=592)
[2026-06-08T08:28:09] Filtering fusions with no coverage around the breakpoints (remaining=583)
[2026-06-08T08:28:10] Indexing gene sequences 
[2026-06-08T08:28:14] Filtering genes with >=30% identity (remaining=191)
[2026-06-08T08:28:16] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=66)
[2026-06-08T08:28:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=66)
[2026-06-08T08:28:20] Searching for additional isoforms (remaining=82)
[2026-06-08T08:28:22] Assigning confidence scores to events 
[2026-06-08T08:28:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:28:26] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s43.arriba.fusions.tsv' 
[2026-06-08T08:28:28] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s43.arriba.fusions.discarded.tsv'
[2026-06-08T08:29:08] Freeing resources
[2026-06-08T08:29:36] Done (elapsed time=00:14:01, CPU time=00:13:59, peak memory=16.8gb)