[2026-05-28T20:09:13] Launching Arriba 2.4.0
[2026-05-28T20:09:13] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:09:29] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:09:35] Reading chimeric alignments from 'SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1364188)
[2026-05-28T20:10:05] Marking multi-mapping alignments (marked=1174334)
[2026-05-28T20:10:06] Detecting strandedness (no)
[2026-05-28T20:10:06] Annotating alignments 
[2026-05-28T20:10:12] Filtering duplicates (remaining=581158)
[2026-05-28T20:10:13] 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=461514)
[2026-05-28T20:10:13] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=461514)
[2026-05-28T20:10:13] Filtering viral contigs with expression lower than the top 5 (remaining=461514)
[2026-05-28T20:10:14] Filtering viral contigs with less than 5% coverage (remaining=461514)
[2026-05-28T20:10:15] Estimating fragment length (mate gap mean=-47.8922, mate gap stddev=34.225, read length mean=81.5507)
[2026-05-28T20:10:15] Filtering read-through fragments with a distance <=10000bp (remaining=455043)
[2026-05-28T20:10:15] Filtering inconsistently clipped mates (remaining=439389)
[2026-05-28T20:10:15] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=408171)
[2026-05-28T20:10:16] Filtering fragments with small insert size (remaining=407580)
[2026-05-28T20:10:16] Filtering alignments with long gaps (remaining=407580)
[2026-05-28T20:10:16] Filtering fragments with both mates in the same gene (remaining=406800)
[2026-05-28T20:10:17] Filtering fusions arising from hairpin structures (remaining=383827)
[2026-05-28T20:10:17] Filtering reads with a mismatch p-value <=0.01 (remaining=48760)
[2026-05-28T20:10:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=17498)
[2026-05-28T20:10:19] Finding fusions and counting supporting reads (total=17398)
[2026-05-28T20:10:21] Merging adjacent fusion breakpoints (remaining=17269)
[2026-05-28T20:10:21] Filtering multi-mapping fusions by alignment score and read support (remaining=8000)
[2026-05-28T20:10:26] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:10:27] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=7824)
[2026-05-28T20:10:27] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=5920)
[2026-05-28T20:10:27] Filtering fusions with <2 supporting reads (remaining=143)
[2026-05-28T20:10:27] Filtering fusions with an e-value >=0.3 (remaining=79)
[2026-05-28T20:10:27] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=79)
[2026-05-28T20:10:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=53)
[2026-05-28T20:10:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=53)
[2026-05-28T20:10:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=43)
[2026-05-28T20:10:28] Searching for fusions with spliced split reads (remaining=43)
[2026-05-28T20:10:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=38)
[2026-05-28T20:10:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=37)
[2026-05-28T20:10:29] Searching for fusions with >=4 spliced events (remaining=37)
[2026-05-28T20:10:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=6)
[2026-05-28T20:10:50] Filtering fusions with anchors <=23nt (remaining=3)
[2026-05-28T20:10:50] Filtering end-to-end fusions with low support (remaining=3)
[2026-05-28T20:10:50] Filtering fusions with no coverage around the breakpoints (remaining=2)
[2026-05-28T20:10:50] Indexing gene sequences 
[2026-05-28T20:10:50] Filtering genes with >=30% identity (remaining=1)
[2026-05-28T20:10:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:10:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:10:50] Searching for additional isoforms (remaining=0)
[2026-05-28T20:10:50] Assigning confidence scores to events 
[2026-05-28T20:10:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:10:51] Writing fusions to file 'SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:10:51] Writing discarded fusions to file 'SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:10:55] Freeing resources
[2026-05-28T20:10:58] Done (elapsed time=00:01:45, CPU time=00:01:44, peak memory=5.49gb)