[2026-06-08T09:01:28] Launching Arriba 2.4.0
[2026-06-08T09:01:28] Loading assembly from 'ref_genome.fa' 
[2026-06-08T09:01:38] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T09:01:42] Reading chimeric alignments from 'FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam' (total=11415143)
[2026-06-08T09:09:13] Marking multi-mapping alignments (marked=7630647)
[2026-06-08T09:09:18] Detecting strandedness (reverse)
[2026-06-08T09:09:18] Assigning strands to alignments 
[2026-06-08T09:09:21] Annotating alignments 
[2026-06-08T09:09:59] Filtering duplicates (remaining=6533050)
[2026-06-08T09:10:07] 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=5993280)
[2026-06-08T09:10:09] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5993280)
[2026-06-08T09:10:11] Filtering viral contigs with expression lower than the top 5 (remaining=5993280)
[2026-06-08T09:10:16] Filtering viral contigs with less than 5% coverage (remaining=5993280)
[2026-06-08T09:10:19] Estimating fragment length (mate gap mean=-86.0426, mate gap stddev=32.3561, read length mean=133.116)
[2026-06-08T09:10:19] Filtering read-through fragments with a distance <=10000bp (remaining=5746719)
[2026-06-08T09:10:21] Filtering inconsistently clipped mates (remaining=5642805)
[2026-06-08T09:10:23] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=5435870)
[2026-06-08T09:10:28] Filtering fragments with small insert size (remaining=5435106)
[2026-06-08T09:10:30] Filtering alignments with long gaps (remaining=5435105)
[2026-06-08T09:10:32] Filtering fragments with both mates in the same gene (remaining=5434170)
[2026-06-08T09:10:34] Filtering fusions arising from hairpin structures (remaining=5068711)
[2026-06-08T09:10:37] Filtering reads with a mismatch p-value <=0.01 (remaining=2404754)
[2026-06-08T09:10:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=928991)
[2026-06-08T09:11:02] Finding fusions and counting supporting reads (total=681172)
[2026-06-08T09:11:19] Merging adjacent fusion breakpoints (remaining=674380)
[2026-06-08T09:11:21] Filtering multi-mapping fusions by alignment score and read support (remaining=416775)
[2026-06-08T09:11:57] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:12:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=413978)
[2026-06-08T09:12:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=241379)
[2026-06-08T09:12:06] Filtering fusions with <2 supporting reads (remaining=33860)
[2026-06-08T09:12:06] Filtering fusions with an e-value >=0.3 (remaining=11764)
[2026-06-08T09:12:07] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=11816)
[2026-06-08T09:12:11] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=11730)
[2026-06-08T09:12:12] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=11755)
[2026-06-08T09:12:13] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=8319)
[2026-06-08T09:12:18] Searching for fusions with spliced split reads (remaining=8455)
[2026-06-08T09:12:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=4415)
[2026-06-08T09:12:25] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4374)
[2026-06-08T09:12:26] Searching for fusions with >=4 spliced events (remaining=5192)
[2026-06-08T09:12:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2050)
[2026-06-08T09:12:43] Filtering fusions with anchors <=23nt (remaining=1512)
[2026-06-08T09:12:44] Filtering end-to-end fusions with low support (remaining=1438)
[2026-06-08T09:12:45] Filtering fusions with no coverage around the breakpoints (remaining=1394)
[2026-06-08T09:12:45] Indexing gene sequences 
[2026-06-08T09:12:51] Filtering genes with >=30% identity (remaining=401)
[2026-06-08T09:12:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=132)
[2026-06-08T09:12:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=127)
[2026-06-08T09:12:57] Searching for additional isoforms (remaining=161)
[2026-06-08T09:12:59] Assigning confidence scores to events 
[2026-06-08T09:13:02] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:13:02] Writing fusions to file 'FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.arriba.fusions.tsv' 
[2026-06-08T09:13:04] Writing discarded fusions to file 'FFPE_V4_0002_RNA_0006_A23WJ53LT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:13:32] Freeing resources
[2026-06-08T09:13:50] Done (elapsed time=00:12:22, CPU time=00:12:20, peak memory=16.1gb)