[2026-05-28T21:23:48] Launching Arriba 2.4.0
[2026-05-28T21:23:48] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:24:03] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:24:07] Reading chimeric alignments from 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=10831319)
[2026-05-28T21:32:17] Marking multi-mapping alignments (marked=7060858)
[2026-05-28T21:32:21] Detecting strandedness (reverse)
[2026-05-28T21:32:21] Assigning strands to alignments 
[2026-05-28T21:32:23] Annotating alignments 
[2026-05-28T21:32:58] Filtering duplicates (remaining=8023009)
[2026-05-28T21:33:08] 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=7501486)
[2026-05-28T21:33:10] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7501486)
[2026-05-28T21:33:12] Filtering viral contigs with expression lower than the top 5 (remaining=7501486)
[2026-05-28T21:33:17] Filtering viral contigs with less than 5% coverage (remaining=7501486)
[2026-05-28T21:33:20] Estimating fragment length (mate gap mean=-83.7273, mate gap stddev=29.9166, read length mean=128.202)
[2026-05-28T21:33:20] Filtering read-through fragments with a distance <=10000bp (remaining=7132850)
[2026-05-28T21:33:22] Filtering inconsistently clipped mates (remaining=7022480)
[2026-05-28T21:33:24] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6704069)
[2026-05-28T21:33:29] Filtering fragments with small insert size (remaining=6702854)
[2026-05-28T21:33:31] Filtering alignments with long gaps (remaining=6702853)
[2026-05-28T21:33:33] Filtering fragments with both mates in the same gene (remaining=6701385)
[2026-05-28T21:33:36] Filtering fusions arising from hairpin structures (remaining=6365590)
[2026-05-28T21:33:38] Filtering reads with a mismatch p-value <=0.01 (remaining=3139564)
[2026-05-28T21:33:54] Filtering reads with low entropy (k-mer content >=60%) (remaining=1317454)
[2026-05-28T21:34:08] Finding fusions and counting supporting reads (total=979173)
[2026-05-28T21:34:26] Merging adjacent fusion breakpoints (remaining=973305)
[2026-05-28T21:34:28] Filtering multi-mapping fusions by alignment score and read support (remaining=594657)
[2026-05-28T21:35:02] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:35:11] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=591969)
[2026-05-28T21:35:11] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=373391)
[2026-05-28T21:35:13] Filtering fusions with <2 supporting reads (remaining=39431)
[2026-05-28T21:35:14] Filtering fusions with an e-value >=0.3 (remaining=9001)
[2026-05-28T21:35:15] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9045)
[2026-05-28T21:35:19] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8864)
[2026-05-28T21:35:19] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8864)
[2026-05-28T21:35:21] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7677)
[2026-05-28T21:35:27] Searching for fusions with spliced split reads (remaining=7700)
[2026-05-28T21:35:33] Selecting best breakpoints from genes with multiple breakpoints (remaining=4385)
[2026-05-28T21:35:35] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4360)
[2026-05-28T21:35:36] Searching for fusions with >=4 spliced events (remaining=5531)
[2026-05-28T21:35:38] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2464)
[2026-05-28T21:35:54] Filtering fusions with anchors <=23nt (remaining=1968)
[2026-05-28T21:35:55] Filtering end-to-end fusions with low support (remaining=1930)
[2026-05-28T21:35:56] Filtering fusions with no coverage around the breakpoints (remaining=1898)
[2026-05-28T21:35:57] Indexing gene sequences 
[2026-05-28T21:36:04] Filtering genes with >=30% identity (remaining=561)
[2026-05-28T21:36:08] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=248)
[2026-05-28T21:36:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=171)
[2026-05-28T21:36:13] Searching for additional isoforms (remaining=249)
[2026-05-28T21:36:14] Assigning confidence scores to events 
[2026-05-28T21:36:19] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:36:19] Writing fusions to file 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-05-28T21:36:22] Writing discarded fusions to file 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-05-28T21:36:58] Freeing resources
[2026-05-28T21:37:17] Done (elapsed time=00:13:29, CPU time=00:13:28, peak memory=15.6gb)