[2026-06-08T08:22:38] Launching Arriba 2.4.0
[2026-06-08T08:22:38] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:22:54] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:22:59] Reading chimeric alignments from 'GM24385_0001_RNA_0001_23H5VFLT4_s08.Aligned.sortedByCoord.out.bam' (total=13975908)
[2026-06-08T08:31:31] Marking multi-mapping alignments (marked=10377361)
[2026-06-08T08:31:37] Detecting strandedness (no)
[2026-06-08T08:31:37] Annotating alignments 
[2026-06-08T08:32:28] Filtering duplicates (remaining=6874914)
[2026-06-08T08:32:37] 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=5898735)
[2026-06-08T08:32:40] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5898735)
[2026-06-08T08:32:42] Filtering viral contigs with expression lower than the top 5 (remaining=5898735)
[2026-06-08T08:32:48] Filtering viral contigs with less than 5% coverage (remaining=5898735)
[2026-06-08T08:32:51] Estimating fragment length (mate gap mean=-82.6291, mate gap stddev=30.1174, read length mean=122.972)
[2026-06-08T08:32:51] Filtering read-through fragments with a distance <=10000bp (remaining=5659336)
[2026-06-08T08:32:54] Filtering inconsistently clipped mates (remaining=5544608)
[2026-06-08T08:32:56] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4856097)
[2026-06-08T08:33:01] Filtering fragments with small insert size (remaining=4854402)
[2026-06-08T08:33:04] Filtering alignments with long gaps (remaining=4854402)
[2026-06-08T08:33:07] Filtering fragments with both mates in the same gene (remaining=4852651)
[2026-06-08T08:33:10] Filtering fusions arising from hairpin structures (remaining=4474437)
[2026-06-08T08:33:13] Filtering reads with a mismatch p-value <=0.01 (remaining=1677205)
[2026-06-08T08:33:26] Filtering reads with low entropy (k-mer content >=60%) (remaining=941380)
[2026-06-08T08:33:37] Finding fusions and counting supporting reads (total=838475)
[2026-06-08T08:33:55] Merging adjacent fusion breakpoints (remaining=830534)
[2026-06-08T08:33:57] Filtering multi-mapping fusions by alignment score and read support (remaining=389912)
[2026-06-08T08:34:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:34:46] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=386588)
[2026-06-08T08:34:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=269756)
[2026-06-08T08:34:48] Filtering fusions with <2 supporting reads (remaining=18772)
[2026-06-08T08:34:48] Filtering fusions with an e-value >=0.3 (remaining=4123)
[2026-06-08T08:34:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4151)
[2026-06-08T08:34:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3677)
[2026-06-08T08:34:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3677)
[2026-06-08T08:34:56] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3483)
[2026-06-08T08:35:02] Searching for fusions with spliced split reads (remaining=3545)
[2026-06-08T08:35:09] Selecting best breakpoints from genes with multiple breakpoints (remaining=2465)
[2026-06-08T08:35:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2430)
[2026-06-08T08:35:11] Searching for fusions with >=4 spliced events (remaining=2900)
[2026-06-08T08:35:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1013)
[2026-06-08T08:35:29] Filtering fusions with anchors <=23nt (remaining=795)
[2026-06-08T08:35:30] Filtering end-to-end fusions with low support (remaining=759)
[2026-06-08T08:35:31] Filtering fusions with no coverage around the breakpoints (remaining=745)
[2026-06-08T08:35:32] Indexing gene sequences 
[2026-06-08T08:35:36] Filtering genes with >=30% identity (remaining=202)
[2026-06-08T08:35:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=39)
[2026-06-08T08:35:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=39)
[2026-06-08T08:35:41] Searching for additional isoforms (remaining=50)
[2026-06-08T08:35:42] Assigning confidence scores to events 
[2026-06-08T08:35:47] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:35:47] Writing fusions to file 'GM24385_0001_RNA_0001_23H5VFLT4_s08.arriba.fusions.tsv' 
[2026-06-08T08:35:48] Writing discarded fusions to file 'GM24385_0001_RNA_0001_23H5VFLT4_s08.arriba.fusions.discarded.tsv'
[2026-06-08T08:36:15] Freeing resources
[2026-06-08T08:36:37] Done (elapsed time=00:13:59, CPU time=00:13:58, peak memory=19.3gb)