[2026-05-28T21:25:51] Launching Arriba 2.4.0
[2026-05-28T21:25:51] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:26:08] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:26:14] Reading chimeric alignments from 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=11821572)
[2026-05-28T21:38:14] Marking multi-mapping alignments (marked=7759093)
[2026-05-28T21:38:19] Detecting strandedness (reverse)
[2026-05-28T21:38:19] Assigning strands to alignments 
[2026-05-28T21:38:21] Annotating alignments 
[2026-05-28T21:39:05] Filtering duplicates (remaining=8706256)
[2026-05-28T21:39:16] 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=8114858)
[2026-05-28T21:39:18] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8114858)
[2026-05-28T21:39:21] Filtering viral contigs with expression lower than the top 5 (remaining=8114858)
[2026-05-28T21:39:27] Filtering viral contigs with less than 5% coverage (remaining=8114858)
[2026-05-28T21:39:30] Estimating fragment length (mate gap mean=-85.1766, mate gap stddev=29.7517, read length mean=129.832)
[2026-05-28T21:39:30] Filtering read-through fragments with a distance <=10000bp (remaining=7706806)
[2026-05-28T21:39:32] Filtering inconsistently clipped mates (remaining=7586960)
[2026-05-28T21:39:35] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7278359)
[2026-05-28T21:39:41] Filtering fragments with small insert size (remaining=7277017)
[2026-05-28T21:39:43] Filtering alignments with long gaps (remaining=7277014)
[2026-05-28T21:39:46] Filtering fragments with both mates in the same gene (remaining=7275506)
[2026-05-28T21:39:48] Filtering fusions arising from hairpin structures (remaining=6874149)
[2026-05-28T21:39:52] Filtering reads with a mismatch p-value <=0.01 (remaining=3240999)
[2026-05-28T21:40:09] Filtering reads with low entropy (k-mer content >=60%) (remaining=1440504)
[2026-05-28T21:40:24] Finding fusions and counting supporting reads (total=1104645)
[2026-05-28T21:40:45] Merging adjacent fusion breakpoints (remaining=1097427)
[2026-05-28T21:40:48] Filtering multi-mapping fusions by alignment score and read support (remaining=676977)
[2026-05-28T21:41:34] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:41:44] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=673937)
[2026-05-28T21:41:45] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=428018)
[2026-05-28T21:41:46] Filtering fusions with <2 supporting reads (remaining=42287)
[2026-05-28T21:41:47] Filtering fusions with an e-value >=0.3 (remaining=9549)
[2026-05-28T21:41:48] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=9596)
[2026-05-28T21:41:52] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=9446)
[2026-05-28T21:41:53] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=9446)
[2026-05-28T21:41:55] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7901)
[2026-05-28T21:42:02] Searching for fusions with spliced split reads (remaining=7924)
[2026-05-28T21:42:08] Selecting best breakpoints from genes with multiple breakpoints (remaining=4394)
[2026-05-28T21:42:10] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4371)
[2026-05-28T21:42:11] Searching for fusions with >=4 spliced events (remaining=5674)
[2026-05-28T21:42:13] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2550)
[2026-05-28T21:42:31] Filtering fusions with anchors <=23nt (remaining=1995)
[2026-05-28T21:42:32] Filtering end-to-end fusions with low support (remaining=1946)
[2026-05-28T21:42:33] Filtering fusions with no coverage around the breakpoints (remaining=1917)
[2026-05-28T21:42:34] Indexing gene sequences 
[2026-05-28T21:42:41] Filtering genes with >=30% identity (remaining=445)
[2026-05-28T21:42:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=153)
[2026-05-28T21:42:47] Selecting best breakpoints from genes with multiple breakpoints (remaining=128)
[2026-05-28T21:42:49] Searching for additional isoforms (remaining=187)
[2026-05-28T21:42:51] Assigning confidence scores to events 
[2026-05-28T21:42:56] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:42:56] Writing fusions to file 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T21:42:59] Writing discarded fusions to file 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T21:43:55] Freeing resources
[2026-05-28T21:44:23] Done (elapsed time=00:18:32, CPU time=00:18:31, peak memory=16.9gb)