[2026-05-28T20:15:15] Launching Arriba 2.4.0
[2026-05-28T20:15:15] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:15:28] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:15:33] Reading chimeric alignments from 'BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=3681535)
[2026-05-28T20:16:42] Marking multi-mapping alignments (marked=3005325)
[2026-05-28T20:16:44] Detecting strandedness (no)
[2026-05-28T20:16:44] Annotating alignments 
[2026-05-28T20:16:57] Filtering duplicates (remaining=856246)
[2026-05-28T20:16:58] 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=683381)
[2026-05-28T20:16:59] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=683381)
[2026-05-28T20:17:00] Filtering viral contigs with expression lower than the top 5 (remaining=683381)
[2026-05-28T20:17:01] Filtering viral contigs with less than 5% coverage (remaining=683381)
[2026-05-28T20:17:02] Estimating fragment length (mate gap mean=-53.9413, mate gap stddev=30.2728, read length mean=89.8976)
[2026-05-28T20:17:02] Filtering read-through fragments with a distance <=10000bp (remaining=669862)
[2026-05-28T20:17:02] Filtering inconsistently clipped mates (remaining=640330)
[2026-05-28T20:17:03] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=590141)
[2026-05-28T20:17:04] Filtering fragments with small insert size (remaining=588887)
[2026-05-28T20:17:05] Filtering alignments with long gaps (remaining=588887)
[2026-05-28T20:17:05] Filtering fragments with both mates in the same gene (remaining=587887)
[2026-05-28T20:17:06] Filtering fusions arising from hairpin structures (remaining=550333)
[2026-05-28T20:17:07] Filtering reads with a mismatch p-value <=0.01 (remaining=111458)
[2026-05-28T20:17:08] Filtering reads with low entropy (k-mer content >=60%) (remaining=34420)
[2026-05-28T20:17:09] Finding fusions and counting supporting reads (total=31994)
[2026-05-28T20:17:13] Merging adjacent fusion breakpoints (remaining=31463)
[2026-05-28T20:17:14] Filtering multi-mapping fusions by alignment score and read support (remaining=12848)
[2026-05-28T20:17:24] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:17:25] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=12613)
[2026-05-28T20:17:25] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=9625)
[2026-05-28T20:17:25] Filtering fusions with <2 supporting reads (remaining=588)
[2026-05-28T20:17:25] Filtering fusions with an e-value >=0.3 (remaining=167)
[2026-05-28T20:17:25] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=168)
[2026-05-28T20:17:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=139)
[2026-05-28T20:17:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=139)
[2026-05-28T20:17:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=128)
[2026-05-28T20:17:27] Searching for fusions with spliced split reads (remaining=130)
[2026-05-28T20:17:28] Selecting best breakpoints from genes with multiple breakpoints (remaining=96)
[2026-05-28T20:17:29] Filtering read-through fusions with breakpoints near the gene boundary (remaining=95)
[2026-05-28T20:17:29] Searching for fusions with >=4 spliced events (remaining=95)
[2026-05-28T20:17:29] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=30)
[2026-05-28T20:17:44] Filtering fusions with anchors <=23nt (remaining=22)
[2026-05-28T20:17:44] Filtering end-to-end fusions with low support (remaining=18)
[2026-05-28T20:17:44] Filtering fusions with no coverage around the breakpoints (remaining=18)
[2026-05-28T20:17:44] Indexing gene sequences 
[2026-05-28T20:17:45] Filtering genes with >=30% identity (remaining=13)
[2026-05-28T20:17:45] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=4)
[2026-05-28T20:17:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=4)
[2026-05-28T20:17:45] Searching for additional isoforms (remaining=4)
[2026-05-28T20:17:45] Assigning confidence scores to events 
[2026-05-28T20:17:46] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:17:46] Writing fusions to file 'BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:17:46] Writing discarded fusions to file 'BreastNP_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:17:50] Freeing resources
[2026-05-28T20:17:56] Done (elapsed time=00:02:41, CPU time=00:02:40, peak memory=7.75gb)