[2026-05-28T21:01:02] Launching Arriba 2.4.0
[2026-05-28T21:01:02] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:01:17] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:01:22] Reading chimeric alignments from 'SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=7863563)
[2026-05-28T21:04:28] Marking multi-mapping alignments (marked=6407536)
[2026-05-28T21:04:31] Detecting strandedness (reverse)
[2026-05-28T21:04:31] Assigning strands to alignments 
[2026-05-28T21:04:33] Annotating alignments 
[2026-05-28T21:04:58] Filtering duplicates (remaining=1168111)
[2026-05-28T21:05:02] 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=928804)
[2026-05-28T21:05:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=928804)
[2026-05-28T21:05:05] Filtering viral contigs with expression lower than the top 5 (remaining=928804)
[2026-05-28T21:05:08] Filtering viral contigs with less than 5% coverage (remaining=928804)
[2026-05-28T21:05:09] Estimating fragment length (mate gap mean=-65.0682, mate gap stddev=29.1495, read length mean=101.57)
[2026-05-28T21:05:10] Filtering read-through fragments with a distance <=10000bp (remaining=898180)
[2026-05-28T21:05:11] Filtering inconsistently clipped mates (remaining=865811)
[2026-05-28T21:05:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=787609)
[2026-05-28T21:05:15] Filtering fragments with small insert size (remaining=786514)
[2026-05-28T21:05:16] Filtering alignments with long gaps (remaining=786514)
[2026-05-28T21:05:18] Filtering fragments with both mates in the same gene (remaining=785793)
[2026-05-28T21:05:19] Filtering fusions arising from hairpin structures (remaining=731913)
[2026-05-28T21:05:21] Filtering reads with a mismatch p-value <=0.01 (remaining=176235)
[2026-05-28T21:05:23] Filtering reads with low entropy (k-mer content >=60%) (remaining=63218)
[2026-05-28T21:05:27] Finding fusions and counting supporting reads (total=60035)
[2026-05-28T21:05:37] Merging adjacent fusion breakpoints (remaining=59323)
[2026-05-28T21:05:37] Filtering multi-mapping fusions by alignment score and read support (remaining=22947)
[2026-05-28T21:06:00] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:06:02] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=22523)
[2026-05-28T21:06:03] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=16914)
[2026-05-28T21:06:03] Filtering fusions with <2 supporting reads (remaining=628)
[2026-05-28T21:06:03] Filtering fusions with an e-value >=0.3 (remaining=139)
[2026-05-28T21:06:03] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=140)
[2026-05-28T21:06:05] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=102)
[2026-05-28T21:06:05] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=102)
[2026-05-28T21:06:05] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=101)
[2026-05-28T21:06:08] Searching for fusions with spliced split reads (remaining=101)
[2026-05-28T21:06:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=83)
[2026-05-28T21:06:11] Filtering read-through fusions with breakpoints near the gene boundary (remaining=79)
[2026-05-28T21:06:11] Searching for fusions with >=4 spliced events (remaining=79)
[2026-05-28T21:06:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=25)
[2026-05-28T21:06:28] Filtering fusions with anchors <=23nt (remaining=20)
[2026-05-28T21:06:28] Filtering end-to-end fusions with low support (remaining=20)
[2026-05-28T21:06:28] Filtering fusions with no coverage around the breakpoints (remaining=19)
[2026-05-28T21:06:28] Indexing gene sequences 
[2026-05-28T21:06:29] Filtering genes with >=30% identity (remaining=12)
[2026-05-28T21:06:29] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-05-28T21:06:29] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-05-28T21:06:30] Searching for additional isoforms (remaining=7)
[2026-05-28T21:06:30] Assigning confidence scores to events 
[2026-05-28T21:06:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:06:31] Writing fusions to file 'SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:06:31] Writing discarded fusions to file 'SkinN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:06:39] Freeing resources
[2026-05-28T21:06:53] Done (elapsed time=00:05:51, CPU time=00:05:49, peak memory=11.9gb)