[2026-06-08T08:19:42] Launching Arriba 2.4.0
[2026-06-08T08:19:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:19:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:04] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s04.Aligned.sortedByCoord.out.bam' (total=13369663)
[2026-06-08T08:29:16] Marking multi-mapping alignments (marked=9640096)
[2026-06-08T08:29:22] Detecting strandedness (reverse)
[2026-06-08T08:29:22] Assigning strands to alignments 
[2026-06-08T08:29:25] Annotating alignments 
[2026-06-08T08:30:18] Filtering duplicates (remaining=6666812)
[2026-06-08T08:30:27] 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=5783620)
[2026-06-08T08:30:30] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5783620)
[2026-06-08T08:30:33] Filtering viral contigs with expression lower than the top 5 (remaining=5783620)
[2026-06-08T08:30:40] Filtering viral contigs with less than 5% coverage (remaining=5783620)
[2026-06-08T08:30:43] Estimating fragment length (mate gap mean=-84.0017, mate gap stddev=30.882, read length mean=126.718)
[2026-06-08T08:30:43] Filtering read-through fragments with a distance <=10000bp (remaining=5542854)
[2026-06-08T08:30:46] Filtering inconsistently clipped mates (remaining=5433610)
[2026-06-08T08:30:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4838572)
[2026-06-08T08:30:55] Filtering fragments with small insert size (remaining=4837326)
[2026-06-08T08:30:58] Filtering alignments with long gaps (remaining=4837325)
[2026-06-08T08:31:01] Filtering fragments with both mates in the same gene (remaining=4835534)
[2026-06-08T08:31:04] Filtering fusions arising from hairpin structures (remaining=4445431)
[2026-06-08T08:31:07] Filtering reads with a mismatch p-value <=0.01 (remaining=1748580)
[2026-06-08T08:31:21] Filtering reads with low entropy (k-mer content >=60%) (remaining=971546)
[2026-06-08T08:31:35] Finding fusions and counting supporting reads (total=858189)
[2026-06-08T08:32:01] Merging adjacent fusion breakpoints (remaining=850865)
[2026-06-08T08:32:04] Filtering multi-mapping fusions by alignment score and read support (remaining=428729)
[2026-06-08T08:32:50] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=425438)
[2026-06-08T08:33:01] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=292981)
[2026-06-08T08:33:02] Filtering fusions with <2 supporting reads (remaining=21054)
[2026-06-08T08:33:03] Filtering fusions with an e-value >=0.3 (remaining=4664)
[2026-06-08T08:33:04] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4697)
[2026-06-08T08:33:09] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=4321)
[2026-06-08T08:33:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4325)
[2026-06-08T08:33:12] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3948)
[2026-06-08T08:33:19] Searching for fusions with spliced split reads (remaining=4033)
[2026-06-08T08:33:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=2630)
[2026-06-08T08:33:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2599)
[2026-06-08T08:33:30] Searching for fusions with >=4 spliced events (remaining=3029)
[2026-06-08T08:33:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1068)
[2026-06-08T08:33:50] Filtering fusions with anchors <=23nt (remaining=814)
[2026-06-08T08:33:51] Filtering end-to-end fusions with low support (remaining=777)
[2026-06-08T08:33:52] Filtering fusions with no coverage around the breakpoints (remaining=764)
[2026-06-08T08:33:53] Indexing gene sequences 
[2026-06-08T08:33:59] Filtering genes with >=30% identity (remaining=242)
[2026-06-08T08:34:00] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=85)
[2026-06-08T08:34:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=79)
[2026-06-08T08:34:05] Searching for additional isoforms (remaining=99)
[2026-06-08T08:34:06] Assigning confidence scores to events 
[2026-06-08T08:34:11] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:12] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s04.arriba.fusions.tsv' 
[2026-06-08T08:34:13] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s04.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:55] Freeing resources
[2026-06-08T08:35:25] Done (elapsed time=00:15:43, CPU time=00:15:41, peak memory=18.6gb)