[2026-06-08T07:36:23] Launching Arriba 2.4.0
[2026-06-08T07:36:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:36:36] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:36:41] Reading chimeric alignments from 'BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=4468174)
[2026-06-08T07:38:32] Marking multi-mapping alignments (marked=3570653)
[2026-06-08T07:38:34] Detecting strandedness (no)
[2026-06-08T07:38:34] Annotating alignments 
[2026-06-08T07:38:52] Filtering duplicates (remaining=1048679)
[2026-06-08T07:38:54] 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)
[2026-06-08T07:38:55] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=816949)
[2026-06-08T07:38:55] Filtering viral contigs with expression lower than the top 5 (remaining=816949)
[2026-06-08T07:38:57] Filtering viral contigs with less than 5% coverage (remaining=816949)
[2026-06-08T07:38:58] Estimating fragment length (mate gap mean=-59.2614, mate gap stddev=29.821, read length mean=96.7765)
[2026-06-08T07:38:58] Filtering read-through fragments with a distance <=10000bp (remaining=801813)
[2026-06-08T07:38:59] Filtering inconsistently clipped mates (remaining=770454)
[2026-06-08T07:39:00] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=690199)
[2026-06-08T07:39:01] Filtering fragments with small insert size (remaining=689109)
[2026-06-08T07:39:02] Filtering alignments with long gaps (remaining=689109)
[2026-06-08T07:39:03] Filtering fragments with both mates in the same gene (remaining=688390)
[2026-06-08T07:39:04] Filtering fusions arising from hairpin structures (remaining=640873)
[2026-06-08T07:39:05] Filtering reads with a mismatch p-value <=0.01 (remaining=160483)
[2026-06-08T07:39:06] Filtering reads with low entropy (k-mer content >=60%) (remaining=60301)
[2026-06-08T07:39:09] Finding fusions and counting supporting reads (total=60459)
[2026-06-08T07:39:15] Merging adjacent fusion breakpoints (remaining=60120)
[2026-06-08T07:39:15] Filtering multi-mapping fusions by alignment score and read support (remaining=21903)
[2026-06-08T07:39:29] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:39:30] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=21313)
[2026-06-08T07:39:30] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=17586)
[2026-06-08T07:39:30] Filtering fusions with <2 supporting reads (remaining=410)
[2026-06-08T07:39:30] Filtering fusions with an e-value >=0.3 (remaining=144)
[2026-06-08T07:39:31] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=146)
[2026-06-08T07:39:32] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=94)
[2026-06-08T07:39:32] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=94)
[2026-06-08T07:39:32] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=90)
[2026-06-08T07:39:34] Searching for fusions with spliced split reads (remaining=94)
[2026-06-08T07:39:36] Selecting best breakpoints from genes with multiple breakpoints (remaining=80)
[2026-06-08T07:39:36] Filtering read-through fusions with breakpoints near the gene boundary (remaining=79)
[2026-06-08T07:39:37] Searching for fusions with >=4 spliced events (remaining=79)
[2026-06-08T07:39:37] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=21)
[2026-06-08T07:39:55] Filtering fusions with anchors <=23nt (remaining=19)
[2026-06-08T07:39:55] Filtering end-to-end fusions with low support (remaining=17)
[2026-06-08T07:39:55] Filtering fusions with no coverage around the breakpoints (remaining=17)
[2026-06-08T07:39:55] Indexing gene sequences 
[2026-06-08T07:39:56] Filtering genes with >=30% identity (remaining=8)
[2026-06-08T07:39:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=3)
[2026-06-08T07:39:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=3)
[2026-06-08T07:39:56] Searching for additional isoforms (remaining=3)
[2026-06-08T07:39:56] Assigning confidence scores to events 
[2026-06-08T07:39:57] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:39:57] Writing fusions to file 'BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:39:58] Writing discarded fusions to file 'BreastNB_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:40:03] Freeing resources
[2026-06-08T07:40:12] Done (elapsed time=00:03:49, CPU time=00:03:48, peak memory=8.56gb)