[2026-06-08T08:32:12] Launching Arriba 2.4.0
[2026-06-08T08:32:12] Loading assembly from 'ref_genome.fa' 
[2026-06-08T08:32:26] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T08:32:32] Reading chimeric alignments from '786-O_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=11440821)
[2026-06-08T08:41:05] Marking multi-mapping alignments (marked=7619584)
[2026-06-08T08:41:10] Detecting strandedness (reverse)
[2026-06-08T08:41:10] Assigning strands to alignments 
[2026-06-08T08:41:13] Annotating alignments 
[2026-06-08T08:41:59] Filtering duplicates (remaining=8268049)
[2026-06-08T08:42:09] 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=7686467)
[2026-06-08T08:42:12] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=7686467)
[2026-06-08T08:42:14] Filtering viral contigs with expression lower than the top 5 (remaining=7686467)
[2026-06-08T08:42:21] Filtering viral contigs with less than 5% coverage (remaining=7686467)
[2026-06-08T08:42:24] Estimating fragment length (mate gap mean=-85.473, mate gap stddev=30.4133, read length mean=128.514)
[2026-06-08T08:42:24] Filtering read-through fragments with a distance <=10000bp (remaining=7309398)
[2026-06-08T08:42:26] Filtering inconsistently clipped mates (remaining=7188717)
[2026-06-08T08:42:29] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=6932961)
[2026-06-08T08:42:35] Filtering fragments with small insert size (remaining=6931652)
[2026-06-08T08:42:38] Filtering alignments with long gaps (remaining=6931652)
[2026-06-08T08:42:40] Filtering fragments with both mates in the same gene (remaining=6930420)
[2026-06-08T08:42:43] Filtering fusions arising from hairpin structures (remaining=6507423)
[2026-06-08T08:42:46] Filtering reads with a mismatch p-value <=0.01 (remaining=2958657)
[2026-06-08T08:43:04] Filtering reads with low entropy (k-mer content >=60%) (remaining=1196196)
[2026-06-08T08:43:19] Finding fusions and counting supporting reads (total=958683)
[2026-06-08T08:43:45] Merging adjacent fusion breakpoints (remaining=951029)
[2026-06-08T08:43:48] Filtering multi-mapping fusions by alignment score and read support (remaining=599881)
[2026-06-08T08:44:31] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T08:44:45] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=597458)
[2026-06-08T08:44:46] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=357157)
[2026-06-08T08:44:48] Filtering fusions with <2 supporting reads (remaining=33237)
[2026-06-08T08:44:50] Filtering fusions with an e-value >=0.3 (remaining=7282)
[2026-06-08T08:44:51] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=7323)
[2026-06-08T08:44:57] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=7150)
[2026-06-08T08:44:59] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=7150)
[2026-06-08T08:45:02] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6629)
[2026-06-08T08:45:12] Searching for fusions with spliced split reads (remaining=6653)
[2026-06-08T08:45:21] Selecting best breakpoints from genes with multiple breakpoints (remaining=4258)
[2026-06-08T08:45:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4226)
[2026-06-08T08:45:25] Searching for fusions with >=4 spliced events (remaining=5272)
[2026-06-08T08:45:28] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2389)
[2026-06-08T08:45:55] Filtering fusions with anchors <=23nt (remaining=1900)
[2026-06-08T08:45:56] Filtering end-to-end fusions with low support (remaining=1872)
[2026-06-08T08:45:57] Filtering fusions with no coverage around the breakpoints (remaining=1853)
[2026-06-08T08:45:59] Indexing gene sequences 
[2026-06-08T08:46:10] Filtering genes with >=30% identity (remaining=573)
[2026-06-08T08:46:15] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=259)
[2026-06-08T08:46:30] Selecting best breakpoints from genes with multiple breakpoints (remaining=216)
[2026-06-08T08:46:33] Searching for additional isoforms (remaining=302)
[2026-06-08T08:46:35] Assigning confidence scores to events 
[2026-06-08T08:46:42] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T08:46:42] Writing fusions to file '786-O_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-06-08T08:46:47] Writing discarded fusions to file '786-O_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-06-08T08:47:47] Freeing resources
[2026-06-08T08:48:17] Done (elapsed time=00:16:05, CPU time=00:16:05, peak memory=16.4gb)