[2026-05-28T22:35:03] Launching Arriba 2.4.0
[2026-05-28T22:35:03] Loading assembly from 'ref_genome.fa' 
[2026-05-28T22:35:10] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T22:35:14] Reading chimeric alignments from 'SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=21172725)
[2026-05-28T22:42:41] Marking multi-mapping alignments (marked=16465484)
[2026-05-28T22:42:50] Detecting strandedness (no)
[2026-05-28T22:42:50] Annotating alignments 
[2026-05-28T22:44:26] Filtering duplicates (remaining=4349122)
[2026-05-28T22:44:40] 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=3391351)
[2026-05-28T22:44:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=3391351)
[2026-05-28T22:44:49] Filtering viral contigs with expression lower than the top 5 (remaining=3391351)
[2026-05-28T22:44:59] Filtering viral contigs with less than 5% coverage (remaining=3391351)
[2026-05-28T22:45:04] Estimating fragment length (mate gap mean=-73.873, mate gap stddev=30.5497, read length mean=107.544)
[2026-05-28T22:45:05] Filtering read-through fragments with a distance <=10000bp (remaining=3313755)
[2026-05-28T22:45:09] Filtering inconsistently clipped mates (remaining=3220755)
[2026-05-28T22:45:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=2961901)
[2026-05-28T22:45:19] Filtering fragments with small insert size (remaining=2959714)
[2026-05-28T22:45:24] Filtering alignments with long gaps (remaining=2959714)
[2026-05-28T22:45:29] Filtering fragments with both mates in the same gene (remaining=2958150)
[2026-05-28T22:45:34] Filtering fusions arising from hairpin structures (remaining=2794129)
[2026-05-28T22:45:39] Filtering reads with a mismatch p-value <=0.01 (remaining=782840)
[2026-05-28T22:45:50] Filtering reads with low entropy (k-mer content >=60%) (remaining=250856)
[2026-05-28T22:46:03] Finding fusions and counting supporting reads (total=217473)
[2026-05-28T22:46:29] Merging adjacent fusion breakpoints (remaining=214968)
[2026-05-28T22:46:31] Filtering multi-mapping fusions by alignment score and read support (remaining=100957)
[2026-05-28T22:47:36] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T22:47:43] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=99749)
[2026-05-28T22:47:43] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=72249)
[2026-05-28T22:47:44] Filtering fusions with <2 supporting reads (remaining=4174)
[2026-05-28T22:47:45] Filtering fusions with an e-value >=0.3 (remaining=892)
[2026-05-28T22:47:45] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=905)
[2026-05-28T22:47:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=807)
[2026-05-28T22:47:52] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=807)
[2026-05-28T22:47:53] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=806)
[2026-05-28T22:48:03] Searching for fusions with spliced split reads (remaining=862)
[2026-05-28T22:48:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=684)
[2026-05-28T22:48:14] Filtering read-through fusions with breakpoints near the gene boundary (remaining=670)
[2026-05-28T22:48:14] Searching for fusions with >=4 spliced events (remaining=696)
[2026-05-28T22:48:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=240)
[2026-05-28T22:48:39] Filtering fusions with anchors <=23nt (remaining=195)
[2026-05-28T22:48:39] Filtering end-to-end fusions with low support (remaining=174)
[2026-05-28T22:48:40] Filtering fusions with no coverage around the breakpoints (remaining=166)
[2026-05-28T22:48:40] Indexing gene sequences 
[2026-05-28T22:48:43] Filtering genes with >=30% identity (remaining=55)
[2026-05-28T22:48:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=18)
[2026-05-28T22:48:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=15)
[2026-05-28T22:48:46] Searching for additional isoforms (remaining=15)
[2026-05-28T22:48:47] Assigning confidence scores to events 
[2026-05-28T22:48:50] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T22:48:50] Writing fusions to file 'SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T22:48:50] Writing discarded fusions to file 'SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T22:49:15] Freeing resources
[2026-05-28T22:49:54] Done (elapsed time=00:14:51, CPU time=00:14:51, peak memory=25.6gb)