[2026-05-28T21:06:21] Launching Arriba 2.4.0
[2026-05-28T21:06:21] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:06:34] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:06:39] Reading chimeric alignments from 'SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=13148700)
[2026-05-28T21:13:29] Marking multi-mapping alignments (marked=10066288)
[2026-05-28T21:13:34] Detecting strandedness (reverse)
[2026-05-28T21:13:34] Assigning strands to alignments 
[2026-05-28T21:13:37] Annotating alignments 
[2026-05-28T21:14:23] Filtering duplicates (remaining=2695132)
[2026-05-28T21:14:30] 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=2321688)
[2026-05-28T21:14:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=2321688)
[2026-05-28T21:14:35] Filtering viral contigs with expression lower than the top 5 (remaining=2321688)
[2026-05-28T21:14:40] Filtering viral contigs with less than 5% coverage (remaining=2321688)
[2026-05-28T21:14:43] Estimating fragment length (mate gap mean=-73.72, mate gap stddev=28.5823, read length mean=110.192)
[2026-05-28T21:14:43] Filtering read-through fragments with a distance <=10000bp (remaining=2259554)
[2026-05-28T21:14:46] Filtering inconsistently clipped mates (remaining=2195345)
[2026-05-28T21:14:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1912447)
[2026-05-28T21:14:52] Filtering fragments with small insert size (remaining=1911199)
[2026-05-28T21:14:54] Filtering alignments with long gaps (remaining=1911199)
[2026-05-28T21:14:56] Filtering fragments with both mates in the same gene (remaining=1910154)
[2026-05-28T21:14:59] Filtering fusions arising from hairpin structures (remaining=1817623)
[2026-05-28T21:15:01] Filtering reads with a mismatch p-value <=0.01 (remaining=579842)
[2026-05-28T21:15:07] Filtering reads with low entropy (k-mer content >=60%) (remaining=200496)
[2026-05-28T21:15:13] Finding fusions and counting supporting reads (total=197225)
[2026-05-28T21:15:29] Merging adjacent fusion breakpoints (remaining=195892)
[2026-05-28T21:15:30] Filtering multi-mapping fusions by alignment score and read support (remaining=76362)
[2026-05-28T21:16:11] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:16:16] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=75168)
[2026-05-28T21:16:16] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=58930)
[2026-05-28T21:16:17] Filtering fusions with <2 supporting reads (remaining=2348)
[2026-05-28T21:16:17] Filtering fusions with an e-value >=0.3 (remaining=553)
[2026-05-28T21:16:17] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=558)
[2026-05-28T21:16:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=452)
[2026-05-28T21:16:21] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=452)
[2026-05-28T21:16:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=452)
[2026-05-28T21:16:26] Searching for fusions with spliced split reads (remaining=484)
[2026-05-28T21:16:32] Selecting best breakpoints from genes with multiple breakpoints (remaining=381)
[2026-05-28T21:16:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=374)
[2026-05-28T21:16:33] Searching for fusions with >=4 spliced events (remaining=385)
[2026-05-28T21:16:33] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=96)
[2026-05-28T21:16:51] Filtering fusions with anchors <=23nt (remaining=67)
[2026-05-28T21:16:51] Filtering end-to-end fusions with low support (remaining=65)
[2026-05-28T21:16:52] Filtering fusions with no coverage around the breakpoints (remaining=64)
[2026-05-28T21:16:52] Indexing gene sequences 
[2026-05-28T21:16:53] Filtering genes with >=30% identity (remaining=27)
[2026-05-28T21:16:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=5)
[2026-05-28T21:16:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=5)
[2026-05-28T21:16:55] Searching for additional isoforms (remaining=5)
[2026-05-28T21:16:55] Assigning confidence scores to events 
[2026-05-28T21:16:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:16:57] Writing fusions to file 'SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:16:57] Writing discarded fusions to file 'SkinN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:17:13] Freeing resources
[2026-05-28T21:17:34] Done (elapsed time=00:11:13, CPU time=00:11:13, peak memory=17.3gb)