[2026-06-08T08:17:42] Launching Arriba 2.4.0
[2026-06-08T08:17:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:17:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:17:55] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s18.Aligned.sortedByCoord.out.bam' (total=12072147)
[2026-06-08T08:25:05] Marking multi-mapping alignments (marked=8400699)
[2026-06-08T08:25:10] Detecting strandedness (reverse)
[2026-06-08T08:25:10] Assigning strands to alignments 
[2026-06-08T08:25:12] Annotating alignments 
[2026-06-08T08:25:54] Filtering duplicates (remaining=6786699)
[2026-06-08T08:26:02] 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=6033557)
[2026-06-08T08:26:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6033557)
[2026-06-08T08:26:07] Filtering viral contigs with expression lower than the top 5 (remaining=6033557)
[2026-06-08T08:26:12] Filtering viral contigs with less than 5% coverage (remaining=6033557)
[2026-06-08T08:26:15] Estimating fragment length (mate gap mean=-84.4899, mate gap stddev=31.921, read length mean=130.244)
[2026-06-08T08:26:15] Filtering read-through fragments with a distance <=10000bp (remaining=5772921)
[2026-06-08T08:26:17] Filtering inconsistently clipped mates (remaining=5668534)
[2026-06-08T08:26:20] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5205380)
[2026-06-08T08:26:25] Filtering fragments with small insert size (remaining=5204237)
[2026-06-08T08:26:27] Filtering alignments with long gaps (remaining=5204237)
[2026-06-08T08:26:30] Filtering fragments with both mates in the same gene (remaining=5202292)
[2026-06-08T08:26:32] Filtering fusions arising from hairpin structures (remaining=4834170)
[2026-06-08T08:26:35] Filtering reads with a mismatch p-value <=0.01 (remaining=1991731)
[2026-06-08T08:26:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=1081561)
[2026-06-08T08:27:00] Finding fusions and counting supporting reads (total=938472)
[2026-06-08T08:27:19] Merging adjacent fusion breakpoints (remaining=932478)
[2026-06-08T08:27:21] Filtering multi-mapping fusions by alignment score and read support (remaining=529568)
[2026-06-08T08:27:58] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:28:06] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=526494)
[2026-06-08T08:28:07] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=359249)
[2026-06-08T08:28:08] Filtering fusions with <2 supporting reads (remaining=26786)
[2026-06-08T08:28:09] Filtering fusions with an e-value >=0.3 (remaining=6630)
[2026-06-08T08:28:10] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=6664)
[2026-06-08T08:28:14] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=6437)
[2026-06-08T08:28:15] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6465)
[2026-06-08T08:28:16] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5032)
[2026-06-08T08:28:22] Searching for fusions with spliced split reads (remaining=5112)
[2026-06-08T08:28:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=3015)
[2026-06-08T08:28:30] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2981)
[2026-06-08T08:28:30] Searching for fusions with >=4 spliced events (remaining=3668)
[2026-06-08T08:28:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1420)
[2026-06-08T08:28:46] Filtering fusions with anchors <=23nt (remaining=1053)
[2026-06-08T08:28:47] Filtering end-to-end fusions with low support (remaining=1022)
[2026-06-08T08:28:47] Filtering fusions with no coverage around the breakpoints (remaining=1007)
[2026-06-08T08:28:48] Indexing gene sequences 
[2026-06-08T08:28:53] Filtering genes with >=30% identity (remaining=262)
[2026-06-08T08:28:55] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=80)
[2026-06-08T08:28:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=78)
[2026-06-08T08:28:59] Searching for additional isoforms (remaining=97)
[2026-06-08T08:29:00] Assigning confidence scores to events 
[2026-06-08T08:29:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:29:04] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s18.arriba.fusions.tsv' 
[2026-06-08T08:29:05] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s18.arriba.fusions.discarded.tsv'
[2026-06-08T08:29:36] Freeing resources
[2026-06-08T08:29:57] Done (elapsed time=00:12:15, CPU time=00:12:14, peak memory=17.3gb)