[2026-06-08T08:26:41] Launching Arriba 2.4.0
[2026-06-08T08:26:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:50] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:26:54] Reading chimeric alignments from 'HD789_0002_RNA_0008_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam' (total=9298153)
[2026-06-08T08:33:53] Marking multi-mapping alignments (marked=6065547)
[2026-06-08T08:33:57] Detecting strandedness (no)
[2026-06-08T08:33:57] Annotating alignments 
[2026-06-08T08:34:34] Filtering duplicates (remaining=6042747)
[2026-06-08T08:34:41] 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=5576526)
[2026-06-08T08:34:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5576526)
[2026-06-08T08:34:44] Filtering viral contigs with expression lower than the top 5 (remaining=5576526)
[2026-06-08T08:34:48] Filtering viral contigs with less than 5% coverage (remaining=5576526)
[2026-06-08T08:34:50] Estimating fragment length (mate gap mean=-84.9969, mate gap stddev=33.0802, read length mean=137.657)
[2026-06-08T08:34:51] Filtering read-through fragments with a distance <=10000bp (remaining=5277390)
[2026-06-08T08:34:52] Filtering inconsistently clipped mates (remaining=5188934)
[2026-06-08T08:34:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4825143)
[2026-06-08T08:34:59] Filtering fragments with small insert size (remaining=4824500)
[2026-06-08T08:35:00] Filtering alignments with long gaps (remaining=4824500)
[2026-06-08T08:35:02] Filtering fragments with both mates in the same gene (remaining=4823097)
[2026-06-08T08:35:04] Filtering fusions arising from hairpin structures (remaining=4386610)
[2026-06-08T08:35:07] Filtering reads with a mismatch p-value <=0.01 (remaining=2069321)
[2026-06-08T08:35:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=1074059)
[2026-06-08T08:35:28] Finding fusions and counting supporting reads (total=846122)
[2026-06-08T08:35:43] Merging adjacent fusion breakpoints (remaining=840538)
[2026-06-08T08:35:45] Filtering multi-mapping fusions by alignment score and read support (remaining=530022)
[2026-06-08T08:36:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:36:22] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=525506)
[2026-06-08T08:36:23] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=322259)
[2026-06-08T08:36:24] Filtering fusions with <2 supporting reads (remaining=43970)
[2026-06-08T08:36:24] Filtering fusions with an e-value >=0.3 (remaining=17239)
[2026-06-08T08:36:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=17291)
[2026-06-08T08:36:29] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=17159)
[2026-06-08T08:36:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17172)
[2026-06-08T08:36:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8434)
[2026-06-08T08:36:35] Searching for fusions with spliced split reads (remaining=8461)
[2026-06-08T08:36:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=4373)
[2026-06-08T08:36:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4333)
[2026-06-08T08:36:42] Searching for fusions with >=4 spliced events (remaining=5497)
[2026-06-08T08:36:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2190)
[2026-06-08T08:36:56] Filtering fusions with anchors <=23nt (remaining=1770)
[2026-06-08T08:36:57] Filtering end-to-end fusions with low support (remaining=1731)
[2026-06-08T08:36:58] Filtering fusions with no coverage around the breakpoints (remaining=1700)
[2026-06-08T08:36:58] Indexing gene sequences 
[2026-06-08T08:37:05] Filtering genes with >=30% identity (remaining=596)
[2026-06-08T08:37:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=353)
[2026-06-08T08:37:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=256)
[2026-06-08T08:37:14] Searching for additional isoforms (remaining=403)
[2026-06-08T08:37:15] Assigning confidence scores to events 
[2026-06-08T08:37:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:37:18] Writing fusions to file 'HD789_0002_RNA_0008_23H5VFLT4_s19.arriba.fusions.tsv' 
[2026-06-08T08:37:21] Writing discarded fusions to file 'HD789_0002_RNA_0008_23H5VFLT4_s19.arriba.fusions.discarded.tsv'
[2026-06-08T08:37:48] Freeing resources
[2026-06-08T08:38:05] Done (elapsed time=00:11:24, CPU time=00:11:23, peak memory=14.3gb)