[2026-05-28T20:12:13] Launching Arriba 2.4.0
[2026-05-28T20:12:13] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:12:30] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:12:36] Reading chimeric alignments from 'HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=2342492)
[2026-05-28T20:13:22] Marking multi-mapping alignments (marked=1984572)
[2026-05-28T20:13:23] Detecting strandedness (reverse)
[2026-05-28T20:13:23] Assigning strands to alignments 
[2026-05-28T20:13:24] Annotating alignments 
[2026-05-28T20:13:31] Filtering duplicates (remaining=599502)
[2026-05-28T20:13:33] 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=463897)
[2026-05-28T20:13:33] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=463897)
[2026-05-28T20:13:33] Filtering viral contigs with expression lower than the top 5 (remaining=463897)
[2026-05-28T20:13:34] Filtering viral contigs with less than 5% coverage (remaining=463897)
[2026-05-28T20:13:35] Estimating fragment length (mate gap mean=-47.3317, mate gap stddev=27.397, read length mean=86.4494)
[2026-05-28T20:13:35] Filtering read-through fragments with a distance <=10000bp (remaining=456113)
[2026-05-28T20:13:35] Filtering inconsistently clipped mates (remaining=433940)
[2026-05-28T20:13:36] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=398053)
[2026-05-28T20:13:36] Filtering fragments with small insert size (remaining=397240)
[2026-05-28T20:13:37] Filtering alignments with long gaps (remaining=397240)
[2026-05-28T20:13:37] Filtering fragments with both mates in the same gene (remaining=396534)
[2026-05-28T20:13:37] Filtering fusions arising from hairpin structures (remaining=368208)
[2026-05-28T20:13:38] Filtering reads with a mismatch p-value <=0.01 (remaining=62871)
[2026-05-28T20:13:39] Filtering reads with low entropy (k-mer content >=60%) (remaining=20432)
[2026-05-28T20:13:40] Finding fusions and counting supporting reads (total=19170)
[2026-05-28T20:13:42] Merging adjacent fusion breakpoints (remaining=19012)
[2026-05-28T20:13:42] Filtering multi-mapping fusions by alignment score and read support (remaining=7404)
[2026-05-28T20:13:49] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:13:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=7228)
[2026-05-28T20:13:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=5491)
[2026-05-28T20:13:49] Filtering fusions with <2 supporting reads (remaining=180)
[2026-05-28T20:13:49] Filtering fusions with an e-value >=0.3 (remaining=69)
[2026-05-28T20:13:49] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=70)
[2026-05-28T20:13:50] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=49)
[2026-05-28T20:13:50] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=50)
[2026-05-28T20:13:50] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=48)
[2026-05-28T20:13:51] Searching for fusions with spliced split reads (remaining=48)
[2026-05-28T20:13:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=43)
[2026-05-28T20:13:52] Filtering read-through fusions with breakpoints near the gene boundary (remaining=42)
[2026-05-28T20:13:52] Searching for fusions with >=4 spliced events (remaining=42)
[2026-05-28T20:13:52] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15)
[2026-05-28T20:14:07] Filtering fusions with anchors <=23nt (remaining=11)
[2026-05-28T20:14:08] Filtering end-to-end fusions with low support (remaining=11)
[2026-05-28T20:14:08] Filtering fusions with no coverage around the breakpoints (remaining=11)
[2026-05-28T20:14:08] Indexing gene sequences 
[2026-05-28T20:14:08] Filtering genes with >=30% identity (remaining=7)
[2026-05-28T20:14:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:14:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:14:08] Searching for additional isoforms (remaining=0)
[2026-05-28T20:14:08] Assigning confidence scores to events 
[2026-05-28T20:14:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:14:09] Writing fusions to file 'HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:14:09] Writing discarded fusions to file 'HeadNeckN_FFPE_L05_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:14:12] Freeing resources
[2026-05-28T20:14:15] Done (elapsed time=00:02:02, CPU time=00:02:01, peak memory=6.39gb)