[2026-06-08T07:56:41] Launching Arriba 2.4.0
[2026-06-08T07:56:41] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:56:51] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:56:55] Reading chimeric alignments from 'HeadNeckN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=10852087)
[2026-06-08T08:01:20] Marking multi-mapping alignments (marked=8555647)
[2026-06-08T08:01:25] Detecting strandedness (reverse)
[2026-06-08T08:01:25] Assigning strands to alignments 
[2026-06-08T08:01:28] Annotating alignments 
[2026-06-08T08:02:10] Filtering duplicates (remaining=2273116)
[2026-06-08T08:02:17] 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=1773891)
[2026-06-08T08:02:19] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1773891)
[2026-06-08T08:02:21] Filtering viral contigs with expression lower than the top 5 (remaining=1773891)
[2026-06-08T08:02:25] Filtering viral contigs with less than 5% coverage (remaining=1773891)
[2026-06-08T08:02:28] Estimating fragment length (mate gap mean=-67.6046, mate gap stddev=28.9525, read length mean=104.074)
[2026-06-08T08:02:28] Filtering read-through fragments with a distance <=10000bp (remaining=1735818)
[2026-06-08T08:02:31] Filtering inconsistently clipped mates (remaining=1682193)
[2026-06-08T08:02:33] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1515240)
[2026-06-08T08:02:36] Filtering fragments with small insert size (remaining=1513653)
[2026-06-08T08:02:38] Filtering alignments with long gaps (remaining=1513653)
[2026-06-08T08:02:41] Filtering fragments with both mates in the same gene (remaining=1512651)
[2026-06-08T08:02:43] Filtering fusions arising from hairpin structures (remaining=1431073)
[2026-06-08T08:02:46] Filtering reads with a mismatch p-value <=0.01 (remaining=411933)
[2026-06-08T08:02:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=136574)
[2026-06-08T08:02:56] Finding fusions and counting supporting reads (total=126576)
[2026-06-08T08:03:11] Merging adjacent fusion breakpoints (remaining=125214)
[2026-06-08T08:03:12] Filtering multi-mapping fusions by alignment score and read support (remaining=50922)
[2026-06-08T08:03:49] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:03:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=49880)
[2026-06-08T08:03:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=39160)
[2026-06-08T08:03:53] Filtering fusions with <2 supporting reads (remaining=1887)
[2026-06-08T08:03:54] Filtering fusions with an e-value >=0.3 (remaining=439)
[2026-06-08T08:03:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=445)
[2026-06-08T08:03:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=349)
[2026-06-08T08:03:57] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=349)
[2026-06-08T08:03:58] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=349)
[2026-06-08T08:04:02] Searching for fusions with spliced split reads (remaining=365)
[2026-06-08T08:04:07] Selecting best breakpoints from genes with multiple breakpoints (remaining=312)
[2026-06-08T08:04:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=307)
[2026-06-08T08:04:08] Searching for fusions with >=4 spliced events (remaining=311)
[2026-06-08T08:04:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=68)
[2026-06-08T08:04:28] Filtering fusions with anchors <=23nt (remaining=47)
[2026-06-08T08:04:28] Filtering end-to-end fusions with low support (remaining=45)
[2026-06-08T08:04:29] Filtering fusions with no coverage around the breakpoints (remaining=45)
[2026-06-08T08:04:29] Indexing gene sequences 
[2026-06-08T08:04:30] Filtering genes with >=30% identity (remaining=18)
[2026-06-08T08:04:30] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-06-08T08:04:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-06-08T08:04:32] Searching for additional isoforms (remaining=3)
[2026-06-08T08:04:32] Assigning confidence scores to events 
[2026-06-08T08:04:34] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:04:34] Writing fusions to file 'HeadNeckN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:04:34] Writing discarded fusions to file 'HeadNeckN_FFPE_L09_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:04:48] Freeing resources
[2026-06-08T08:05:10] Done (elapsed time=00:08:29, CPU time=00:08:27, peak memory=15gb)