[2026-06-08T08:17:37] Launching Arriba 2.4.0
[2026-06-08T08:17:37] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:47] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:52] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s36.Aligned.sortedByCoord.out.bam' (total=11868327)
[2026-06-08T08:24:28] Marking multi-mapping alignments (marked=8494208)
[2026-06-08T08:24:33] Detecting strandedness (reverse)
[2026-06-08T08:24:33] Assigning strands to alignments 
[2026-06-08T08:24:35] Annotating alignments 
[2026-06-08T08:25:17] Filtering duplicates (remaining=5468115)
[2026-06-08T08:25:23] 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=4809205)
[2026-06-08T08:25:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4809205)
[2026-06-08T08:25:28] Filtering viral contigs with expression lower than the top 5 (remaining=4809205)
[2026-06-08T08:25:33] Filtering viral contigs with less than 5% coverage (remaining=4809205)
[2026-06-08T08:25:36] Estimating fragment length (mate gap mean=-82.0251, mate gap stddev=31.8901, read length mean=125.829)
[2026-06-08T08:25:36] Filtering read-through fragments with a distance <=10000bp (remaining=4619736)
[2026-06-08T08:25:38] Filtering inconsistently clipped mates (remaining=4534069)
[2026-06-08T08:25:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3979923)
[2026-06-08T08:25:45] Filtering fragments with small insert size (remaining=3978843)
[2026-06-08T08:25:47] Filtering alignments with long gaps (remaining=3978843)
[2026-06-08T08:25:50] Filtering fragments with both mates in the same gene (remaining=3976953)
[2026-06-08T08:25:52] Filtering fusions arising from hairpin structures (remaining=3736037)
[2026-06-08T08:25:54] Filtering reads with a mismatch p-value <=0.01 (remaining=1424672)
[2026-06-08T08:26:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=733620)
[2026-06-08T08:26:14] Finding fusions and counting supporting reads (total=660212)
[2026-06-08T08:26:32] Merging adjacent fusion breakpoints (remaining=656551)
[2026-06-08T08:26:34] Filtering multi-mapping fusions by alignment score and read support (remaining=322166)
[2026-06-08T08:27:12] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=319557)
[2026-06-08T08:27:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=228211)
[2026-06-08T08:27:20] Filtering fusions with <2 supporting reads (remaining=15082)
[2026-06-08T08:27:20] Filtering fusions with an e-value >=0.3 (remaining=3662)
[2026-06-08T08:27:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3688)
[2026-06-08T08:27:25] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3312)
[2026-06-08T08:27:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3314)
[2026-06-08T08:27:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2969)
[2026-06-08T08:27:32] Searching for fusions with spliced split reads (remaining=3029)
[2026-06-08T08:27:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=2094)
[2026-06-08T08:27:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2064)
[2026-06-08T08:27:40] Searching for fusions with >=4 spliced events (remaining=2309)
[2026-06-08T08:27:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=765)
[2026-06-08T08:27:55] Filtering fusions with anchors <=23nt (remaining=568)
[2026-06-08T08:27:55] Filtering end-to-end fusions with low support (remaining=552)
[2026-06-08T08:27:56] Filtering fusions with no coverage around the breakpoints (remaining=544)
[2026-06-08T08:27:57] Indexing gene sequences 
[2026-06-08T08:28:00] Filtering genes with >=30% identity (remaining=210)
[2026-06-08T08:28:01] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=104)
[2026-06-08T08:28:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=76)
[2026-06-08T08:28:04] Searching for additional isoforms (remaining=92)
[2026-06-08T08:28:05] Assigning confidence scores to events 
[2026-06-08T08:28:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:28:09] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s36.arriba.fusions.tsv' 
[2026-06-08T08:28:10] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s36.arriba.fusions.discarded.tsv'
[2026-06-08T08:28:36] Freeing resources
[2026-06-08T08:28:55] Done (elapsed time=00:11:18, CPU time=00:11:17, peak memory=16.8gb)