[2026-05-28T20:21:24] Launching Arriba 2.4.0
[2026-05-28T20:21:24] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:21:39] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:21:44] Reading chimeric alignments from 'HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=5767714)
[2026-05-28T20:23:48] Marking multi-mapping alignments (marked=4723427)
[2026-05-28T20:23:50] Detecting strandedness (reverse)
[2026-05-28T20:23:50] Assigning strands to alignments 
[2026-05-28T20:23:51] Annotating alignments 
[2026-05-28T20:24:11] Filtering duplicates (remaining=1346433)
[2026-05-28T20:24:15] 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=1012524)
[2026-05-28T20:24:16] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1012524)
[2026-05-28T20:24:17] Filtering viral contigs with expression lower than the top 5 (remaining=1012524)
[2026-05-28T20:24:19] Filtering viral contigs with less than 5% coverage (remaining=1012524)
[2026-05-28T20:24:20] Estimating fragment length (mate gap mean=-60.0396, mate gap stddev=29.93, read length mean=96.1638)
[2026-05-28T20:24:20] Filtering read-through fragments with a distance <=10000bp (remaining=992651)
[2026-05-28T20:24:21] Filtering inconsistently clipped mates (remaining=951763)
[2026-05-28T20:24:22] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=872606)
[2026-05-28T20:24:23] Filtering fragments with small insert size (remaining=870840)
[2026-05-28T20:24:24] Filtering alignments with long gaps (remaining=870840)
[2026-05-28T20:24:25] Filtering fragments with both mates in the same gene (remaining=869811)
[2026-05-28T20:24:26] Filtering fusions arising from hairpin structures (remaining=812333)
[2026-05-28T20:24:27] Filtering reads with a mismatch p-value <=0.01 (remaining=184698)
[2026-05-28T20:24:29] Filtering reads with low entropy (k-mer content >=60%) (remaining=61929)
[2026-05-28T20:24:32] Finding fusions and counting supporting reads (total=56791)
[2026-05-28T20:24:38] Merging adjacent fusion breakpoints (remaining=56078)
[2026-05-28T20:24:38] Filtering multi-mapping fusions by alignment score and read support (remaining=23464)
[2026-05-28T20:24:58] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:25:00] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=22966)
[2026-05-28T20:25:00] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=17390)
[2026-05-28T20:25:00] Filtering fusions with <2 supporting reads (remaining=738)
[2026-05-28T20:25:00] Filtering fusions with an e-value >=0.3 (remaining=196)
[2026-05-28T20:25:00] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=197)
[2026-05-28T20:25:02] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=154)
[2026-05-28T20:25:02] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=154)
[2026-05-28T20:25:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=152)
[2026-05-28T20:25:05] Searching for fusions with spliced split reads (remaining=158)
[2026-05-28T20:25:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=137)
[2026-05-28T20:25:08] Filtering read-through fusions with breakpoints near the gene boundary (remaining=135)
[2026-05-28T20:25:08] Searching for fusions with >=4 spliced events (remaining=135)
[2026-05-28T20:25:08] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=40)
[2026-05-28T20:25:26] Filtering fusions with anchors <=23nt (remaining=28)
[2026-05-28T20:25:26] Filtering end-to-end fusions with low support (remaining=26)
[2026-05-28T20:25:26] Filtering fusions with no coverage around the breakpoints (remaining=24)
[2026-05-28T20:25:26] Indexing gene sequences 
[2026-05-28T20:25:26] Filtering genes with >=30% identity (remaining=12)
[2026-05-28T20:25:26] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-05-28T20:25:27] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-05-28T20:25:27] Searching for additional isoforms (remaining=3)
[2026-05-28T20:25:27] Assigning confidence scores to events 
[2026-05-28T20:25:28] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:25:28] Writing fusions to file 'HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:25:28] Writing discarded fusions to file 'HeadNeckN_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:25:36] Freeing resources
[2026-05-28T20:25:46] Done (elapsed time=00:04:22, CPU time=00:04:20, peak memory=9.94gb)