[2026-06-08T08:20:40] Launching Arriba 2.4.0
[2026-06-08T08:20:40] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:20:53] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:20:57] Reading chimeric alignments from 'V4_0001_RNA_0005_23H5VFLT4_s05.Aligned.sortedByCoord.out.bam' (total=14550916)
[2026-06-08T08:28:12] Marking multi-mapping alignments (marked=10786868)
[2026-06-08T08:28:18] Detecting strandedness (reverse)
[2026-06-08T08:28:18] Assigning strands to alignments 
[2026-06-08T08:28:21] Annotating alignments 
[2026-06-08T08:29:05] Filtering duplicates (remaining=7124265)
[2026-06-08T08:29:14] 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=6094349)
[2026-06-08T08:29:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=6094349)
[2026-06-08T08:29:19] Filtering viral contigs with expression lower than the top 5 (remaining=6094349)
[2026-06-08T08:29:24] Filtering viral contigs with less than 5% coverage (remaining=6094349)
[2026-06-08T08:29:27] Estimating fragment length (mate gap mean=-82.1095, mate gap stddev=31.5433, read length mean=122.566)
[2026-06-08T08:29:27] Filtering read-through fragments with a distance <=10000bp (remaining=5857817)
[2026-06-08T08:29:30] Filtering inconsistently clipped mates (remaining=5741163)
[2026-06-08T08:29:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5112170)
[2026-06-08T08:29:39] Filtering fragments with small insert size (remaining=5110350)
[2026-06-08T08:29:41] Filtering alignments with long gaps (remaining=5110350)
[2026-06-08T08:29:44] Filtering fragments with both mates in the same gene (remaining=5108174)
[2026-06-08T08:29:47] Filtering fusions arising from hairpin structures (remaining=4707467)
[2026-06-08T08:29:50] Filtering reads with a mismatch p-value <=0.01 (remaining=1709189)
[2026-06-08T08:30:03] Filtering reads with low entropy (k-mer content >=60%) (remaining=965726)
[2026-06-08T08:30:14] Finding fusions and counting supporting reads (total=857072)
[2026-06-08T08:30:34] Merging adjacent fusion breakpoints (remaining=848176)
[2026-06-08T08:30:36] Filtering multi-mapping fusions by alignment score and read support (remaining=411660)
[2026-06-08T08:31:16] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:31:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=408380)
[2026-06-08T08:31:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=279032)
[2026-06-08T08:31:26] Filtering fusions with <2 supporting reads (remaining=19623)
[2026-06-08T08:31:26] Filtering fusions with an e-value >=0.3 (remaining=4324)
[2026-06-08T08:31:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=4355)
[2026-06-08T08:31:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=3948)
[2026-06-08T08:31:32] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=3948)
[2026-06-08T08:31:34] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=3701)
[2026-06-08T08:31:40] Searching for fusions with spliced split reads (remaining=3762)
[2026-06-08T08:31:46] Selecting best breakpoints from genes with multiple breakpoints (remaining=2604)
[2026-06-08T08:31:48] Filtering read-through fusions with breakpoints near the gene boundary (remaining=2570)
[2026-06-08T08:31:49] Searching for fusions with >=4 spliced events (remaining=2997)
[2026-06-08T08:31:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1049)
[2026-06-08T08:32:04] Filtering fusions with anchors <=23nt (remaining=793)
[2026-06-08T08:32:05] Filtering end-to-end fusions with low support (remaining=757)
[2026-06-08T08:32:06] Filtering fusions with no coverage around the breakpoints (remaining=745)
[2026-06-08T08:32:07] Indexing gene sequences 
[2026-06-08T08:32:11] Filtering genes with >=30% identity (remaining=203)
[2026-06-08T08:32:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=49)
[2026-06-08T08:32:14] Selecting best breakpoints from genes with multiple breakpoints (remaining=49)
[2026-06-08T08:32:16] Searching for additional isoforms (remaining=65)
[2026-06-08T08:32:17] Assigning confidence scores to events 
[2026-06-08T08:32:21] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:32:21] Writing fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s05.arriba.fusions.tsv' 
[2026-06-08T08:32:22] Writing discarded fusions to file 'V4_0001_RNA_0005_23H5VFLT4_s05.arriba.fusions.discarded.tsv'
[2026-06-08T08:32:53] Freeing resources
[2026-06-08T08:33:15] Done (elapsed time=00:12:35, CPU time=00:12:33, peak memory=20gb)