[2026-06-08T08:23:28] Launching Arriba 2.4.0
[2026-06-08T08:23:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:42] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s23.Aligned.sortedByCoord.out.bam' (total=13416324)
[2026-06-08T08:31:13] Marking multi-mapping alignments (marked=9832889)
[2026-06-08T08:31:20] Detecting strandedness (reverse)
[2026-06-08T08:31:20] Assigning strands to alignments 
[2026-06-08T08:31:24] Annotating alignments 
[2026-06-08T08:32:31] Filtering duplicates (remaining=6195198)
[2026-06-08T08:32:43] 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=5333571)
[2026-06-08T08:32:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5333571)
[2026-06-08T08:32:51] Filtering viral contigs with expression lower than the top 5 (remaining=5333571)
[2026-06-08T08:33:01] Filtering viral contigs with less than 5% coverage (remaining=5333571)
[2026-06-08T08:33:05] Estimating fragment length (mate gap mean=-83.1585, mate gap stddev=30.801, read length mean=125.397)
[2026-06-08T08:33:05] Filtering read-through fragments with a distance <=10000bp (remaining=5112687)
[2026-06-08T08:33:09] Filtering inconsistently clipped mates (remaining=5011963)
[2026-06-08T08:33:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4387490)
[2026-06-08T08:33:21] Filtering fragments with small insert size (remaining=4385998)
[2026-06-08T08:33:25] Filtering alignments with long gaps (remaining=4385998)
[2026-06-08T08:33:29] Filtering fragments with both mates in the same gene (remaining=4384243)
[2026-06-08T08:33:33] Filtering fusions arising from hairpin structures (remaining=4077997)
[2026-06-08T08:33:37] Filtering reads with a mismatch p-value <=0.01 (remaining=1567995)
[2026-06-08T08:33:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=864316)
[2026-06-08T08:34:05] Finding fusions and counting supporting reads (total=779112)
[2026-06-08T08:34:33] Merging adjacent fusion breakpoints (remaining=772778)
[2026-06-08T08:34:36] Filtering multi-mapping fusions by alignment score and read support (remaining=366347)
[2026-06-08T08:35:34] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:35:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=363143)
[2026-06-08T08:35:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=263835)
[2026-06-08T08:35:49] Filtering fusions with <2 supporting reads (remaining=17073)
[2026-06-08T08:35:50] Filtering fusions with an e-value >=0.3 (remaining=3714)
[2026-06-08T08:35:52] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3741)
[2026-06-08T08:35:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3331)
[2026-06-08T08:36:00] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3331)
[2026-06-08T08:36:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3071)
[2026-06-08T08:36:12] Searching for fusions with spliced split reads (remaining=3141)
[2026-06-08T08:36:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=2208)
[2026-06-08T08:36:23] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2179)
[2026-06-08T08:36:24] Searching for fusions with >=4 spliced events (remaining=2522)
[2026-06-08T08:36:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=838)
[2026-06-08T08:36:44] Filtering fusions with anchors <=23nt (remaining=653)
[2026-06-08T08:36:45] Filtering end-to-end fusions with low support (remaining=629)
[2026-06-08T08:36:46] Filtering fusions with no coverage around the breakpoints (remaining=614)
[2026-06-08T08:36:48] Indexing gene sequences 
[2026-06-08T08:36:53] Filtering genes with >=30% identity (remaining=209)
[2026-06-08T08:36:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=68)
[2026-06-08T08:36:58] Selecting best breakpoints from genes with multiple breakpoints (remaining=67)
[2026-06-08T08:37:00] Searching for additional isoforms (remaining=90)
[2026-06-08T08:37:02] Assigning confidence scores to events 
[2026-06-08T08:37:08] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:09] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s23.arriba.fusions.tsv' 
[2026-06-08T08:37:10] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s23.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:59] Freeing resources
[2026-06-08T08:38:32] Done (elapsed time=00:15:04, CPU time=00:15:03, peak memory=18.6gb)