[2026-06-08T08:08:27] Launching Arriba 2.4.0
[2026-06-08T08:08:27] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:08:42] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:08:47] Reading chimeric alignments from 'GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam' (total=10307298)
[2026-06-08T08:15:02] Marking multi-mapping alignments (marked=7511758)
[2026-06-08T08:15:06] Detecting strandedness (reverse)
[2026-06-08T08:15:06] Assigning strands to alignments 
[2026-06-08T08:15:08] Annotating alignments 
[2026-06-08T08:15:40] Filtering duplicates (remaining=5404949)
[2026-06-08T08:15:46] 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=4705218)
[2026-06-08T08:15:48] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4705218)
[2026-06-08T08:15:50] Filtering viral contigs with expression lower than the top 5 (remaining=4705218)
[2026-06-08T08:15:54] Filtering viral contigs with less than 5% coverage (remaining=4705218)
[2026-06-08T08:15:56] Estimating fragment length (mate gap mean=-81.7598, mate gap stddev=30.3894, read length mean=121.975)
[2026-06-08T08:15:56] Filtering read-through fragments with a distance <=10000bp (remaining=4516348)
[2026-06-08T08:15:58] Filtering inconsistently clipped mates (remaining=4415731)
[2026-06-08T08:16:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3871150)
[2026-06-08T08:16:04] Filtering fragments with small insert size (remaining=3869891)
[2026-06-08T08:16:06] Filtering alignments with long gaps (remaining=3869891)
[2026-06-08T08:16:07] Filtering fragments with both mates in the same gene (remaining=3868284)
[2026-06-08T08:16:09] Filtering fusions arising from hairpin structures (remaining=3583427)
[2026-06-08T08:16:11] Filtering reads with a mismatch p-value <=0.01 (remaining=1410172)
[2026-06-08T08:16:19] Filtering reads with low entropy (k-mer content >=60%) (remaining=767955)
[2026-06-08T08:16:27] Finding fusions and counting supporting reads (total=688387)
[2026-06-08T08:16:41] Merging adjacent fusion breakpoints (remaining=683184)
[2026-06-08T08:16:42] Filtering multi-mapping fusions by alignment score and read support (remaining=336946)
[2026-06-08T08:17:10] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:17:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=334368)
[2026-06-08T08:17:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=236321)
[2026-06-08T08:17:17] Filtering fusions with <2 supporting reads (remaining=15311)
[2026-06-08T08:17:18] Filtering fusions with an e-value >=0.3 (remaining=3262)
[2026-06-08T08:17:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=3294)
[2026-06-08T08:17:21] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=2934)
[2026-06-08T08:17:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2934)
[2026-06-08T08:17:23] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=2805)
[2026-06-08T08:17:27] Searching for fusions with spliced split reads (remaining=2858)
[2026-06-08T08:17:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=2028)
[2026-06-08T08:17:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1999)
[2026-06-08T08:17:34] Searching for fusions with >=4 spliced events (remaining=2257)
[2026-06-08T08:17:35] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=722)
[2026-06-08T08:17:48] Filtering fusions with anchors <=23nt (remaining=541)
[2026-06-08T08:17:48] Filtering end-to-end fusions with low support (remaining=523)
[2026-06-08T08:17:49] Filtering fusions with no coverage around the breakpoints (remaining=513)
[2026-06-08T08:17:49] Indexing gene sequences 
[2026-06-08T08:17:53] Filtering genes with >=30% identity (remaining=125)
[2026-06-08T08:17:54] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=31)
[2026-06-08T08:17:55] Selecting best breakpoints from genes with multiple breakpoints (remaining=31)
[2026-06-08T08:17:56] Searching for additional isoforms (remaining=48)
[2026-06-08T08:17:57] Assigning confidence scores to events 
[2026-06-08T08:18:00] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:18:00] Writing fusions to file 'GM24385_0001_RNA_0001_23H5VFLT4_s24.arriba.fusions.tsv' 
[2026-06-08T08:18:01] Writing discarded fusions to file 'GM24385_0001_RNA_0001_23H5VFLT4_s24.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:24] Freeing resources
[2026-06-08T08:18:40] Done (elapsed time=00:10:13, CPU time=00:10:11, peak memory=15.3gb)