[2026-05-28T21:20:34] Launching Arriba 2.4.0
[2026-05-28T21:20:34] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:20:47] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:20:52] Reading chimeric alignments from 'HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=20166465)
[2026-05-28T21:32:23] Marking multi-mapping alignments (marked=15388124)
[2026-05-28T21:32:33] Detecting strandedness (reverse)
[2026-05-28T21:32:33] Assigning strands to alignments 
[2026-05-28T21:32:38] Annotating alignments 
[2026-05-28T21:34:07] Filtering duplicates (remaining=5507530)
[2026-05-28T21:34:21] 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=4781356)
[2026-05-28T21:34:25] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4781356)
[2026-05-28T21:34:29] Filtering viral contigs with expression lower than the top 5 (remaining=4781356)
[2026-05-28T21:34:38] Filtering viral contigs with less than 5% coverage (remaining=4781356)
[2026-05-28T21:34:43] Estimating fragment length (mate gap mean=-74.8133, mate gap stddev=28.3492, read length mean=110.003)
[2026-05-28T21:34:43] Filtering read-through fragments with a distance <=10000bp (remaining=4681079)
[2026-05-28T21:34:47] Filtering inconsistently clipped mates (remaining=4570147)
[2026-05-28T21:34:51] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4035961)
[2026-05-28T21:34:58] Filtering fragments with small insert size (remaining=4033351)
[2026-05-28T21:35:02] Filtering alignments with long gaps (remaining=4033351)
[2026-05-28T21:35:07] Filtering fragments with both mates in the same gene (remaining=4031862)
[2026-05-28T21:35:11] Filtering fusions arising from hairpin structures (remaining=3848900)
[2026-05-28T21:35:16] Filtering reads with a mismatch p-value <=0.01 (remaining=1105481)
[2026-05-28T21:35:27] Filtering reads with low entropy (k-mer content >=60%) (remaining=434346)
[2026-05-28T21:35:38] Finding fusions and counting supporting reads (total=415596)
[2026-05-28T21:36:09] Merging adjacent fusion breakpoints (remaining=411975)
[2026-05-28T21:36:11] Filtering multi-mapping fusions by alignment score and read support (remaining=172200)
[2026-05-28T21:37:21] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:37:29] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=170049)
[2026-05-28T21:37:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=134877)
[2026-05-28T21:37:30] Filtering fusions with <2 supporting reads (remaining=6146)
[2026-05-28T21:37:31] Filtering fusions with an e-value >=0.3 (remaining=1297)
[2026-05-28T21:37:32] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1308)
[2026-05-28T21:37:37] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1135)
[2026-05-28T21:37:38] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1135)
[2026-05-28T21:37:39] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1134)
[2026-05-28T21:37:47] Searching for fusions with spliced split reads (remaining=1212)
[2026-05-28T21:37:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=939)
[2026-05-28T21:37:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=931)
[2026-05-28T21:37:56] Searching for fusions with >=4 spliced events (remaining=983)
[2026-05-28T21:37:58] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=318)
[2026-05-28T21:38:16] Filtering fusions with anchors <=23nt (remaining=283)
[2026-05-28T21:38:17] Filtering end-to-end fusions with low support (remaining=277)
[2026-05-28T21:38:18] Filtering fusions with no coverage around the breakpoints (remaining=276)
[2026-05-28T21:38:18] Indexing gene sequences 
[2026-05-28T21:38:21] Filtering genes with >=30% identity (remaining=135)
[2026-05-28T21:38:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=79)
[2026-05-28T21:38:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=79)
[2026-05-28T21:38:25] Searching for additional isoforms (remaining=84)
[2026-05-28T21:38:26] Assigning confidence scores to events 
[2026-05-28T21:38:30] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:38:30] Writing fusions to file 'HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:38:31] Writing discarded fusions to file 'HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:39:02] Freeing resources
[2026-05-28T21:39:40] Done (elapsed time=00:19:06, CPU time=00:19:05, peak memory=24.9gb)