[2026-06-08T08:26:41] Launching Arriba 2.4.0
[2026-06-08T08:26:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:26:55] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:27:00] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s26.Aligned.sortedByCoord.out.bam' (total=12175698)
[2026-06-08T08:35:44] Marking multi-mapping alignments (marked=8465360)
[2026-06-08T08:35:50] Detecting strandedness (reverse)
[2026-06-08T08:35:50] Assigning strands to alignments 
[2026-06-08T08:35:53] Annotating alignments 
[2026-06-08T08:36:44] Filtering duplicates (remaining=6159775)
[2026-06-08T08:36:54] 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=5488247)
[2026-06-08T08:36:57] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5488247)
[2026-06-08T08:37:00] Filtering viral contigs with expression lower than the top 5 (remaining=5488247)
[2026-06-08T08:37:07] Filtering viral contigs with less than 5% coverage (remaining=5488247)
[2026-06-08T08:37:10] Estimating fragment length (mate gap mean=-83.8141, mate gap stddev=32.4366, read length mean=131.052)
[2026-06-08T08:37:10] Filtering read-through fragments with a distance <=10000bp (remaining=5268559)
[2026-06-08T08:37:13] Filtering inconsistently clipped mates (remaining=5181082)
[2026-06-08T08:37:16] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4723185)
[2026-06-08T08:37:22] Filtering fragments with small insert size (remaining=4722269)
[2026-06-08T08:37:25] Filtering alignments with long gaps (remaining=4722269)
[2026-06-08T08:37:28] Filtering fragments with both mates in the same gene (remaining=4720426)
[2026-06-08T08:37:31] Filtering fusions arising from hairpin structures (remaining=4427090)
[2026-06-08T08:37:35] Filtering reads with a mismatch p-value <=0.01 (remaining=1788077)
[2026-06-08T08:37:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=909701)
[2026-06-08T08:38:01] Finding fusions and counting supporting reads (total=807367)
[2026-06-08T08:38:24] Merging adjacent fusion breakpoints (remaining=802606)
[2026-06-08T08:38:26] Filtering multi-mapping fusions by alignment score and read support (remaining=447859)
[2026-06-08T08:39:11] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:39:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=444932)
[2026-06-08T08:39:20] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=313762)
[2026-06-08T08:39:22] Filtering fusions with <2 supporting reads (remaining=22024)
[2026-06-08T08:39:23] Filtering fusions with an e-value >=0.3 (remaining=5525)
[2026-06-08T08:39:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=5558)
[2026-06-08T08:39:28] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=5305)
[2026-06-08T08:39:29] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=5315)
[2026-06-08T08:39:31] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=4114)
[2026-06-08T08:39:38] Searching for fusions with spliced split reads (remaining=4202)
[2026-06-08T08:39:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=2546)
[2026-06-08T08:39:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2516)
[2026-06-08T08:39:48] Searching for fusions with >=4 spliced events (remaining=3028)
[2026-06-08T08:39:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1153)
[2026-06-08T08:40:09] Filtering fusions with anchors <=23nt (remaining=878)
[2026-06-08T08:40:10] Filtering end-to-end fusions with low support (remaining=846)
[2026-06-08T08:40:11] Filtering fusions with no coverage around the breakpoints (remaining=838)
[2026-06-08T08:40:12] Indexing gene sequences 
[2026-06-08T08:40:17] Filtering genes with >=30% identity (remaining=240)
[2026-06-08T08:40:19] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=77)
[2026-06-08T08:40:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=77)
[2026-06-08T08:40:24] Searching for additional isoforms (remaining=102)
[2026-06-08T08:40:26] Assigning confidence scores to events 
[2026-06-08T08:40:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:40:30] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s26.arriba.fusions.tsv' 
[2026-06-08T08:40:32] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s26.arriba.fusions.discarded.tsv'
[2026-06-08T08:41:13] Freeing resources
[2026-06-08T08:41:40] Done (elapsed time=00:14:59, CPU time=00:14:57, peak memory=17.2gb)