[2026-05-28T20:21:59] Launching Arriba 2.4.0
[2026-05-28T20:21:59] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:22:16] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:22:22] Reading chimeric alignments from 'BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=4468174)
[2026-05-28T20:24:27] Marking multi-mapping alignments (marked=3570653)
[2026-05-28T20:24:29] Detecting strandedness (no)
[2026-05-28T20:24:29] Annotating alignments 
[2026-05-28T20:24:46] Filtering duplicates (remaining=1048679)
[2026-05-28T20:24:48] 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=816949)
[2026-05-28T20:24:49] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=816949)
[2026-05-28T20:24:50] Filtering viral contigs with expression lower than the top 5 (remaining=816949)
[2026-05-28T20:24:52] Filtering viral contigs with less than 5% coverage (remaining=816949)
[2026-05-28T20:24:53] Estimating fragment length (mate gap mean=-59.2614, mate gap stddev=29.821, read length mean=96.7765)
[2026-05-28T20:24:53] Filtering read-through fragments with a distance <=10000bp (remaining=801813)
[2026-05-28T20:24:54] Filtering inconsistently clipped mates (remaining=770454)
[2026-05-28T20:24:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=690199)
[2026-05-28T20:24:56] Filtering fragments with small insert size (remaining=689109)
[2026-05-28T20:24:57] Filtering alignments with long gaps (remaining=689109)
[2026-05-28T20:24:58] Filtering fragments with both mates in the same gene (remaining=688390)
[2026-05-28T20:24:58] Filtering fusions arising from hairpin structures (remaining=640873)
[2026-05-28T20:24:59] Filtering reads with a mismatch p-value <=0.01 (remaining=160483)
[2026-05-28T20:25:01] Filtering reads with low entropy (k-mer content >=60%) (remaining=60301)
[2026-05-28T20:25:04] Finding fusions and counting supporting reads (total=60459)
[2026-05-28T20:25:09] Merging adjacent fusion breakpoints (remaining=60120)
[2026-05-28T20:25:09] Filtering multi-mapping fusions by alignment score and read support (remaining=21903)
[2026-05-28T20:25:24] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:25:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=21313)
[2026-05-28T20:25:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=17586)
[2026-05-28T20:25:25] Filtering fusions with <2 supporting reads (remaining=410)
[2026-05-28T20:25:25] Filtering fusions with an e-value >=0.3 (remaining=144)
[2026-05-28T20:25:26] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=146)
[2026-05-28T20:25:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=94)
[2026-05-28T20:25:27] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=94)
[2026-05-28T20:25:27] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=90)
[2026-05-28T20:25:29] Searching for fusions with spliced split reads (remaining=94)
[2026-05-28T20:25:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=80)
[2026-05-28T20:25:31] Filtering read-through fusions with breakpoints near the gene boundary (remaining=79)
[2026-05-28T20:25:31] Searching for fusions with >=4 spliced events (remaining=79)
[2026-05-28T20:25:31] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=21)
[2026-05-28T20:25:49] Filtering fusions with anchors <=23nt (remaining=19)
[2026-05-28T20:25:49] Filtering end-to-end fusions with low support (remaining=17)
[2026-05-28T20:25:49] Filtering fusions with no coverage around the breakpoints (remaining=17)
[2026-05-28T20:25:49] Indexing gene sequences 
[2026-05-28T20:25:50] Filtering genes with >=30% identity (remaining=8)
[2026-05-28T20:25:50] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-05-28T20:25:50] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-05-28T20:25:51] Searching for additional isoforms (remaining=3)
[2026-05-28T20:25:51] Assigning confidence scores to events 
[2026-05-28T20:25:51] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:25:52] Writing fusions to file 'BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:25:52] Writing discarded fusions to file 'BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:25:58] Freeing resources
[2026-05-28T20:26:05] Done (elapsed time=00:04:06, CPU time=00:04:05, peak memory=8.59gb)