[2026-05-28T20:31:02] Launching Arriba 2.4.0
[2026-05-28T20:31:02] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:31:17] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:31:23] Reading chimeric alignments from 'HeadNeckN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=5148035)
[2026-05-28T20:33:37] Marking multi-mapping alignments (marked=3908255)
[2026-05-28T20:33:40] Detecting strandedness (no)
[2026-05-28T20:33:40] Annotating alignments 
[2026-05-28T20:34:02] Filtering duplicates (remaining=1075225)
[2026-05-28T20:34:05] 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=925798)
[2026-05-28T20:34:06] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=925798)
[2026-05-28T20:34:07] Filtering viral contigs with expression lower than the top 5 (remaining=925798)
[2026-05-28T20:34:09] Filtering viral contigs with less than 5% coverage (remaining=925798)
[2026-05-28T20:34:11] Estimating fragment length (mate gap mean=-65.3681, mate gap stddev=29.7538, read length mean=100.885)
[2026-05-28T20:34:11] Filtering read-through fragments with a distance <=10000bp (remaining=903589)
[2026-05-28T20:34:12] Filtering inconsistently clipped mates (remaining=868842)
[2026-05-28T20:34:13] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=787807)
[2026-05-28T20:34:14] Filtering fragments with small insert size (remaining=786807)
[2026-05-28T20:34:15] Filtering alignments with long gaps (remaining=786807)
[2026-05-28T20:34:16] Filtering fragments with both mates in the same gene (remaining=785968)
[2026-05-28T20:34:17] Filtering fusions arising from hairpin structures (remaining=736272)
[2026-05-28T20:34:18] Filtering reads with a mismatch p-value <=0.01 (remaining=179732)
[2026-05-28T20:34:20] Filtering reads with low entropy (k-mer content >=60%) (remaining=63836)
[2026-05-28T20:34:22] Finding fusions and counting supporting reads (total=65279)
[2026-05-28T20:34:29] Merging adjacent fusion breakpoints (remaining=64911)
[2026-05-28T20:34:30] Filtering multi-mapping fusions by alignment score and read support (remaining=26903)
[2026-05-28T20:34:46] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:34:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=26535)
[2026-05-28T20:34:47] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=20097)
[2026-05-28T20:34:47] Filtering fusions with <2 supporting reads (remaining=589)
[2026-05-28T20:34:48] Filtering fusions with an e-value >=0.3 (remaining=173)
[2026-05-28T20:34:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=175)
[2026-05-28T20:34:49] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=137)
[2026-05-28T20:34:49] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=137)
[2026-05-28T20:34:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=135)
[2026-05-28T20:34:51] Searching for fusions with spliced split reads (remaining=138)
[2026-05-28T20:34:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=118)
[2026-05-28T20:34:53] Filtering read-through fusions with breakpoints near the gene boundary (remaining=115)
[2026-05-28T20:34:54] Searching for fusions with >=4 spliced events (remaining=115)
[2026-05-28T20:34:54] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=28)
[2026-05-28T20:35:11] Filtering fusions with anchors <=23nt (remaining=20)
[2026-05-28T20:35:11] Filtering end-to-end fusions with low support (remaining=18)
[2026-05-28T20:35:11] Filtering fusions with no coverage around the breakpoints (remaining=16)
[2026-05-28T20:35:11] Indexing gene sequences 
[2026-05-28T20:35:12] Filtering genes with >=30% identity (remaining=4)
[2026-05-28T20:35:12] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=2)
[2026-05-28T20:35:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=2)
[2026-05-28T20:35:12] Searching for additional isoforms (remaining=2)
[2026-05-28T20:35:12] Assigning confidence scores to events 
[2026-05-28T20:35:13] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:35:13] Writing fusions to file 'HeadNeckN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:35:14] Writing discarded fusions to file 'HeadNeckN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:35:20] Freeing resources
[2026-05-28T20:35:29] Done (elapsed time=00:04:27, CPU time=00:04:26, peak memory=9.26gb)