[2026-05-28T20:14:06] Launching Arriba 2.4.0
[2026-05-28T20:14:06] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:14:19] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:14:23] Reading chimeric alignments from 'BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=3508132)
[2026-05-28T20:15:29] Marking multi-mapping alignments (marked=2877480)
[2026-05-28T20:15:31] Detecting strandedness (no)
[2026-05-28T20:15:31] Annotating alignments 
[2026-05-28T20:15:42] Filtering duplicates (remaining=958800)
[2026-05-28T20:15:44] 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=739020)
[2026-05-28T20:15:44] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=739020)
[2026-05-28T20:15:45] Filtering viral contigs with expression lower than the top 5 (remaining=739020)
[2026-05-28T20:15:46] Filtering viral contigs with less than 5% coverage (remaining=739020)
[2026-05-28T20:15:47] Estimating fragment length (mate gap mean=-51.1329, mate gap stddev=28.8609, read length mean=88.1228)
[2026-05-28T20:15:47] Filtering read-through fragments with a distance <=10000bp (remaining=727835)
[2026-05-28T20:15:48] Filtering inconsistently clipped mates (remaining=701190)
[2026-05-28T20:15:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=636534)
[2026-05-28T20:15:49] Filtering fragments with small insert size (remaining=635584)
[2026-05-28T20:15:50] Filtering alignments with long gaps (remaining=635584)
[2026-05-28T20:15:50] Filtering fragments with both mates in the same gene (remaining=634939)
[2026-05-28T20:15:51] Filtering fusions arising from hairpin structures (remaining=597798)
[2026-05-28T20:15:52] Filtering reads with a mismatch p-value <=0.01 (remaining=108437)
[2026-05-28T20:15:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=39606)
[2026-05-28T20:15:54] Finding fusions and counting supporting reads (total=38752)
[2026-05-28T20:15:58] Merging adjacent fusion breakpoints (remaining=38476)
[2026-05-28T20:15:58] Filtering multi-mapping fusions by alignment score and read support (remaining=16339)
[2026-05-28T20:16:08] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:16:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=15955)
[2026-05-28T20:16:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=13163)
[2026-05-28T20:16:09] Filtering fusions with <2 supporting reads (remaining=359)
[2026-05-28T20:16:09] Filtering fusions with an e-value >=0.3 (remaining=122)
[2026-05-28T20:16:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=122)
[2026-05-28T20:16:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=90)
[2026-05-28T20:16:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=90)
[2026-05-28T20:16:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=85)
[2026-05-28T20:16:11] Searching for fusions with spliced split reads (remaining=85)
[2026-05-28T20:16:13] Selecting best breakpoints from genes with multiple breakpoints (remaining=79)
[2026-05-28T20:16:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=77)
[2026-05-28T20:16:13] Searching for fusions with >=4 spliced events (remaining=77)
[2026-05-28T20:16:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=21)
[2026-05-28T20:16:27] Filtering fusions with anchors <=23nt (remaining=14)
[2026-05-28T20:16:27] Filtering end-to-end fusions with low support (remaining=14)
[2026-05-28T20:16:27] Filtering fusions with no coverage around the breakpoints (remaining=13)
[2026-05-28T20:16:27] Indexing gene sequences 
[2026-05-28T20:16:27] Filtering genes with >=30% identity (remaining=4)
[2026-05-28T20:16:28] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:16:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:16:28] Searching for additional isoforms (remaining=0)
[2026-05-28T20:16:28] Assigning confidence scores to events 
[2026-05-28T20:16:29] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:16:29] Writing fusions to file 'BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:16:29] Writing discarded fusions to file 'BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:16:33] Freeing resources
[2026-05-28T20:16:38] Done (elapsed time=00:02:32, CPU time=00:02:31, peak memory=7.64gb)