[2026-05-28T21:19:03] Launching Arriba 2.4.0
[2026-05-28T21:19:03] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:19:17] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:19:21] Reading chimeric alignments from 'SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=12302997)
[2026-05-28T21:29:28] Marking multi-mapping alignments (marked=8167071)
[2026-05-28T21:29:33] Detecting strandedness (reverse)
[2026-05-28T21:29:33] Assigning strands to alignments 
[2026-05-28T21:29:36] Annotating alignments 
[2026-05-28T21:30:22] Filtering duplicates (remaining=9188307)
[2026-05-28T21:30:36] 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)
[2026-05-28T21:30:39] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8433106)
[2026-05-28T21:30:42] Filtering viral contigs with expression lower than the top 5 (remaining=8433106)
[2026-05-28T21:30:48] Filtering viral contigs with less than 5% coverage (remaining=8433106)
[2026-05-28T21:30:52] Estimating fragment length (mate gap mean=-84.1639, mate gap stddev=30.6241, read length mean=129.857)
[2026-05-28T21:30:52] Filtering read-through fragments with a distance <=10000bp (remaining=7987279)
[2026-05-28T21:30:55] Filtering inconsistently clipped mates (remaining=7869278)
[2026-05-28T21:30:58] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7625683)
[2026-05-28T21:31:04] Filtering fragments with small insert size (remaining=7624385)
[2026-05-28T21:31:07] Filtering alignments with long gaps (remaining=7624385)
[2026-05-28T21:31:09] Filtering fragments with both mates in the same gene (remaining=7623048)
[2026-05-28T21:31:12] Filtering fusions arising from hairpin structures (remaining=7153752)
[2026-05-28T21:31:16] Filtering reads with a mismatch p-value <=0.01 (remaining=3476022)
[2026-05-28T21:31:35] Filtering reads with low entropy (k-mer content >=60%) (remaining=1700623)
[2026-05-28T21:31:50] Finding fusions and counting supporting reads (total=1363605)
[2026-05-28T21:32:20] Merging adjacent fusion breakpoints (remaining=1351479)
[2026-05-28T21:32:23] Filtering multi-mapping fusions by alignment score and read support (remaining=855243)
[2026-05-28T21:33:15] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:33:28] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=852639)
[2026-05-28T21:33:29] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=582600)
[2026-05-28T21:33:31] Filtering fusions with <2 supporting reads (remaining=43047)
[2026-05-28T21:33:32] Filtering fusions with an e-value >=0.3 (remaining=8404)
[2026-05-28T21:33:33] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8446)
[2026-05-28T21:33:38] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8300)
[2026-05-28T21:33:39] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8301)
[2026-05-28T21:33:41] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6316)
[2026-05-28T21:33:49] Searching for fusions with spliced split reads (remaining=6338)
[2026-05-28T21:33:57] Selecting best breakpoints from genes with multiple breakpoints (remaining=3814)
[2026-05-28T21:33:59] Filtering read-through fusions with breakpoints near the gene boundary (remaining=3796)
[2026-05-28T21:34:00] Searching for fusions with >=4 spliced events (remaining=4923)
[2026-05-28T21:34:02] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2291)
[2026-05-28T21:34:24] Filtering fusions with anchors <=23nt (remaining=1844)
[2026-05-28T21:34:25] Filtering end-to-end fusions with low support (remaining=1807)
[2026-05-28T21:34:26] Filtering fusions with no coverage around the breakpoints (remaining=1796)
[2026-05-28T21:34:27] Indexing gene sequences 
[2026-05-28T21:34:36] Filtering genes with >=30% identity (remaining=615)
[2026-05-28T21:34:43] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=342)
[2026-05-28T21:34:54] Selecting best breakpoints from genes with multiple breakpoints (remaining=194)
[2026-05-28T21:34:56] Searching for additional isoforms (remaining=389)
[2026-05-28T21:34:58] Assigning confidence scores to events 
[2026-05-28T21:35:04] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:35:04] Writing fusions to file 'SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:35:10] Writing discarded fusions to file 'SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:36:03] Freeing resources
[2026-05-28T21:36:29] Done (elapsed time=00:17:26, CPU time=00:17:26, peak memory=17.4gb)