[2026-06-08T08:24:40] Launching Arriba 2.4.0
[2026-06-08T08:24:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:24:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:25:01] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s01.Aligned.sortedByCoord.out.bam' (total=12866085)
[2026-06-08T08:34:22] Marking multi-mapping alignments (marked=9074905)
[2026-06-08T08:34:28] Detecting strandedness (reverse)
[2026-06-08T08:34:28] Assigning strands to alignments 
[2026-06-08T08:34:31] Annotating alignments 
[2026-06-08T08:35:30] Filtering duplicates (remaining=7134012)
[2026-06-08T08:35:41] 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=6265847)
[2026-06-08T08:35:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6265847)
[2026-06-08T08:35:48] Filtering viral contigs with expression lower than the top 5 (remaining=6265847)
[2026-06-08T08:35:54] Filtering viral contigs with less than 5% coverage (remaining=6265847)
[2026-06-08T08:35:58] Estimating fragment length (mate gap mean=-85.2235, mate gap stddev=31.2488, read length mean=131.426)
[2026-06-08T08:35:58] Filtering read-through fragments with a distance <=10000bp (remaining=6008363)
[2026-06-08T08:36:01] Filtering inconsistently clipped mates (remaining=5898038)
[2026-06-08T08:36:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5441999)
[2026-06-08T08:36:11] Filtering fragments with small insert size (remaining=5440811)
[2026-06-08T08:36:14] Filtering alignments with long gaps (remaining=5440811)
[2026-06-08T08:36:17] Filtering fragments with both mates in the same gene (remaining=5438996)
[2026-06-08T08:36:20] Filtering fusions arising from hairpin structures (remaining=4983560)
[2026-06-08T08:36:23] Filtering reads with a mismatch p-value <=0.01 (remaining=2041092)
[2026-06-08T08:36:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=1146597)
[2026-06-08T08:36:53] Finding fusions and counting supporting reads (total=984434)
[2026-06-08T08:37:18] Merging adjacent fusion breakpoints (remaining=974995)
[2026-06-08T08:37:20] Filtering multi-mapping fusions by alignment score and read support (remaining=547079)
[2026-06-08T08:38:07] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:38:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=543575)
[2026-06-08T08:38:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=371794)
[2026-06-08T08:38:20] Filtering fusions with <2 supporting reads (remaining=28719)
[2026-06-08T08:38:21] Filtering fusions with an e-value >=0.3 (remaining=6883)
[2026-06-08T08:38:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6921)
[2026-06-08T08:38:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6627)
[2026-06-08T08:38:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6657)
[2026-06-08T08:38:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5561)
[2026-06-08T08:38:38] Searching for fusions with spliced split reads (remaining=5671)
[2026-06-08T08:38:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=3146)
[2026-06-08T08:38:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3113)
[2026-06-08T08:38:48] Searching for fusions with >=4 spliced events (remaining=3819)
[2026-06-08T08:38:51] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1511)
[2026-06-08T08:39:10] Filtering fusions with anchors <=23nt (remaining=1142)
[2026-06-08T08:39:11] Filtering end-to-end fusions with low support (remaining=1105)
[2026-06-08T08:39:12] Filtering fusions with no coverage around the breakpoints (remaining=1088)
[2026-06-08T08:39:13] Indexing gene sequences 
[2026-06-08T08:39:20] Filtering genes with >=30% identity (remaining=285)
[2026-06-08T08:39:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=93)
[2026-06-08T08:39:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=90)
[2026-06-08T08:39:28] Searching for additional isoforms (remaining=127)
[2026-06-08T08:39:30] Assigning confidence scores to events 
[2026-06-08T08:39:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:39:35] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s01.arriba.fusions.tsv' 
[2026-06-08T08:39:37] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s01.arriba.fusions.discarded.tsv'
[2026-06-08T08:40:28] Freeing resources
[2026-06-08T08:40:55] Done (elapsed time=00:16:15, CPU time=00:16:13, peak memory=18.1gb)