[2026-05-28T21:23:51] Launching Arriba 2.4.0
[2026-05-28T21:23:51] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:24:05] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:24:10] Reading chimeric alignments from 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=12179069)
[2026-05-28T21:32:57] Marking multi-mapping alignments (marked=8027667)
[2026-05-28T21:33:04] Detecting strandedness (reverse)
[2026-05-28T21:33:04] Assigning strands to alignments 
[2026-05-28T21:33:06] Annotating alignments 
[2026-05-28T21:33:50] Filtering duplicates (remaining=8974816)
[2026-05-28T21:34:00] 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)
[2026-05-28T21:34:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8345878)
[2026-05-28T21:34:05] Filtering viral contigs with expression lower than the top 5 (remaining=8345878)
[2026-05-28T21:34:11] Filtering viral contigs with less than 5% coverage (remaining=8345878)
[2026-05-28T21:34:14] Estimating fragment length (mate gap mean=-86.6103, mate gap stddev=29.9059, read length mean=130.741)
[2026-05-28T21:34:14] Filtering read-through fragments with a distance <=10000bp (remaining=7941007)
[2026-05-28T21:34:17] Filtering inconsistently clipped mates (remaining=7815768)
[2026-05-28T21:34:19] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7509132)
[2026-05-28T21:34:27] Filtering fragments with small insert size (remaining=7507805)
[2026-05-28T21:34:29] Filtering alignments with long gaps (remaining=7507804)
[2026-05-28T21:34:32] Filtering fragments with both mates in the same gene (remaining=7506464)
[2026-05-28T21:34:35] Filtering fusions arising from hairpin structures (remaining=7080632)
[2026-05-28T21:34:39] Filtering reads with a mismatch p-value <=0.01 (remaining=3262016)
[2026-05-28T21:35:00] Filtering reads with low entropy (k-mer content >=60%) (remaining=1456177)
[2026-05-28T21:35:17] Finding fusions and counting supporting reads (total=1125940)
[2026-05-28T21:35:42] Merging adjacent fusion breakpoints (remaining=1117640)
[2026-05-28T21:35:44] Filtering multi-mapping fusions by alignment score and read support (remaining=689449)
[2026-05-28T21:36:26] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:36:36] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=686311)
[2026-05-28T21:36:37] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=436390)
[2026-05-28T21:36:38] Filtering fusions with <2 supporting reads (remaining=41590)
[2026-05-28T21:36:39] Filtering fusions with an e-value >=0.3 (remaining=8912)
[2026-05-28T21:36:40] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8959)
[2026-05-28T21:36:46] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8781)
[2026-05-28T21:36:47] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8781)
[2026-05-28T21:36:49] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=7521)
[2026-05-28T21:36:56] Searching for fusions with spliced split reads (remaining=7548)
[2026-05-28T21:37:03] Selecting best breakpoints from genes with multiple breakpoints (remaining=4374)
[2026-05-28T21:37:05] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4351)
[2026-05-28T21:37:06] Searching for fusions with >=4 spliced events (remaining=5664)
[2026-05-28T21:37:08] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2609)
[2026-05-28T21:37:26] Filtering fusions with anchors <=23nt (remaining=2057)
[2026-05-28T21:37:27] Filtering end-to-end fusions with low support (remaining=2011)
[2026-05-28T21:37:28] Filtering fusions with no coverage around the breakpoints (remaining=1980)
[2026-05-28T21:37:29] Indexing gene sequences 
[2026-05-28T21:37:37] Filtering genes with >=30% identity (remaining=516)
[2026-05-28T21:37:40] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=194)
[2026-05-28T21:37:43] Selecting best breakpoints from genes with multiple breakpoints (remaining=151)
[2026-05-28T21:37:45] Searching for additional isoforms (remaining=216)
[2026-05-28T21:37:47] Assigning confidence scores to events 
[2026-05-28T21:37:52] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:37:53] Writing fusions to file 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T21:37:55] Writing discarded fusions to file 'KG1_FFPE_01_RNA_0003_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T21:38:38] Freeing resources
[2026-05-28T21:39:00] Done (elapsed time=00:15:09, CPU time=00:15:08, peak memory=17.3gb)