[2026-06-08T08:08:34] Launching Arriba 2.4.0
[2026-06-08T08:08:34] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:08:48] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:08:53] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s30.Aligned.sortedByCoord.out.bam' (total=10980814)
[2026-06-08T08:15:57] Marking multi-mapping alignments (marked=8060572)
[2026-06-08T08:16:01] Detecting strandedness (reverse)
[2026-06-08T08:16:01] Assigning strands to alignments 
[2026-06-08T08:16:03] Annotating alignments 
[2026-06-08T08:16:41] Filtering duplicates (remaining=5090461)
[2026-06-08T08:16:47] 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=4422138)
[2026-06-08T08:16:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4422138)
[2026-06-08T08:16:51] Filtering viral contigs with expression lower than the top 5 (remaining=4422138)
[2026-06-08T08:16:55] Filtering viral contigs with less than 5% coverage (remaining=4422138)
[2026-06-08T08:16:58] Estimating fragment length (mate gap mean=-81.3965, mate gap stddev=31.9076, read length mean=122.962)
[2026-06-08T08:16:58] Filtering read-through fragments with a distance <=10000bp (remaining=4245728)
[2026-06-08T08:17:00] Filtering inconsistently clipped mates (remaining=4164034)
[2026-06-08T08:17:02] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3617718)
[2026-06-08T08:17:06] Filtering fragments with small insert size (remaining=3616577)
[2026-06-08T08:17:08] Filtering alignments with long gaps (remaining=3616577)
[2026-06-08T08:17:10] Filtering fragments with both mates in the same gene (remaining=3614722)
[2026-06-08T08:17:12] Filtering fusions arising from hairpin structures (remaining=3379041)
[2026-06-08T08:17:14] Filtering reads with a mismatch p-value <=0.01 (remaining=1231040)
[2026-06-08T08:17:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=651036)
[2026-06-08T08:17:31] Finding fusions and counting supporting reads (total=589887)
[2026-06-08T08:17:45] Merging adjacent fusion breakpoints (remaining=585804)
[2026-06-08T08:17:46] Filtering multi-mapping fusions by alignment score and read support (remaining=271165)
[2026-06-08T08:18:16] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:18:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=268646)
[2026-06-08T08:18:22] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=189357)
[2026-06-08T08:18:23] Filtering fusions with <2 supporting reads (remaining=13139)
[2026-06-08T08:18:23] Filtering fusions with an e-value >=0.3 (remaining=3202)
[2026-06-08T08:18:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3226)
[2026-06-08T08:18:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2869)
[2026-06-08T08:18:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2870)
[2026-06-08T08:18:28] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2633)
[2026-06-08T08:18:33] Searching for fusions with spliced split reads (remaining=2682)
[2026-06-08T08:18:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=1866)
[2026-06-08T08:18:39] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1833)
[2026-06-08T08:18:39] Searching for fusions with >=4 spliced events (remaining=2121)
[2026-06-08T08:18:40] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=692)
[2026-06-08T08:18:54] Filtering fusions with anchors <=23nt (remaining=530)
[2026-06-08T08:18:54] Filtering end-to-end fusions with low support (remaining=512)
[2026-06-08T08:18:55] Filtering fusions with no coverage around the breakpoints (remaining=502)
[2026-06-08T08:18:55] Indexing gene sequences 
[2026-06-08T08:18:59] Filtering genes with >=30% identity (remaining=137)
[2026-06-08T08:19:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=50)
[2026-06-08T08:19:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=50)
[2026-06-08T08:19:02] Searching for additional isoforms (remaining=66)
[2026-06-08T08:19:03] Assigning confidence scores to events 
[2026-06-08T08:19:07] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:19:07] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s30.arriba.fusions.tsv' 
[2026-06-08T08:19:08] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s30.arriba.fusions.discarded.tsv'
[2026-06-08T08:19:33] Freeing resources
[2026-06-08T08:19:50] Done (elapsed time=00:11:16, CPU time=00:11:15, peak memory=16gb)