[2026-06-08T08:19:40] Launching Arriba 2.4.0
[2026-06-08T08:19:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:56] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:01] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s02.Aligned.sortedByCoord.out.bam' (total=12435245)
[2026-06-08T08:28:56] Marking multi-mapping alignments (marked=8747468)
[2026-06-08T08:29:01] Detecting strandedness (reverse)
[2026-06-08T08:29:01] Assigning strands to alignments 
[2026-06-08T08:29:04] Annotating alignments 
[2026-06-08T08:29:52] Filtering duplicates (remaining=6794096)
[2026-06-08T08:30:01] 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=5994186)
[2026-06-08T08:30:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5994186)
[2026-06-08T08:30:06] Filtering viral contigs with expression lower than the top 5 (remaining=5994186)
[2026-06-08T08:30:12] Filtering viral contigs with less than 5% coverage (remaining=5994186)
[2026-06-08T08:30:15] Estimating fragment length (mate gap mean=-85.1641, mate gap stddev=30.8829, read length mean=128.614)
[2026-06-08T08:30:16] Filtering read-through fragments with a distance <=10000bp (remaining=5751077)
[2026-06-08T08:30:18] Filtering inconsistently clipped mates (remaining=5641997)
[2026-06-08T08:30:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5161521)
[2026-06-08T08:30:27] Filtering fragments with small insert size (remaining=5160399)
[2026-06-08T08:30:30] Filtering alignments with long gaps (remaining=5160399)
[2026-06-08T08:30:33] Filtering fragments with both mates in the same gene (remaining=5158552)
[2026-06-08T08:30:36] Filtering fusions arising from hairpin structures (remaining=4731411)
[2026-06-08T08:30:39] Filtering reads with a mismatch p-value <=0.01 (remaining=1907072)
[2026-06-08T08:30:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=1060817)
[2026-06-08T08:31:05] Finding fusions and counting supporting reads (total=923666)
[2026-06-08T08:31:29] Merging adjacent fusion breakpoints (remaining=914416)
[2026-06-08T08:31:31] Filtering multi-mapping fusions by alignment score and read support (remaining=503625)
[2026-06-08T08:32:15] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:32:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=500632)
[2026-06-08T08:32:26] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=337708)
[2026-06-08T08:32:28] Filtering fusions with <2 supporting reads (remaining=25409)
[2026-06-08T08:32:29] Filtering fusions with an e-value >=0.3 (remaining=5426)
[2026-06-08T08:32:29] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5460)
[2026-06-08T08:32:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5156)
[2026-06-08T08:32:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5168)
[2026-06-08T08:32:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4581)
[2026-06-08T08:32:44] Searching for fusions with spliced split reads (remaining=4669)
[2026-06-08T08:32:51] Selecting best breakpoints from genes with multiple breakpoints (remaining=2886)
[2026-06-08T08:32:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2849)
[2026-06-08T08:32:54] Searching for fusions with >=4 spliced events (remaining=3408)
[2026-06-08T08:32:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1234)
[2026-06-08T08:33:14] Filtering fusions with anchors <=23nt (remaining=917)
[2026-06-08T08:33:15] Filtering end-to-end fusions with low support (remaining=881)
[2026-06-08T08:33:16] Filtering fusions with no coverage around the breakpoints (remaining=872)
[2026-06-08T08:33:16] Indexing gene sequences 
[2026-06-08T08:33:22] Filtering genes with >=30% identity (remaining=239)
[2026-06-08T08:33:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=81)
[2026-06-08T08:33:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=80)
[2026-06-08T08:33:29] Searching for additional isoforms (remaining=106)
[2026-06-08T08:33:31] Assigning confidence scores to events 
[2026-06-08T08:33:36] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:33:36] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s02.arriba.fusions.tsv' 
[2026-06-08T08:33:37] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s02.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:21] Freeing resources
[2026-06-08T08:34:46] Done (elapsed time=00:15:06, CPU time=00:15:06, peak memory=17.7gb)