[2026-05-28T21:21:48] Launching Arriba 2.4.0
[2026-05-28T21:21:48] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:22:03] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:22:07] Reading chimeric alignments from '786-O_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam' (total=11110656)
[2026-05-28T21:30:37] Marking multi-mapping alignments (marked=7339022)
[2026-05-28T21:30:42] Detecting strandedness (reverse)
[2026-05-28T21:30:42] Assigning strands to alignments 
[2026-05-28T21:30:44] Annotating alignments 
[2026-05-28T21:31:23] Filtering duplicates (remaining=8039565)
[2026-05-28T21:31:32] 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=7483173)
[2026-05-28T21:31:35] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7483173)
[2026-05-28T21:31:37] Filtering viral contigs with expression lower than the top 5 (remaining=7483173)
[2026-05-28T21:31:43] Filtering viral contigs with less than 5% coverage (remaining=7483173)
[2026-05-28T21:31:45] Estimating fragment length (mate gap mean=-85.8982, mate gap stddev=29.9928, read length mean=129.132)
[2026-05-28T21:31:45] Filtering read-through fragments with a distance <=10000bp (remaining=7108992)
[2026-05-28T21:31:48] Filtering inconsistently clipped mates (remaining=6986951)
[2026-05-28T21:31:50] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6725027)
[2026-05-28T21:31:56] Filtering fragments with small insert size (remaining=6723934)
[2026-05-28T21:31:58] Filtering alignments with long gaps (remaining=6723934)
[2026-05-28T21:32:01] Filtering fragments with both mates in the same gene (remaining=6722697)
[2026-05-28T21:32:03] Filtering fusions arising from hairpin structures (remaining=6279708)
[2026-05-28T21:32:06] Filtering reads with a mismatch p-value <=0.01 (remaining=2917983)
[2026-05-28T21:32:24] Filtering reads with low entropy (k-mer content >=60%) (remaining=1205309)
[2026-05-28T21:32:40] Finding fusions and counting supporting reads (total=962783)
[2026-05-28T21:33:01] Merging adjacent fusion breakpoints (remaining=954429)
[2026-05-28T21:33:03] Filtering multi-mapping fusions by alignment score and read support (remaining=601783)
[2026-05-28T21:33:38] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:33:47] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=599335)
[2026-05-28T21:33:48] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=354321)
[2026-05-28T21:33:49] Filtering fusions with <2 supporting reads (remaining=33774)
[2026-05-28T21:33:50] Filtering fusions with an e-value >=0.3 (remaining=7230)
[2026-05-28T21:33:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7260)
[2026-05-28T21:33:56] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7130)
[2026-05-28T21:33:56] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7130)
[2026-05-28T21:33:59] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6553)
[2026-05-28T21:34:05] Searching for fusions with spliced split reads (remaining=6569)
[2026-05-28T21:34:11] Selecting best breakpoints from genes with multiple breakpoints (remaining=4158)
[2026-05-28T21:34:13] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4133)
[2026-05-28T21:34:14] Searching for fusions with >=4 spliced events (remaining=5114)
[2026-05-28T21:34:16] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2215)
[2026-05-28T21:34:33] Filtering fusions with anchors <=23nt (remaining=1778)
[2026-05-28T21:34:33] Filtering end-to-end fusions with low support (remaining=1750)
[2026-05-28T21:34:34] Filtering fusions with no coverage around the breakpoints (remaining=1731)
[2026-05-28T21:34:35] Indexing gene sequences 
[2026-05-28T21:34:43] Filtering genes with >=30% identity (remaining=551)
[2026-05-28T21:34:47] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=268)
[2026-05-28T21:35:00] Selecting best breakpoints from genes with multiple breakpoints (remaining=224)
[2026-05-28T21:35:02] Searching for additional isoforms (remaining=298)
[2026-05-28T21:35:04] Assigning confidence scores to events 
[2026-05-28T21:35:09] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:35:09] Writing fusions to file '786-O_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.tsv' 
[2026-05-28T21:35:12] Writing discarded fusions to file '786-O_FFPE_RNA_0001_B23LG7FLT4_2.arriba.fusions.discarded.tsv'
[2026-05-28T21:35:52] Freeing resources
[2026-05-28T21:36:12] Done (elapsed time=00:14:24, CPU time=00:14:22, peak memory=16gb)