[2026-06-08T08:07:29] Launching Arriba 2.4.0
[2026-06-08T08:07:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:07:43] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:07:48] Reading chimeric alignments from 'GM24385_0001_RNA_0001_23H5VFLT4_s40.Aligned.sortedByCoord.out.bam' (total=10644616)
[2026-06-08T08:14:43] Marking multi-mapping alignments (marked=7866498)
[2026-06-08T08:14:47] Detecting strandedness (reverse)
[2026-06-08T08:14:47] Assigning strands to alignments 
[2026-06-08T08:14:49] Annotating alignments 
[2026-06-08T08:15:24] Filtering duplicates (remaining=4641382)
[2026-06-08T08:15:30] 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=4077436)
[2026-06-08T08:15:32] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4077436)
[2026-06-08T08:15:34] Filtering viral contigs with expression lower than the top 5 (remaining=4077436)
[2026-06-08T08:15:38] Filtering viral contigs with less than 5% coverage (remaining=4077436)
[2026-06-08T08:15:41] Estimating fragment length (mate gap mean=-79.2932, mate gap stddev=32.4011, read length mean=118.465)
[2026-06-08T08:15:41] Filtering read-through fragments with a distance <=10000bp (remaining=3947459)
[2026-06-08T08:15:43] Filtering inconsistently clipped mates (remaining=3864951)
[2026-06-08T08:15:45] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=3266715)
[2026-06-08T08:15:49] Filtering fragments with small insert size (remaining=3265519)
[2026-06-08T08:15:51] Filtering alignments with long gaps (remaining=3265519)
[2026-06-08T08:15:53] Filtering fragments with both mates in the same gene (remaining=3263055)
[2026-06-08T08:15:55] Filtering fusions arising from hairpin structures (remaining=3090679)
[2026-06-08T08:15:57] Filtering reads with a mismatch p-value <=0.01 (remaining=1046550)
[2026-06-08T08:16:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=518004)
[2026-06-08T08:16:12] Finding fusions and counting supporting reads (total=476595)
[2026-06-08T08:16:25] Merging adjacent fusion breakpoints (remaining=474179)
[2026-06-08T08:16:27] Filtering multi-mapping fusions by alignment score and read support (remaining=213721)
[2026-06-08T08:16:56] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:17:01] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=211775)
[2026-06-08T08:17:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=156588)
[2026-06-08T08:17:02] Filtering fusions with <2 supporting reads (remaining=9137)
[2026-06-08T08:17:02] Filtering fusions with an e-value >=0.3 (remaining=2138)
[2026-06-08T08:17:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=2154)
[2026-06-08T08:17:06] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1771)
[2026-06-08T08:17:07] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1771)
[2026-06-08T08:17:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1728)
[2026-06-08T08:17:12] Searching for fusions with spliced split reads (remaining=1845)
[2026-06-08T08:17:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=1406)
[2026-06-08T08:17:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1381)
[2026-06-08T08:17:18] Searching for fusions with >=4 spliced events (remaining=1469)
[2026-06-08T08:17:19] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=416)
[2026-06-08T08:17:32] Filtering fusions with anchors <=23nt (remaining=303)
[2026-06-08T08:17:33] Filtering end-to-end fusions with low support (remaining=287)
[2026-06-08T08:17:33] Filtering fusions with no coverage around the breakpoints (remaining=282)
[2026-06-08T08:17:34] Indexing gene sequences 
[2026-06-08T08:17:36] Filtering genes with >=30% identity (remaining=89)
[2026-06-08T08:17:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=29)
[2026-06-08T08:17:38] Selecting best breakpoints from genes with multiple breakpoints (remaining=29)
[2026-06-08T08:17:39] Searching for additional isoforms (remaining=35)
[2026-06-08T08:17:40] Assigning confidence scores to events 
[2026-06-08T08:17:43] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:17:43] Writing fusions to file 'GM24385_0001_RNA_0001_23H5VFLT4_s40.arriba.fusions.tsv' 
[2026-06-08T08:17:43] Writing discarded fusions to file 'GM24385_0001_RNA_0001_23H5VFLT4_s40.arriba.fusions.discarded.tsv'
[2026-06-08T08:18:04] Freeing resources
[2026-06-08T08:18:23] Done (elapsed time=00:10:54, CPU time=00:10:52, peak memory=15.5gb)