[2026-06-08T08:16:41] Launching Arriba 2.4.0
[2026-06-08T08:16:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:16:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:16:58] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s42.Aligned.sortedByCoord.out.bam' (total=11823885)
[2026-06-08T08:25:10] Marking multi-mapping alignments (marked=8226209)
[2026-06-08T08:25:14] Detecting strandedness (reverse)
[2026-06-08T08:25:15] Assigning strands to alignments 
[2026-06-08T08:25:17] Annotating alignments 
[2026-06-08T08:25:53] Filtering duplicates (remaining=5873039)
[2026-06-08T08:25:59] 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=5201406)
[2026-06-08T08:26:02] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5201406)
[2026-06-08T08:26:04] Filtering viral contigs with expression lower than the top 5 (remaining=5201406)
[2026-06-08T08:26:08] Filtering viral contigs with less than 5% coverage (remaining=5201406)
[2026-06-08T08:26:11] Estimating fragment length (mate gap mean=-82.818, mate gap stddev=31.4255, read length mean=130.77)
[2026-06-08T08:26:11] Filtering read-through fragments with a distance <=10000bp (remaining=4983139)
[2026-06-08T08:26:13] Filtering inconsistently clipped mates (remaining=4898757)
[2026-06-08T08:26:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4427766)
[2026-06-08T08:26:19] Filtering fragments with small insert size (remaining=4426867)
[2026-06-08T08:26:21] Filtering alignments with long gaps (remaining=4426867)
[2026-06-08T08:26:24] Filtering fragments with both mates in the same gene (remaining=4425141)
[2026-06-08T08:26:26] Filtering fusions arising from hairpin structures (remaining=4168609)
[2026-06-08T08:26:28] Filtering reads with a mismatch p-value <=0.01 (remaining=1735393)
[2026-06-08T08:26:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=869415)
[2026-06-08T08:26:49] Finding fusions and counting supporting reads (total=765259)
[2026-06-08T08:27:06] Merging adjacent fusion breakpoints (remaining=761621)
[2026-06-08T08:27:08] Filtering multi-mapping fusions by alignment score and read support (remaining=420267)
[2026-06-08T08:27:42] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:27:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=417361)
[2026-06-08T08:27:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=291865)
[2026-06-08T08:27:49] Filtering fusions with <2 supporting reads (remaining=20725)
[2026-06-08T08:27:50] Filtering fusions with an e-value >=0.3 (remaining=5112)
[2026-06-08T08:27:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5139)
[2026-06-08T08:27:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4887)
[2026-06-08T08:27:55] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4899)
[2026-06-08T08:27:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3852)
[2026-06-08T08:28:01] Searching for fusions with spliced split reads (remaining=3929)
[2026-06-08T08:28:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=2384)
[2026-06-08T08:28:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2353)
[2026-06-08T08:28:09] Searching for fusions with >=4 spliced events (remaining=2802)
[2026-06-08T08:28:10] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1031)
[2026-06-08T08:28:25] Filtering fusions with anchors <=23nt (remaining=758)
[2026-06-08T08:28:26] Filtering end-to-end fusions with low support (remaining=732)
[2026-06-08T08:28:26] Filtering fusions with no coverage around the breakpoints (remaining=719)
[2026-06-08T08:28:27] Indexing gene sequences 
[2026-06-08T08:28:31] Filtering genes with >=30% identity (remaining=199)
[2026-06-08T08:28:33] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=67)
[2026-06-08T08:28:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=67)
[2026-06-08T08:28:36] Searching for additional isoforms (remaining=86)
[2026-06-08T08:28:37] Assigning confidence scores to events 
[2026-06-08T08:28:41] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:28:41] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s42.arriba.fusions.tsv' 
[2026-06-08T08:28:42] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s42.arriba.fusions.discarded.tsv'
[2026-06-08T08:29:11] Freeing resources
[2026-06-08T08:29:34] Done (elapsed time=00:12:53, CPU time=00:12:52, peak memory=16.8gb)