[2026-06-08T08:36:10] Launching Arriba 2.4.0
[2026-06-08T08:36:10] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:36:19] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:36:23] Reading chimeric alignments from 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=12179069)
[2026-06-08T08:43:27] Marking multi-mapping alignments (marked=8027667)
[2026-06-08T08:43:32] Detecting strandedness (reverse)
[2026-06-08T08:43:32] Assigning strands to alignments 
[2026-06-08T08:43:34] Annotating alignments 
[2026-06-08T08:44:15] Filtering duplicates (remaining=8974816)
[2026-06-08T08:44:25] 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=8345878)
[2026-06-08T08:44:27] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8345878)
[2026-06-08T08:44:29] Filtering viral contigs with expression lower than the top 5 (remaining=8345878)
[2026-06-08T08:44:35] Filtering viral contigs with less than 5% coverage (remaining=8345878)
[2026-06-08T08:44:37] Estimating fragment length (mate gap mean=-86.6103, mate gap stddev=29.9059, read length mean=130.741)
[2026-06-08T08:44:38] Filtering read-through fragments with a distance <=10000bp (remaining=7941007)
[2026-06-08T08:44:40] Filtering inconsistently clipped mates (remaining=7815768)
[2026-06-08T08:44:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7509132)
[2026-06-08T08:44:48] Filtering fragments with small insert size (remaining=7507805)
[2026-06-08T08:44:51] Filtering alignments with long gaps (remaining=7507804)
[2026-06-08T08:44:53] Filtering fragments with both mates in the same gene (remaining=7506464)
[2026-06-08T08:44:56] Filtering fusions arising from hairpin structures (remaining=7080632)
[2026-06-08T08:44:59] Filtering reads with a mismatch p-value <=0.01 (remaining=3262016)
[2026-06-08T08:45:18] Filtering reads with low entropy (k-mer content >=60%) (remaining=1456177)
[2026-06-08T08:45:32] Finding fusions and counting supporting reads (total=1125940)
[2026-06-08T08:45:54] Merging adjacent fusion breakpoints (remaining=1117640)
[2026-06-08T08:45:57] Filtering multi-mapping fusions by alignment score and read support (remaining=689449)
[2026-06-08T08:46:38] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:46:48] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=686311)
[2026-06-08T08:46:49] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=436390)
[2026-06-08T08:46:51] Filtering fusions with <2 supporting reads (remaining=41590)
[2026-06-08T08:46:52] Filtering fusions with an e-value >=0.3 (remaining=8912)
[2026-06-08T08:46:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8959)
[2026-06-08T08:46:58] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8781)
[2026-06-08T08:46:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8781)
[2026-06-08T08:47:01] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7521)
[2026-06-08T08:47:08] Searching for fusions with spliced split reads (remaining=7548)
[2026-06-08T08:47:15] Selecting best breakpoints from genes with multiple breakpoints (remaining=4374)
[2026-06-08T08:47:17] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4351)
[2026-06-08T08:47:18] Searching for fusions with >=4 spliced events (remaining=5664)
[2026-06-08T08:47:20] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2609)
[2026-06-08T08:47:35] Filtering fusions with anchors <=23nt (remaining=2057)
[2026-06-08T08:47:36] Filtering end-to-end fusions with low support (remaining=2011)
[2026-06-08T08:47:37] Filtering fusions with no coverage around the breakpoints (remaining=1980)
[2026-06-08T08:47:38] Indexing gene sequences 
[2026-06-08T08:47:45] Filtering genes with >=30% identity (remaining=516)
[2026-06-08T08:47:49] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=194)
[2026-06-08T08:47:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=151)
[2026-06-08T08:47:54] Searching for additional isoforms (remaining=216)
[2026-06-08T08:47:56] Assigning confidence scores to events 
[2026-06-08T08:48:01] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:48:01] Writing fusions to file 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T08:48:04] Writing discarded fusions to file 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T08:48:46] Freeing resources
[2026-06-08T08:49:10] Done (elapsed time=00:13:00, CPU time=00:12:58, peak memory=17.2gb)