[2026-05-28T20:10:39] Launching Arriba 2.4.0
[2026-05-28T20:10:39] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:10:57] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:11:03] Reading chimeric alignments from 'BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=1209181)
[2026-05-28T20:11:38] Marking multi-mapping alignments (marked=1012710)
[2026-05-28T20:11:39] Detecting strandedness (no)
[2026-05-28T20:11:39] Annotating alignments 
[2026-05-28T20:11:46] Filtering duplicates (remaining=312241)
[2026-05-28T20:11:47] 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=250705)
[2026-05-28T20:11:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=250705)
[2026-05-28T20:11:47] Filtering viral contigs with expression lower than the top 5 (remaining=250705)
[2026-05-28T20:11:48] Filtering viral contigs with less than 5% coverage (remaining=250705)
[2026-05-28T20:11:48] Estimating fragment length (mate gap mean=-46.5149, mate gap stddev=27.0343, read length mean=86.965)
[2026-05-28T20:11:49] Filtering read-through fragments with a distance <=10000bp (remaining=246070)
[2026-05-28T20:11:49] Filtering inconsistently clipped mates (remaining=232313)
[2026-05-28T20:11:49] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=213451)
[2026-05-28T20:11:50] Filtering fragments with small insert size (remaining=212862)
[2026-05-28T20:11:50] Filtering alignments with long gaps (remaining=212862)
[2026-05-28T20:11:50] Filtering fragments with both mates in the same gene (remaining=212475)
[2026-05-28T20:11:51] Filtering fusions arising from hairpin structures (remaining=193620)
[2026-05-28T20:11:51] Filtering reads with a mismatch p-value <=0.01 (remaining=38369)
[2026-05-28T20:11:52] Filtering reads with low entropy (k-mer content >=60%) (remaining=12274)
[2026-05-28T20:11:52] Finding fusions and counting supporting reads (total=12520)
[2026-05-28T20:11:54] Merging adjacent fusion breakpoints (remaining=12432)
[2026-05-28T20:11:54] Filtering multi-mapping fusions by alignment score and read support (remaining=4840)
[2026-05-28T20:11:58] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:11:59] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=4716)
[2026-05-28T20:11:59] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=3562)
[2026-05-28T20:11:59] Filtering fusions with <2 supporting reads (remaining=66)
[2026-05-28T20:11:59] Filtering fusions with an e-value >=0.3 (remaining=31)
[2026-05-28T20:11:59] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=31)
[2026-05-28T20:11:59] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=16)
[2026-05-28T20:11:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=16)
[2026-05-28T20:11:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=15)
[2026-05-28T20:12:00] Searching for fusions with spliced split reads (remaining=15)
[2026-05-28T20:12:01] Selecting best breakpoints from genes with multiple breakpoints (remaining=13)
[2026-05-28T20:12:01] Filtering read-through fusions with breakpoints near the gene boundary (remaining=13)
[2026-05-28T20:12:01] Searching for fusions with >=4 spliced events (remaining=13)
[2026-05-28T20:12:01] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=4)
[2026-05-28T20:12:22] Filtering fusions with anchors <=23nt (remaining=4)
[2026-05-28T20:12:22] Filtering end-to-end fusions with low support (remaining=4)
[2026-05-28T20:12:22] Filtering fusions with no coverage around the breakpoints (remaining=4)
[2026-05-28T20:12:22] Indexing gene sequences 
[2026-05-28T20:12:22] Filtering genes with >=30% identity (remaining=3)
[2026-05-28T20:12:22] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:12:22] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:12:22] Searching for additional isoforms (remaining=0)
[2026-05-28T20:12:22] Assigning confidence scores to events 
[2026-05-28T20:12:22] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:12:23] Writing fusions to file 'BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T20:12:23] Writing discarded fusions to file 'BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T20:12:24] Freeing resources
[2026-05-28T20:12:26] Done (elapsed time=00:01:47, CPU time=00:01:46, peak memory=5.28gb)