[2026-05-28T20:10:25] Launching Arriba 2.4.0
[2026-05-28T20:10:25] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:10:41] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:10:48] Reading chimeric alignments from 'ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1584479)
[2026-05-28T20:11:23] Marking multi-mapping alignments (marked=1367866)
[2026-05-28T20:11:24] Detecting strandedness (no)
[2026-05-28T20:11:24] Annotating alignments 
[2026-05-28T20:11:34] Filtering duplicates (remaining=423356)
[2026-05-28T20:11:35] 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=330886)
[2026-05-28T20:11:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=330886)
[2026-05-28T20:11:36] Filtering viral contigs with expression lower than the top 5 (remaining=330886)
[2026-05-28T20:11:37] Filtering viral contigs with less than 5% coverage (remaining=330886)
[2026-05-28T20:11:38] Estimating fragment length (mate gap mean=-41.8918, mate gap stddev=24.5478, read length mean=80.5062)
[2026-05-28T20:11:38] Filtering read-through fragments with a distance <=10000bp (remaining=325345)
[2026-05-28T20:11:38] Filtering inconsistently clipped mates (remaining=306889)
[2026-05-28T20:11:39] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=283341)
[2026-05-28T20:11:39] Filtering fragments with small insert size (remaining=282595)
[2026-05-28T20:11:40] Filtering alignments with long gaps (remaining=282595)
[2026-05-28T20:11:40] Filtering fragments with both mates in the same gene (remaining=282076)
[2026-05-28T20:11:40] Filtering fusions arising from hairpin structures (remaining=259882)
[2026-05-28T20:11:41] Filtering reads with a mismatch p-value <=0.01 (remaining=41904)
[2026-05-28T20:11:42] Filtering reads with low entropy (k-mer content >=60%) (remaining=13236)
[2026-05-28T20:11:43] Finding fusions and counting supporting reads (total=13614)
[2026-05-28T20:11:45] Merging adjacent fusion breakpoints (remaining=13454)
[2026-05-28T20:11:46] Filtering multi-mapping fusions by alignment score and read support (remaining=5124)
[2026-05-28T20:11:53] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:11:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=4966)
[2026-05-28T20:11:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=4087)
[2026-05-28T20:11:53] Filtering fusions with <2 supporting reads (remaining=128)
[2026-05-28T20:11:53] Filtering fusions with an e-value >=0.3 (remaining=51)
[2026-05-28T20:11:54] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=51)
[2026-05-28T20:11:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=33)
[2026-05-28T20:11:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=33)
[2026-05-28T20:11:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=27)
[2026-05-28T20:11:55] Searching for fusions with spliced split reads (remaining=27)
[2026-05-28T20:11:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=24)
[2026-05-28T20:11:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=24)
[2026-05-28T20:11:56] Searching for fusions with >=4 spliced events (remaining=24)
[2026-05-28T20:11:57] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8)
[2026-05-28T20:12:24] Filtering fusions with anchors <=23nt (remaining=5)
[2026-05-28T20:12:24] Filtering end-to-end fusions with low support (remaining=5)
[2026-05-28T20:12:24] Filtering fusions with no coverage around the breakpoints (remaining=5)
[2026-05-28T20:12:24] Indexing gene sequences 
[2026-05-28T20:12:24] Filtering genes with >=30% identity (remaining=4)
[2026-05-28T20:12:24] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:12:25] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:12:25] Searching for additional isoforms (remaining=0)
[2026-05-28T20:12:25] Assigning confidence scores to events 
[2026-05-28T20:12:25] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:12:26] Writing fusions to file 'ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:12:26] Writing discarded fusions to file 'ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:12:29] Freeing resources
[2026-05-28T20:12:34] Done (elapsed time=00:02:09, CPU time=00:02:08, peak memory=5.66gb)