[2026-05-28T20:35:06] Launching Arriba 2.4.0
[2026-05-28T20:35:06] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:35:20] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:35:25] Reading chimeric alignments from 'HeadNeckN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=9009343)
[2026-05-28T20:39:26] Marking multi-mapping alignments (marked=7160444)
[2026-05-28T20:39:30] Detecting strandedness (reverse)
[2026-05-28T20:39:30] Assigning strands to alignments 
[2026-05-28T20:39:32] Annotating alignments 
[2026-05-28T20:40:14] Filtering duplicates (remaining=1824560)
[2026-05-28T20:40:21] 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=1459112)
[2026-05-28T20:40:22] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1459112)
[2026-05-28T20:40:24] Filtering viral contigs with expression lower than the top 5 (remaining=1459112)
[2026-05-28T20:40:28] Filtering viral contigs with less than 5% coverage (remaining=1459112)
[2026-05-28T20:40:30] Estimating fragment length (mate gap mean=-62.6069, mate gap stddev=30.2734, read length mean=95.4619)
[2026-05-28T20:40:31] Filtering read-through fragments with a distance <=10000bp (remaining=1425291)
[2026-05-28T20:40:33] Filtering inconsistently clipped mates (remaining=1375782)
[2026-05-28T20:40:34] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=1255139)
[2026-05-28T20:40:37] Filtering fragments with small insert size (remaining=1253307)
[2026-05-28T20:40:39] Filtering alignments with long gaps (remaining=1253307)
[2026-05-28T20:40:41] Filtering fragments with both mates in the same gene (remaining=1252054)
[2026-05-28T20:40:43] Filtering fusions arising from hairpin structures (remaining=1183481)
[2026-05-28T20:40:45] Filtering reads with a mismatch p-value <=0.01 (remaining=248973)
[2026-05-28T20:40:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=86423)
[2026-05-28T20:40:54] Finding fusions and counting supporting reads (total=76794)
[2026-05-28T20:41:10] Merging adjacent fusion breakpoints (remaining=75628)
[2026-05-28T20:41:11] Filtering multi-mapping fusions by alignment score and read support (remaining=31812)
[2026-05-28T20:41:46] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:41:49] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=31304)
[2026-05-28T20:41:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=24607)
[2026-05-28T20:41:50] Filtering fusions with <2 supporting reads (remaining=1325)
[2026-05-28T20:41:50] Filtering fusions with an e-value >=0.3 (remaining=282)
[2026-05-28T20:41:50] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=287)
[2026-05-28T20:41:53] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=248)
[2026-05-28T20:41:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=248)
[2026-05-28T20:41:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=233)
[2026-05-28T20:41:58] Searching for fusions with spliced split reads (remaining=244)
[2026-05-28T20:42:02] Selecting best breakpoints from genes with multiple breakpoints (remaining=178)
[2026-05-28T20:42:02] Filtering read-through fusions with breakpoints near the gene boundary (remaining=178)
[2026-05-28T20:42:02] Searching for fusions with >=4 spliced events (remaining=182)
[2026-05-28T20:42:03] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=51)
[2026-05-28T20:42:21] Filtering fusions with anchors <=23nt (remaining=33)
[2026-05-28T20:42:21] Filtering end-to-end fusions with low support (remaining=29)
[2026-05-28T20:42:22] Filtering fusions with no coverage around the breakpoints (remaining=29)
[2026-05-28T20:42:22] Indexing gene sequences 
[2026-05-28T20:42:23] Filtering genes with >=30% identity (remaining=18)
[2026-05-28T20:42:23] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=8)
[2026-05-28T20:42:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=5)
[2026-05-28T20:42:24] Searching for additional isoforms (remaining=5)
[2026-05-28T20:42:24] Assigning confidence scores to events 
[2026-05-28T20:42:26] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:42:27] Writing fusions to file 'HeadNeckN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:42:27] Writing discarded fusions to file 'HeadNeckN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:42:39] Freeing resources
[2026-05-28T20:42:55] Done (elapsed time=00:07:49, CPU time=00:07:48, peak memory=13.1gb)