[2026-06-08T08:25:40] Launching Arriba 2.4.0
[2026-06-08T08:25:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:25:49] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:53] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s10.Aligned.sortedByCoord.out.bam' (total=11473378)
[2026-06-08T08:32:51] Marking multi-mapping alignments (marked=7951489)
[2026-06-08T08:32:56] Detecting strandedness (reverse)
[2026-06-08T08:32:56] Assigning strands to alignments 
[2026-06-08T08:32:58] Annotating alignments 
[2026-06-08T08:33:40] Filtering duplicates (remaining=6362489)
[2026-06-08T08:33:48] 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=5654947)
[2026-06-08T08:33:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5654947)
[2026-06-08T08:33:53] Filtering viral contigs with expression lower than the top 5 (remaining=5654947)
[2026-06-08T08:33:59] Filtering viral contigs with less than 5% coverage (remaining=5654947)
[2026-06-08T08:34:02] Estimating fragment length (mate gap mean=-86.1306, mate gap stddev=30.5556, read length mean=131.973)
[2026-06-08T08:34:02] Filtering read-through fragments with a distance <=10000bp (remaining=5397138)
[2026-06-08T08:34:04] Filtering inconsistently clipped mates (remaining=5294865)
[2026-06-08T08:34:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4848874)
[2026-06-08T08:34:12] Filtering fragments with small insert size (remaining=4847892)
[2026-06-08T08:34:15] Filtering alignments with long gaps (remaining=4847891)
[2026-06-08T08:34:17] Filtering fragments with both mates in the same gene (remaining=4846102)
[2026-06-08T08:34:20] Filtering fusions arising from hairpin structures (remaining=4478708)
[2026-06-08T08:34:23] Filtering reads with a mismatch p-value <=0.01 (remaining=1890635)
[2026-06-08T08:34:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=1043877)
[2026-06-08T08:34:47] Finding fusions and counting supporting reads (total=898932)
[2026-06-08T08:35:06] Merging adjacent fusion breakpoints (remaining=892098)
[2026-06-08T08:35:08] Filtering multi-mapping fusions by alignment score and read support (remaining=498562)
[2026-06-08T08:35:48] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:56] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=495298)
[2026-06-08T08:35:57] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=327890)
[2026-06-08T08:35:58] Filtering fusions with <2 supporting reads (remaining=26299)
[2026-06-08T08:35:59] Filtering fusions with an e-value >=0.3 (remaining=6466)
[2026-06-08T08:35:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6502)
[2026-06-08T08:36:04] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6216)
[2026-06-08T08:36:04] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6229)
[2026-06-08T08:36:06] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5003)
[2026-06-08T08:36:12] Searching for fusions with spliced split reads (remaining=5087)
[2026-06-08T08:36:17] Selecting best breakpoints from genes with multiple breakpoints (remaining=3095)
[2026-06-08T08:36:19] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3064)
[2026-06-08T08:36:20] Searching for fusions with >=4 spliced events (remaining=3755)
[2026-06-08T08:36:21] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1477)
[2026-06-08T08:36:35] Filtering fusions with anchors <=23nt (remaining=1106)
[2026-06-08T08:36:36] Filtering end-to-end fusions with low support (remaining=1072)
[2026-06-08T08:36:36] Filtering fusions with no coverage around the breakpoints (remaining=1059)
[2026-06-08T08:36:37] Indexing gene sequences 
[2026-06-08T08:36:42] Filtering genes with >=30% identity (remaining=260)
[2026-06-08T08:36:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=80)
[2026-06-08T08:36:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=80)
[2026-06-08T08:36:48] Searching for additional isoforms (remaining=97)
[2026-06-08T08:36:49] Assigning confidence scores to events 
[2026-06-08T08:36:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:36:53] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s10.arriba.fusions.tsv' 
[2026-06-08T08:36:55] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s10.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:29] Freeing resources
[2026-06-08T08:37:51] Done (elapsed time=00:12:11, CPU time=00:12:09, peak memory=16.6gb)