[2026-06-08T08:21:42] Launching Arriba 2.4.0
[2026-06-08T08:21:42] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:21:59] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:22:04] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s09.Aligned.sortedByCoord.out.bam' (total=11090225)
[2026-06-08T08:30:33] Marking multi-mapping alignments (marked=7621041)
[2026-06-08T08:30:38] Detecting strandedness (reverse)
[2026-06-08T08:30:38] Assigning strands to alignments 
[2026-06-08T08:30:40] Annotating alignments 
[2026-06-08T08:31:18] Filtering duplicates (remaining=6508939)
[2026-06-08T08:31:26] 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=5834936)
[2026-06-08T08:31:28] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5834936)
[2026-06-08T08:31:30] Filtering viral contigs with expression lower than the top 5 (remaining=5834936)
[2026-06-08T08:31:35] Filtering viral contigs with less than 5% coverage (remaining=5834936)
[2026-06-08T08:31:37] Estimating fragment length (mate gap mean=-86.2117, mate gap stddev=30.8505, read length mean=132.956)
[2026-06-08T08:31:37] Filtering read-through fragments with a distance <=10000bp (remaining=5568030)
[2026-06-08T08:31:39] Filtering inconsistently clipped mates (remaining=5465861)
[2026-06-08T08:31:41] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5053592)
[2026-06-08T08:31:46] Filtering fragments with small insert size (remaining=5052771)
[2026-06-08T08:31:48] Filtering alignments with long gaps (remaining=5052771)
[2026-06-08T08:31:51] Filtering fragments with both mates in the same gene (remaining=5050951)
[2026-06-08T08:31:53] Filtering fusions arising from hairpin structures (remaining=4654779)
[2026-06-08T08:31:55] Filtering reads with a mismatch p-value <=0.01 (remaining=1975577)
[2026-06-08T08:32:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=1080605)
[2026-06-08T08:32:20] Finding fusions and counting supporting reads (total=906962)
[2026-06-08T08:32:37] Merging adjacent fusion breakpoints (remaining=900092)
[2026-06-08T08:32:39] Filtering multi-mapping fusions by alignment score and read support (remaining=513136)
[2026-06-08T08:33:13] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:33:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=509937)
[2026-06-08T08:33:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=329492)
[2026-06-08T08:33:22] Filtering fusions with <2 supporting reads (remaining=29788)
[2026-06-08T08:33:22] Filtering fusions with an e-value >=0.3 (remaining=8054)
[2026-06-08T08:33:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8094)
[2026-06-08T08:33:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7817)
[2026-06-08T08:33:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7855)
[2026-06-08T08:33:29] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=5765)
[2026-06-08T08:33:34] Searching for fusions with spliced split reads (remaining=5893)
[2026-06-08T08:33:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=3416)
[2026-06-08T08:33:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3387)
[2026-06-08T08:33:42] Searching for fusions with >=4 spliced events (remaining=4145)
[2026-06-08T08:33:43] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1608)
[2026-06-08T08:34:00] Filtering fusions with anchors <=23nt (remaining=1198)
[2026-06-08T08:34:01] Filtering end-to-end fusions with low support (remaining=1160)
[2026-06-08T08:34:02] Filtering fusions with no coverage around the breakpoints (remaining=1143)
[2026-06-08T08:34:03] Indexing gene sequences 
[2026-06-08T08:34:08] Filtering genes with >=30% identity (remaining=291)
[2026-06-08T08:34:10] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=89)
[2026-06-08T08:34:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=86)
[2026-06-08T08:34:14] Searching for additional isoforms (remaining=106)
[2026-06-08T08:34:16] Assigning confidence scores to events 
[2026-06-08T08:34:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:34:20] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s09.arriba.fusions.tsv' 
[2026-06-08T08:34:21] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s09.arriba.fusions.discarded.tsv'
[2026-06-08T08:34:52] Freeing resources
[2026-06-08T08:35:12] Done (elapsed time=00:13:30, CPU time=00:13:28, peak memory=16.2gb)