[2026-06-08T08:48:29] Launching Arriba 2.4.0
[2026-06-08T08:48:29] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:48:39] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:48:44] Reading chimeric alignments from 'SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=12302997)
[2026-06-08T08:56:21] Marking multi-mapping alignments (marked=8167071)
[2026-06-08T08:56:27] Detecting strandedness (reverse)
[2026-06-08T08:56:27] Assigning strands to alignments 
[2026-06-08T08:56:29] Annotating alignments 
[2026-06-08T08:57:29] Filtering duplicates (remaining=9188307)
[2026-06-08T08:57:42] 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=8433106)
[2026-06-08T08:57:46] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8433106)
[2026-06-08T08:57:48] Filtering viral contigs with expression lower than the top 5 (remaining=8433106)
[2026-06-08T08:57:55] Filtering viral contigs with less than 5% coverage (remaining=8433106)
[2026-06-08T08:57:58] Estimating fragment length (mate gap mean=-84.1639, mate gap stddev=30.6241, read length mean=129.857)
[2026-06-08T08:57:58] Filtering read-through fragments with a distance <=10000bp (remaining=7987279)
[2026-06-08T08:58:01] Filtering inconsistently clipped mates (remaining=7869278)
[2026-06-08T08:58:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7625683)
[2026-06-08T08:58:11] Filtering fragments with small insert size (remaining=7624385)
[2026-06-08T08:58:14] Filtering alignments with long gaps (remaining=7624385)
[2026-06-08T08:58:17] Filtering fragments with both mates in the same gene (remaining=7623048)
[2026-06-08T08:58:20] Filtering fusions arising from hairpin structures (remaining=7153752)
[2026-06-08T08:58:24] Filtering reads with a mismatch p-value <=0.01 (remaining=3476022)
[2026-06-08T08:58:53] Filtering reads with low entropy (k-mer content >=60%) (remaining=1700623)
[2026-06-08T08:59:10] Finding fusions and counting supporting reads (total=1363605)
[2026-06-08T08:59:35] Merging adjacent fusion breakpoints (remaining=1351479)
[2026-06-08T08:59:38] Filtering multi-mapping fusions by alignment score and read support (remaining=855243)
[2026-06-08T09:00:23] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T09:00:34] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=852639)
[2026-06-08T09:00:35] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=582600)
[2026-06-08T09:00:37] Filtering fusions with <2 supporting reads (remaining=43047)
[2026-06-08T09:00:38] Filtering fusions with an e-value >=0.3 (remaining=8404)
[2026-06-08T09:00:39] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8446)
[2026-06-08T09:00:44] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8300)
[2026-06-08T09:00:46] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8301)
[2026-06-08T09:00:48] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6316)
[2026-06-08T09:00:56] Searching for fusions with spliced split reads (remaining=6338)
[2026-06-08T09:01:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=3814)
[2026-06-08T09:01:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3796)
[2026-06-08T09:01:06] Searching for fusions with >=4 spliced events (remaining=4923)
[2026-06-08T09:01:09] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2291)
[2026-06-08T09:01:23] Filtering fusions with anchors <=23nt (remaining=1844)
[2026-06-08T09:01:24] Filtering end-to-end fusions with low support (remaining=1807)
[2026-06-08T09:01:26] Filtering fusions with no coverage around the breakpoints (remaining=1796)
[2026-06-08T09:01:27] Indexing gene sequences 
[2026-06-08T09:01:34] Filtering genes with >=30% identity (remaining=615)
[2026-06-08T09:01:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=342)
[2026-06-08T09:01:49] Selecting best breakpoints from genes with multiple breakpoints (remaining=194)
[2026-06-08T09:01:51] Searching for additional isoforms (remaining=389)
[2026-06-08T09:01:54] Assigning confidence scores to events 
[2026-06-08T09:01:59] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T09:01:59] Writing fusions to file 'SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T09:02:04] Writing discarded fusions to file 'SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T09:02:50] Freeing resources
[2026-06-08T09:03:15] Done (elapsed time=00:14:46, CPU time=00:14:44, peak memory=17.4gb)