[2026-06-08T08:23:38] Launching Arriba 2.4.0
[2026-06-08T08:23:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:23:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:23:58] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s25.Aligned.sortedByCoord.out.bam' (total=11324710)
[2026-06-08T08:32:54] Marking multi-mapping alignments (marked=7903876)
[2026-06-08T08:32:59] Detecting strandedness (reverse)
[2026-06-08T08:32:59] Assigning strands to alignments 
[2026-06-08T08:33:02] Annotating alignments 
[2026-06-08T08:33:49] Filtering duplicates (remaining=5987206)
[2026-06-08T08:33:57] 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=5342315)
[2026-06-08T08:34:00] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5342315)
[2026-06-08T08:34:03] Filtering viral contigs with expression lower than the top 5 (remaining=5342315)
[2026-06-08T08:34:08] Filtering viral contigs with less than 5% coverage (remaining=5342315)
[2026-06-08T08:34:11] Estimating fragment length (mate gap mean=-85.2944, mate gap stddev=31.8469, read length mean=131.106)
[2026-06-08T08:34:11] Filtering read-through fragments with a distance <=10000bp (remaining=5121150)
[2026-06-08T08:34:14] Filtering inconsistently clipped mates (remaining=5033994)
[2026-06-08T08:34:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4646426)
[2026-06-08T08:34:22] Filtering fragments with small insert size (remaining=4645476)
[2026-06-08T08:34:24] Filtering alignments with long gaps (remaining=4645475)
[2026-06-08T08:34:27] Filtering fragments with both mates in the same gene (remaining=4643469)
[2026-06-08T08:34:30] Filtering fusions arising from hairpin structures (remaining=4341715)
[2026-06-08T08:34:33] Filtering reads with a mismatch p-value <=0.01 (remaining=1707255)
[2026-06-08T08:34:45] Filtering reads with low entropy (k-mer content >=60%) (remaining=870764)
[2026-06-08T08:34:56] Finding fusions and counting supporting reads (total=742017)
[2026-06-08T08:35:19] Merging adjacent fusion breakpoints (remaining=737024)
[2026-06-08T08:35:21] Filtering multi-mapping fusions by alignment score and read support (remaining=412468)
[2026-06-08T08:36:05] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:14] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=409600)
[2026-06-08T08:36:15] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=261459)
[2026-06-08T08:36:16] Filtering fusions with <2 supporting reads (remaining=22763)
[2026-06-08T08:36:17] Filtering fusions with an e-value >=0.3 (remaining=6143)
[2026-06-08T08:36:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6178)
[2026-06-08T08:36:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5942)
[2026-06-08T08:36:23] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5957)
[2026-06-08T08:36:25] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4667)
[2026-06-08T08:36:31] Searching for fusions with spliced split reads (remaining=4765)
[2026-06-08T08:36:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=2927)
[2026-06-08T08:36:40] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2892)
[2026-06-08T08:36:40] Searching for fusions with >=4 spliced events (remaining=3428)
[2026-06-08T08:36:42] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1299)
[2026-06-08T08:37:01] Filtering fusions with anchors <=23nt (remaining=926)
[2026-06-08T08:37:02] Filtering end-to-end fusions with low support (remaining=880)
[2026-06-08T08:37:03] Filtering fusions with no coverage around the breakpoints (remaining=866)
[2026-06-08T08:37:04] Indexing gene sequences 
[2026-06-08T08:37:09] Filtering genes with >=30% identity (remaining=231)
[2026-06-08T08:37:11] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=82)
[2026-06-08T08:37:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=80)
[2026-06-08T08:37:15] Searching for additional isoforms (remaining=104)
[2026-06-08T08:37:17] Assigning confidence scores to events 
[2026-06-08T08:37:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:22] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s25.arriba.fusions.tsv' 
[2026-06-08T08:37:23] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s25.arriba.fusions.discarded.tsv'
[2026-06-08T08:38:02] Freeing resources
[2026-06-08T08:38:26] Done (elapsed time=00:14:48, CPU time=00:14:47, peak memory=16.4gb)