[2026-06-04T21:14:00] Launching Arriba 2.4.0
[2026-06-04T21:14:00] Loading assembly from 'ref_genome.fa' 
[2026-06-04T21:14:07] Loading annotation from 'ref_annot.gtf' 
[2026-06-04T21:14:11] Reading chimeric alignments from 'FFPE_V4_0001_RNA_0003_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam' (total=12526205)
[2026-06-04T21:21:11] Marking multi-mapping alignments (marked=7995137)
[2026-06-04T21:21:16] Detecting strandedness (reverse)
[2026-06-04T21:21:16] Assigning strands to alignments 
[2026-06-04T21:21:18] Annotating alignments 
[2026-06-04T21:21:55] Filtering duplicates (remaining=7966164)
[2026-06-04T21:22:03] 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=7460595)
[2026-06-04T21:22:05] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7460595)
[2026-06-04T21:22:08] Filtering viral contigs with expression lower than the top 5 (remaining=7460595)
[2026-06-04T21:22:13] Filtering viral contigs with less than 5% coverage (remaining=7460595)
[2026-06-04T21:22:16] Estimating fragment length (mate gap mean=-86.0959, mate gap stddev=31.9729, read length mean=133.696)
[2026-06-04T21:22:16] Filtering read-through fragments with a distance <=10000bp (remaining=7150051)
[2026-06-04T21:22:19] Filtering inconsistently clipped mates (remaining=7037642)
[2026-06-04T21:22:21] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6852950)
[2026-06-04T21:22:26] Filtering fragments with small insert size (remaining=6851748)
[2026-06-04T21:22:29] Filtering alignments with long gaps (remaining=6851748)
[2026-06-04T21:22:31] Filtering fragments with both mates in the same gene (remaining=6850591)
[2026-06-04T21:22:34] Filtering fusions arising from hairpin structures (remaining=6405032)
[2026-06-04T21:22:37] Filtering reads with a mismatch p-value <=0.01 (remaining=3271342)
[2026-06-04T21:22:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=1182738)
[2026-06-04T21:23:07] Finding fusions and counting supporting reads (total=859771)
[2026-06-04T21:23:24] Merging adjacent fusion breakpoints (remaining=851675)
[2026-06-04T21:23:26] Filtering multi-mapping fusions by alignment score and read support (remaining=549704)
[2026-06-04T21:24:02] Estimating expected number of fusions by random chance (e-value) 
[2026-06-04T21:24:10] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=547040)
[2026-06-04T21:24:10] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=321638)
[2026-06-04T21:24:12] Filtering fusions with <2 supporting reads (remaining=41713)
[2026-06-04T21:24:12] Filtering fusions with an e-value >=0.3 (remaining=12617)
[2026-06-04T21:24:13] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=12668)
[2026-06-04T21:24:18] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=12572)
[2026-06-04T21:24:18] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=12621)
[2026-06-04T21:24:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=9064)
[2026-06-04T21:24:26] Searching for fusions with spliced split reads (remaining=9085)
[2026-06-04T21:24:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=4628)
[2026-06-04T21:24:33] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4588)
[2026-06-04T21:24:34] Searching for fusions with >=4 spliced events (remaining=5861)
[2026-06-04T21:24:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2595)
[2026-06-04T21:24:51] Filtering fusions with anchors <=23nt (remaining=1855)
[2026-06-04T21:24:52] Filtering end-to-end fusions with low support (remaining=1794)
[2026-06-04T21:24:53] Filtering fusions with no coverage around the breakpoints (remaining=1743)
[2026-06-04T21:24:54] Indexing gene sequences 
[2026-06-04T21:24:59] Filtering genes with >=30% identity (remaining=395)
[2026-06-04T21:25:02] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=107)
[2026-06-04T21:25:05] Selecting best breakpoints from genes with multiple breakpoints (remaining=98)
[2026-06-04T21:25:07] Searching for additional isoforms (remaining=148)
[2026-06-04T21:25:09] Assigning confidence scores to events 
[2026-06-04T21:25:12] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-04T21:25:13] Writing fusions to file 'FFPE_V4_0001_RNA_0003_B23MHV2LT4_1.arriba.fusions.tsv' 
[2026-06-04T21:25:14] Writing discarded fusions to file 'FFPE_V4_0001_RNA_0003_B23MHV2LT4_1.arriba.fusions.discarded.tsv'
[2026-06-04T21:25:43] Freeing resources
[2026-06-04T21:26:03] Done (elapsed time=00:12:03, CPU time=00:12:02, peak memory=17.2gb)