[2026-05-28T20:53:10] Launching Arriba 2.4.0
[2026-05-28T20:53:10] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:53:26] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:53:33] Reading chimeric alignments from 'HeadNeckN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=13281451)
[2026-05-28T20:59:39] Marking multi-mapping alignments (marked=10907933)
[2026-05-28T20:59:45] Detecting strandedness (reverse)
[2026-05-28T20:59:45] Assigning strands to alignments 
[2026-05-28T20:59:47] Annotating alignments 
[2026-05-28T21:00:30] Filtering duplicates (remaining=2306239)
[2026-05-28T21:00:36] 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=1699884)
[2026-05-28T21:00:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1699884)
[2026-05-28T21:00:41] Filtering viral contigs with expression lower than the top 5 (remaining=1699884)
[2026-05-28T21:00:45] Filtering viral contigs with less than 5% coverage (remaining=1699884)
[2026-05-28T21:00:48] Estimating fragment length (mate gap mean=-68.4981, mate gap stddev=30.3739, read length mean=100.758)
[2026-05-28T21:00:48] Filtering read-through fragments with a distance <=10000bp (remaining=1655764)
[2026-05-28T21:00:50] Filtering inconsistently clipped mates (remaining=1600127)
[2026-05-28T21:00:52] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1470999)
[2026-05-28T21:00:55] Filtering fragments with small insert size (remaining=1468994)
[2026-05-28T21:00:58] Filtering alignments with long gaps (remaining=1468994)
[2026-05-28T21:01:00] Filtering fragments with both mates in the same gene (remaining=1467914)
[2026-05-28T21:01:02] Filtering fusions arising from hairpin structures (remaining=1385437)
[2026-05-28T21:01:05] Filtering reads with a mismatch p-value <=0.01 (remaining=333091)
[2026-05-28T21:01:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=123864)
[2026-05-28T21:01:15] Finding fusions and counting supporting reads (total=98075)
[2026-05-28T21:01:28] Merging adjacent fusion breakpoints (remaining=95386)
[2026-05-28T21:01:29] Filtering multi-mapping fusions by alignment score and read support (remaining=38053)
[2026-05-28T21:02:01] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:02:04] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=37344)
[2026-05-28T21:02:04] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=29460)
[2026-05-28T21:02:05] Filtering fusions with <2 supporting reads (remaining=2279)
[2026-05-28T21:02:05] Filtering fusions with an e-value >=0.3 (remaining=501)
[2026-05-28T21:02:05] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=503)
[2026-05-28T21:02:08] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=430)
[2026-05-28T21:02:08] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=430)
[2026-05-28T21:02:08] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=342)
[2026-05-28T21:02:12] Searching for fusions with spliced split reads (remaining=360)
[2026-05-28T21:02:16] Selecting best breakpoints from genes with multiple breakpoints (remaining=230)
[2026-05-28T21:02:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=228)
[2026-05-28T21:02:17] Searching for fusions with >=4 spliced events (remaining=232)
[2026-05-28T21:02:17] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=70)
[2026-05-28T21:02:33] Filtering fusions with anchors <=23nt (remaining=49)
[2026-05-28T21:02:33] Filtering end-to-end fusions with low support (remaining=49)
[2026-05-28T21:02:34] Filtering fusions with no coverage around the breakpoints (remaining=45)
[2026-05-28T21:02:34] Indexing gene sequences 
[2026-05-28T21:02:34] Filtering genes with >=30% identity (remaining=26)
[2026-05-28T21:02:35] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=4)
[2026-05-28T21:02:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=4)
[2026-05-28T21:02:35] Searching for additional isoforms (remaining=5)
[2026-05-28T21:02:36] Assigning confidence scores to events 
[2026-05-28T21:02:37] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:02:37] Writing fusions to file 'HeadNeckN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:02:37] Writing discarded fusions to file 'HeadNeckN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:02:48] Freeing resources
[2026-05-28T21:03:06] Done (elapsed time=00:09:56, CPU time=00:09:55, peak memory=17.4gb)