[2026-05-28T20:37:34] Launching Arriba 2.4.0
[2026-05-28T20:37:34] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:37:54] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:38:00] Reading chimeric alignments from 'SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=10327345)
[2026-05-28T20:42:42] Marking multi-mapping alignments (marked=8346350)
[2026-05-28T20:42:46] Detecting strandedness (reverse)
[2026-05-28T20:42:46] Assigning strands to alignments 
[2026-05-28T20:42:49] Annotating alignments 
[2026-05-28T20:43:26] Filtering duplicates (remaining=2148359)
[2026-05-28T20:43:32] 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=1653706)
[2026-05-28T20:43:34] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1653706)
[2026-05-28T20:43:36] Filtering viral contigs with expression lower than the top 5 (remaining=1653706)
[2026-05-28T20:43:40] Filtering viral contigs with less than 5% coverage (remaining=1653706)
[2026-05-28T20:43:43] Estimating fragment length (mate gap mean=-66.134, mate gap stddev=29.1613, read length mean=102.055)
[2026-05-28T20:43:43] Filtering read-through fragments with a distance <=10000bp (remaining=1615187)
[2026-05-28T20:43:45] Filtering inconsistently clipped mates (remaining=1563705)
[2026-05-28T20:43:47] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1399826)
[2026-05-28T20:43:50] Filtering fragments with small insert size (remaining=1397604)
[2026-05-28T20:43:52] Filtering alignments with long gaps (remaining=1397604)
[2026-05-28T20:43:54] Filtering fragments with both mates in the same gene (remaining=1396555)
[2026-05-28T20:43:56] Filtering fusions arising from hairpin structures (remaining=1319011)
[2026-05-28T20:43:59] Filtering reads with a mismatch p-value <=0.01 (remaining=339501)
[2026-05-28T20:44:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=127517)
[2026-05-28T20:44:09] Finding fusions and counting supporting reads (total=120443)
[2026-05-28T20:44:21] Merging adjacent fusion breakpoints (remaining=119154)
[2026-05-28T20:44:22] Filtering multi-mapping fusions by alignment score and read support (remaining=44057)
[2026-05-28T20:44:55] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:44:58] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=43086)
[2026-05-28T20:44:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=34979)
[2026-05-28T20:44:59] Filtering fusions with <2 supporting reads (remaining=1281)
[2026-05-28T20:44:59] Filtering fusions with an e-value >=0.3 (remaining=282)
[2026-05-28T20:44:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=287)
[2026-05-28T20:45:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=202)
[2026-05-28T20:45:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=202)
[2026-05-28T20:45:03] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=201)
[2026-05-28T20:45:06] Searching for fusions with spliced split reads (remaining=216)
[2026-05-28T20:45:10] Selecting best breakpoints from genes with multiple breakpoints (remaining=178)
[2026-05-28T20:45:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=174)
[2026-05-28T20:45:11] Searching for fusions with >=4 spliced events (remaining=176)
[2026-05-28T20:45:11] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=47)
[2026-05-28T20:45:30] Filtering fusions with anchors <=23nt (remaining=41)
[2026-05-28T20:45:30] Filtering end-to-end fusions with low support (remaining=40)
[2026-05-28T20:45:31] Filtering fusions with no coverage around the breakpoints (remaining=40)
[2026-05-28T20:45:31] Indexing gene sequences 
[2026-05-28T20:45:32] Filtering genes with >=30% identity (remaining=20)
[2026-05-28T20:45:32] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=6)
[2026-05-28T20:45:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=6)
[2026-05-28T20:45:33] Searching for additional isoforms (remaining=6)
[2026-05-28T20:45:34] Assigning confidence scores to events 
[2026-05-28T20:45:35] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:45:35] Writing fusions to file 'SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T20:45:35] Writing discarded fusions to file 'SkinN_FFPE_L01_RNA_01_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T20:45:47] Freeing resources
[2026-05-28T20:46:04] Done (elapsed time=00:08:30, CPU time=00:08:28, peak memory=14.5gb)