[2026-05-28T20:20:00] Launching Arriba 2.4.0
[2026-05-28T20:20:00] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:20:20] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:20:26] Reading chimeric alignments from 'BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=4736269)
[2026-05-28T20:22:18] Marking multi-mapping alignments (marked=3872441)
[2026-05-28T20:22:21] Detecting strandedness (no)
[2026-05-28T20:22:21] Annotating alignments 
[2026-05-28T20:22:47] Filtering duplicates (remaining=1185863)
[2026-05-28T20:22:50] 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=934856)
[2026-05-28T20:22:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=934856)
[2026-05-28T20:22:52] Filtering viral contigs with expression lower than the top 5 (remaining=934856)
[2026-05-28T20:22:54] Filtering viral contigs with less than 5% coverage (remaining=934856)
[2026-05-28T20:22:55] Estimating fragment length (mate gap mean=-59.7051, mate gap stddev=29.1254, read length mean=94.9748)
[2026-05-28T20:22:56] Filtering read-through fragments with a distance <=10000bp (remaining=918255)
[2026-05-28T20:22:57] Filtering inconsistently clipped mates (remaining=884757)
[2026-05-28T20:22:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=792285)
[2026-05-28T20:22:59] Filtering fragments with small insert size (remaining=791011)
[2026-05-28T20:23:00] Filtering alignments with long gaps (remaining=791011)
[2026-05-28T20:23:01] Filtering fragments with both mates in the same gene (remaining=790172)
[2026-05-28T20:23:02] Filtering fusions arising from hairpin structures (remaining=741739)
[2026-05-28T20:23:03] Filtering reads with a mismatch p-value <=0.01 (remaining=175085)
[2026-05-28T20:23:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=69244)
[2026-05-28T20:23:07] Finding fusions and counting supporting reads (total=70498)
[2026-05-28T20:23:13] Merging adjacent fusion breakpoints (remaining=70177)
[2026-05-28T20:23:13] Filtering multi-mapping fusions by alignment score and read support (remaining=25636)
[2026-05-28T20:23:28] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:23:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=25078)
[2026-05-28T20:23:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=21219)
[2026-05-28T20:23:30] Filtering fusions with <2 supporting reads (remaining=491)
[2026-05-28T20:23:30] Filtering fusions with an e-value >=0.3 (remaining=169)
[2026-05-28T20:23:30] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=170)
[2026-05-28T20:23:31] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=121)
[2026-05-28T20:23:32] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=121)
[2026-05-28T20:23:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=116)
[2026-05-28T20:23:34] Searching for fusions with spliced split reads (remaining=121)
[2026-05-28T20:23:35] Selecting best breakpoints from genes with multiple breakpoints (remaining=108)
[2026-05-28T20:23:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=105)
[2026-05-28T20:23:36] Searching for fusions with >=4 spliced events (remaining=105)
[2026-05-28T20:23:36] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=27)
[2026-05-28T20:23:52] Filtering fusions with anchors <=23nt (remaining=22)
[2026-05-28T20:23:52] Filtering end-to-end fusions with low support (remaining=22)
[2026-05-28T20:23:52] Filtering fusions with no coverage around the breakpoints (remaining=20)
[2026-05-28T20:23:53] Indexing gene sequences 
[2026-05-28T20:23:53] Filtering genes with >=30% identity (remaining=5)
[2026-05-28T20:23:53] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:23:53] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:23:54] Searching for additional isoforms (remaining=0)
[2026-05-28T20:23:54] Assigning confidence scores to events 
[2026-05-28T20:23:55] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:23:55] Writing fusions to file 'BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:23:55] Writing discarded fusions to file 'BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:24:02] Freeing resources
[2026-05-28T20:24:09] Done (elapsed time=00:04:09, CPU time=00:04:09, peak memory=8.88gb)