[2026-06-08T08:26:42] Launching Arriba 2.4.0
[2026-06-08T08:26:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:59] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s03.Aligned.sortedByCoord.out.bam' (total=13263402)
[2026-06-08T08:35:27] Marking multi-mapping alignments (marked=9507629)
[2026-06-08T08:35:33] Detecting strandedness (reverse)
[2026-06-08T08:35:33] Assigning strands to alignments 
[2026-06-08T08:35:35] Annotating alignments 
[2026-06-08T08:36:20] Filtering duplicates (remaining=6903809)
[2026-06-08T08:36:33] 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=5995404)
[2026-06-08T08:36:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5995404)
[2026-06-08T08:36:38] Filtering viral contigs with expression lower than the top 5 (remaining=5995404)
[2026-06-08T08:36:44] Filtering viral contigs with less than 5% coverage (remaining=5995404)
[2026-06-08T08:36:47] Estimating fragment length (mate gap mean=-85.1863, mate gap stddev=30.5455, read length mean=127.798)
[2026-06-08T08:36:47] Filtering read-through fragments with a distance <=10000bp (remaining=5748116)
[2026-06-08T08:36:50] Filtering inconsistently clipped mates (remaining=5640002)
[2026-06-08T08:36:53] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5111838)
[2026-06-08T08:36:59] Filtering fragments with small insert size (remaining=5110527)
[2026-06-08T08:37:01] Filtering alignments with long gaps (remaining=5110527)
[2026-06-08T08:37:04] Filtering fragments with both mates in the same gene (remaining=5108696)
[2026-06-08T08:37:07] Filtering fusions arising from hairpin structures (remaining=4682176)
[2026-06-08T08:37:11] Filtering reads with a mismatch p-value <=0.01 (remaining=1822660)
[2026-06-08T08:37:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=1017999)
[2026-06-08T08:37:36] Finding fusions and counting supporting reads (total=891885)
[2026-06-08T08:37:58] Merging adjacent fusion breakpoints (remaining=882835)
[2026-06-08T08:38:00] Filtering multi-mapping fusions by alignment score and read support (remaining=463454)
[2026-06-08T08:38:47] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:38:55] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=460066)
[2026-06-08T08:38:55] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=307884)
[2026-06-08T08:38:57] Filtering fusions with <2 supporting reads (remaining=23174)
[2026-06-08T08:38:57] Filtering fusions with an e-value >=0.3 (remaining=5300)
[2026-06-08T08:38:58] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5330)
[2026-06-08T08:39:03] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4967)
[2026-06-08T08:39:03] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4978)
[2026-06-08T08:39:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4175)
[2026-06-08T08:39:12] Searching for fusions with spliced split reads (remaining=4251)
[2026-06-08T08:39:19] Selecting best breakpoints from genes with multiple breakpoints (remaining=2802)
[2026-06-08T08:39:20] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2768)
[2026-06-08T08:39:21] Searching for fusions with >=4 spliced events (remaining=3311)
[2026-06-08T08:39:23] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1222)
[2026-06-08T08:39:39] Filtering fusions with anchors <=23nt (remaining=911)
[2026-06-08T08:39:39] Filtering end-to-end fusions with low support (remaining=868)
[2026-06-08T08:39:40] Filtering fusions with no coverage around the breakpoints (remaining=854)
[2026-06-08T08:39:41] Indexing gene sequences 
[2026-06-08T08:39:46] Filtering genes with >=30% identity (remaining=240)
[2026-06-08T08:39:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=70)
[2026-06-08T08:39:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=70)
[2026-06-08T08:39:51] Searching for additional isoforms (remaining=94)
[2026-06-08T08:39:53] Assigning confidence scores to events 
[2026-06-08T08:39:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:39:57] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s03.arriba.fusions.tsv' 
[2026-06-08T08:39:59] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s03.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:34] Freeing resources
[2026-06-08T08:41:01] Done (elapsed time=00:14:19, CPU time=00:14:18, peak memory=18.6gb)