[2026-06-08T08:29:54] Launching Arriba 2.4.0
[2026-06-08T08:29:54] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:30:03] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:30:07] Reading chimeric alignments from 'HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=20166465)
[2026-06-08T08:37:23] Marking multi-mapping alignments (marked=15388124)
[2026-06-08T08:37:31] Detecting strandedness (reverse)
[2026-06-08T08:37:31] Assigning strands to alignments 
[2026-06-08T08:37:35] Annotating alignments 
[2026-06-08T08:38:41] Filtering duplicates (remaining=5507530)
[2026-06-08T08:38:51] 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)
[2026-06-08T08:38:55] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=4781356)
[2026-06-08T08:38:59] Filtering viral contigs with expression lower than the top 5 (remaining=4781356)
[2026-06-08T08:39:06] Filtering viral contigs with less than 5% coverage (remaining=4781356)
[2026-06-08T08:39:11] Estimating fragment length (mate gap mean=-74.8133, mate gap stddev=28.3492, read length mean=110.003)
[2026-06-08T08:39:11] Filtering read-through fragments with a distance <=10000bp (remaining=4681079)
[2026-06-08T08:39:15] Filtering inconsistently clipped mates (remaining=4570147)
[2026-06-08T08:39:18] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=4035961)
[2026-06-08T08:39:24] Filtering fragments with small insert size (remaining=4033351)
[2026-06-08T08:39:28] Filtering alignments with long gaps (remaining=4033351)
[2026-06-08T08:39:32] Filtering fragments with both mates in the same gene (remaining=4031862)
[2026-06-08T08:39:36] Filtering fusions arising from hairpin structures (remaining=3848900)
[2026-06-08T08:39:40] Filtering reads with a mismatch p-value <=0.01 (remaining=1105481)
[2026-06-08T08:39:51] Filtering reads with low entropy (k-mer content >=60%) (remaining=434346)
[2026-06-08T08:40:02] Finding fusions and counting supporting reads (total=415596)
[2026-06-08T08:40:26] Merging adjacent fusion breakpoints (remaining=411975)
[2026-06-08T08:40:28] Filtering multi-mapping fusions by alignment score and read support (remaining=172200)
[2026-06-08T08:41:27] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:41:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=170049)
[2026-06-08T08:41:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=134877)
[2026-06-08T08:41:35] Filtering fusions with <2 supporting reads (remaining=6146)
[2026-06-08T08:41:36] Filtering fusions with an e-value >=0.3 (remaining=1297)
[2026-06-08T08:41:36] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=1308)
[2026-06-08T08:41:42] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=1135)
[2026-06-08T08:41:43] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=1135)
[2026-06-08T08:41:44] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=1134)
[2026-06-08T08:41:52] Searching for fusions with spliced split reads (remaining=1212)
[2026-06-08T08:42:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=939)
[2026-06-08T08:42:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=931)
[2026-06-08T08:42:03] Searching for fusions with >=4 spliced events (remaining=983)
[2026-06-08T08:42:04] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=318)
[2026-06-08T08:42:18] Filtering fusions with anchors <=23nt (remaining=283)
[2026-06-08T08:42:19] Filtering end-to-end fusions with low support (remaining=277)
[2026-06-08T08:42:19] Filtering fusions with no coverage around the breakpoints (remaining=276)
[2026-06-08T08:42:20] Indexing gene sequences 
[2026-06-08T08:42:22] Filtering genes with >=30% identity (remaining=135)
[2026-06-08T08:42:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=79)
[2026-06-08T08:42:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=79)
[2026-06-08T08:42:27] Searching for additional isoforms (remaining=84)
[2026-06-08T08:42:28] Assigning confidence scores to events 
[2026-06-08T08:42:31] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:42:31] Writing fusions to file 'HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:42:32] Writing discarded fusions to file 'HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:43:01] Freeing resources
[2026-06-08T08:43:31] Done (elapsed time=00:13:37, CPU time=00:13:35, peak memory=24.8gb)