[2026-05-28T20:54:04] Launching Arriba 2.4.0
[2026-05-28T20:54:04] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:54:22] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:54:28] Reading chimeric alignments from 'BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=6285883)
[2026-05-28T20:57:13] Marking multi-mapping alignments (marked=4898094)
[2026-05-28T20:57:16] Detecting strandedness (no)
[2026-05-28T20:57:16] Annotating alignments 
[2026-05-28T20:57:43] Filtering duplicates (remaining=1380632)
[2026-05-28T20:57:46] 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=1158332)
[2026-05-28T20:57:47] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=1158332)
[2026-05-28T20:57:49] Filtering viral contigs with expression lower than the top 5 (remaining=1158332)
[2026-05-28T20:57:51] Filtering viral contigs with less than 5% coverage (remaining=1158332)
[2026-05-28T20:57:53] Estimating fragment length (mate gap mean=-63.6739, mate gap stddev=30.5003, read length mean=98.9408)
[2026-05-28T20:57:53] Filtering read-through fragments with a distance <=10000bp (remaining=1136771)
[2026-05-28T20:57:54] Filtering inconsistently clipped mates (remaining=1090308)
[2026-05-28T20:57:55] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=981426)
[2026-05-28T20:57:57] Filtering fragments with small insert size (remaining=979712)
[2026-05-28T20:57:58] Filtering alignments with long gaps (remaining=979712)
[2026-05-28T20:57:59] Filtering fragments with both mates in the same gene (remaining=978728)
[2026-05-28T20:58:00] Filtering fusions arising from hairpin structures (remaining=912625)
[2026-05-28T20:58:02] Filtering reads with a mismatch p-value <=0.01 (remaining=220793)
[2026-05-28T20:58:05] Filtering reads with low entropy (k-mer content >=60%) (remaining=79551)
[2026-05-28T20:58:08] Finding fusions and counting supporting reads (total=82166)
[2026-05-28T20:58:15] Merging adjacent fusion breakpoints (remaining=81702)
[2026-05-28T20:58:15] Filtering multi-mapping fusions by alignment score and read support (remaining=31825)
[2026-05-28T20:58:32] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:58:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=31300)
[2026-05-28T20:58:34] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=25145)
[2026-05-28T20:58:34] Filtering fusions with <2 supporting reads (remaining=653)
[2026-05-28T20:58:35] Filtering fusions with an e-value >=0.3 (remaining=195)
[2026-05-28T20:58:35] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=195)
[2026-05-28T20:58:36] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=147)
[2026-05-28T20:58:36] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=147)
[2026-05-28T20:58:37] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=144)
[2026-05-28T20:58:39] Searching for fusions with spliced split reads (remaining=154)
[2026-05-28T20:58:40] Selecting best breakpoints from genes with multiple breakpoints (remaining=129)
[2026-05-28T20:58:41] Filtering read-through fusions with breakpoints near the gene boundary (remaining=126)
[2026-05-28T20:58:41] Searching for fusions with >=4 spliced events (remaining=126)
[2026-05-28T20:58:41] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=34)
[2026-05-28T20:58:55] Filtering fusions with anchors <=23nt (remaining=28)
[2026-05-28T20:58:55] Filtering end-to-end fusions with low support (remaining=25)
[2026-05-28T20:58:56] Filtering fusions with no coverage around the breakpoints (remaining=24)
[2026-05-28T20:58:56] Indexing gene sequences 
[2026-05-28T20:58:56] Filtering genes with >=30% identity (remaining=7)
[2026-05-28T20:58:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:58:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:58:57] Searching for additional isoforms (remaining=0)
[2026-05-28T20:58:57] Assigning confidence scores to events 
[2026-05-28T20:58:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:58:58] Writing fusions to file 'BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:58:58] Writing discarded fusions to file 'BreastNB_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:59:05] Freeing resources
[2026-05-28T20:59:14] Done (elapsed time=00:05:10, CPU time=00:05:09, peak memory=10.4gb)