[2026-05-28T20:13:14] Launching Arriba 2.4.0
[2026-05-28T20:13:14] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:13:30] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:13:36] Reading chimeric alignments from 'ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=3602797)
[2026-05-28T20:15:14] Marking multi-mapping alignments (marked=2929202)
[2026-05-28T20:15:16] Detecting strandedness (no)
[2026-05-28T20:15:16] Annotating alignments 
[2026-05-28T20:15:38] Filtering duplicates (remaining=944794)
[2026-05-28T20:15:41] 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=790698)
[2026-05-28T20:15:42] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=790698)
[2026-05-28T20:15:42] Filtering viral contigs with expression lower than the top 5 (remaining=790698)
[2026-05-28T20:15:44] Filtering viral contigs with less than 5% coverage (remaining=790698)
[2026-05-28T20:15:46] Estimating fragment length (mate gap mean=-55.4963, mate gap stddev=28.4836, read length mean=90.4204)
[2026-05-28T20:15:46] Filtering read-through fragments with a distance <=10000bp (remaining=779678)
[2026-05-28T20:15:47] Filtering inconsistently clipped mates (remaining=745659)
[2026-05-28T20:15:48] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=666904)
[2026-05-28T20:15:49] Filtering fragments with small insert size (remaining=665618)
[2026-05-28T20:15:50] Filtering alignments with long gaps (remaining=665618)
[2026-05-28T20:15:51] Filtering fragments with both mates in the same gene (remaining=664949)
[2026-05-28T20:15:52] Filtering fusions arising from hairpin structures (remaining=620122)
[2026-05-28T20:15:53] Filtering reads with a mismatch p-value <=0.01 (remaining=127682)
[2026-05-28T20:15:55] Filtering reads with low entropy (k-mer content >=60%) (remaining=52207)
[2026-05-28T20:15:58] Finding fusions and counting supporting reads (total=54897)
[2026-05-28T20:16:04] Merging adjacent fusion breakpoints (remaining=54677)
[2026-05-28T20:16:05] Filtering multi-mapping fusions by alignment score and read support (remaining=20299)
[2026-05-28T20:16:22] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:16:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=19863)
[2026-05-28T20:16:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=17130)
[2026-05-28T20:16:24] Filtering fusions with <2 supporting reads (remaining=337)
[2026-05-28T20:16:24] Filtering fusions with an e-value >=0.3 (remaining=137)
[2026-05-28T20:16:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=138)
[2026-05-28T20:16:26] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=84)
[2026-05-28T20:16:26] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=84)
[2026-05-28T20:16:26] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=84)
[2026-05-28T20:16:29] Searching for fusions with spliced split reads (remaining=87)
[2026-05-28T20:16:31] Selecting best breakpoints from genes with multiple breakpoints (remaining=80)
[2026-05-28T20:16:32] Filtering read-through fusions with breakpoints near the gene boundary (remaining=78)
[2026-05-28T20:16:32] Searching for fusions with >=4 spliced events (remaining=78)
[2026-05-28T20:16:32] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=34)
[2026-05-28T20:16:55] Filtering fusions with anchors <=23nt (remaining=26)
[2026-05-28T20:16:55] Filtering end-to-end fusions with low support (remaining=23)
[2026-05-28T20:16:55] Filtering fusions with no coverage around the breakpoints (remaining=23)
[2026-05-28T20:16:55] Indexing gene sequences 
[2026-05-28T20:16:56] Filtering genes with >=30% identity (remaining=17)
[2026-05-28T20:16:56] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=13)
[2026-05-28T20:16:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=13)
[2026-05-28T20:16:57] Searching for additional isoforms (remaining=13)
[2026-05-28T20:16:57] Assigning confidence scores to events 
[2026-05-28T20:16:58] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:16:58] Writing fusions to file 'ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:16:59] Writing discarded fusions to file 'ColoN_FFPE_L02_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:17:06] Freeing resources
[2026-05-28T20:17:14] Done (elapsed time=00:04:00, CPU time=00:03:58, peak memory=7.75gb)