[2026-05-28T23:44:04] Launching Arriba 2.4.0
[2026-05-28T23:44:04] Loading assembly from 'ref_genome.fa' 
[2026-05-28T23:44:17] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T23:44:21] Reading chimeric alignments from 'SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=65861431)
[2026-05-28T23:58:55] Marking multi-mapping alignments (marked=58688060)
[2026-05-28T23:59:15] Detecting strandedness (no)
[2026-05-28T23:59:15] Annotating alignments 
[2026-05-29T00:02:22] Filtering duplicates (remaining=8573706)
[2026-05-29T00:02:51] 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=5609556)
[2026-05-29T00:03:01] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=5609556)
[2026-05-29T00:03:10] Filtering viral contigs with expression lower than the top 5 (remaining=5609556)
[2026-05-29T00:03:31] Filtering viral contigs with less than 5% coverage (remaining=5609556)
[2026-05-29T00:03:41] Estimating fragment length (mate gap mean=-64.299, mate gap stddev=28.6649, read length mean=96.393)
[2026-05-29T00:03:41] Filtering read-through fragments with a distance <=10000bp (remaining=5465927)
[2026-05-29T00:03:50] Filtering inconsistently clipped mates (remaining=5335875)
[2026-05-29T00:04:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4938199)
[2026-05-29T00:04:12] Filtering fragments with small insert size (remaining=4934254)
[2026-05-29T00:04:21] Filtering alignments with long gaps (remaining=4934254)
[2026-05-29T00:04:31] Filtering fragments with both mates in the same gene (remaining=4931918)
[2026-05-29T00:04:41] Filtering fusions arising from hairpin structures (remaining=4698534)
[2026-05-29T00:04:51] Filtering reads with a mismatch p-value <=0.01 (remaining=1050442)
[2026-05-29T00:05:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=402241)
[2026-05-29T00:05:30] Finding fusions and counting supporting reads (total=314163)
[2026-05-29T00:06:18] Merging adjacent fusion breakpoints (remaining=308896)
[2026-05-29T00:06:20] Filtering multi-mapping fusions by alignment score and read support (remaining=134425)
[2026-05-29T00:08:11] Estimating expected number of fusions by random chance (e-value) 
[2026-05-29T00:08:20] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=131164)
[2026-05-29T00:08:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=96696)
[2026-05-29T00:08:22] Filtering fusions with <2 supporting reads (remaining=7150)
[2026-05-29T00:08:22] Filtering fusions with an e-value >=0.3 (remaining=1468)
[2026-05-29T00:08:23] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1520)
[2026-05-29T00:08:34] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1348)
[2026-05-29T00:08:35] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1348)
[2026-05-29T00:08:36] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1345)
[2026-05-29T00:08:52] Searching for fusions with spliced split reads (remaining=1428)
[2026-05-29T00:09:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=1087)
[2026-05-29T00:09:09] Filtering read-through fusions with breakpoints near the gene boundary (remaining=1075)
[2026-05-29T00:09:10] Searching for fusions with >=4 spliced events (remaining=1171)
[2026-05-29T00:09:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=401)
[2026-05-29T00:09:28] Filtering fusions with anchors <=23nt (remaining=328)
[2026-05-29T00:09:29] Filtering end-to-end fusions with low support (remaining=318)
[2026-05-29T00:09:30] Filtering fusions with no coverage around the breakpoints (remaining=315)
[2026-05-29T00:09:31] Indexing gene sequences 
[2026-05-29T00:09:33] Filtering genes with >=30% identity (remaining=112)
[2026-05-29T00:09:34] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=49)
[2026-05-29T00:09:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=25)
[2026-05-29T00:09:37] Searching for additional isoforms (remaining=27)
[2026-05-29T00:09:39] Assigning confidence scores to events 
[2026-05-29T00:09:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-29T00:09:42] Writing fusions to file 'SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-29T00:09:43] Writing discarded fusions to file 'SkinN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-29T00:10:12] Freeing resources
[2026-05-29T00:11:27] Done (elapsed time=00:27:23, CPU time=00:27:22, peak memory=71.5gb)