[2026-05-28T20:10:33] Launching Arriba 2.4.0
[2026-05-28T20:10:33] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:10:52] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:11:00] Reading chimeric alignments from 'ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1932822)
[2026-05-28T20:11:49] Marking multi-mapping alignments (marked=1692281)
[2026-05-28T20:11:50] Detecting strandedness (reverse)
[2026-05-28T20:11:50] Assigning strands to alignments 
[2026-05-28T20:11:50] Annotating alignments 
[2026-05-28T20:12:01] Filtering duplicates (remaining=771577)
[2026-05-28T20:12:03] 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=577403)
[2026-05-28T20:12:03] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=577403)
[2026-05-28T20:12:04] Filtering viral contigs with expression lower than the top 5 (remaining=577403)
[2026-05-28T20:12:05] Filtering viral contigs with less than 5% coverage (remaining=577403)
[2026-05-28T20:12:05] Estimating fragment length (mate gap mean=-46.1862, mate gap stddev=30.2392, read length mean=81.9331)
[2026-05-28T20:12:06] Filtering read-through fragments with a distance <=10000bp (remaining=567731)
[2026-05-28T20:12:06] Filtering inconsistently clipped mates (remaining=550858)
[2026-05-28T20:12:06] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=501964)
[2026-05-28T20:12:07] Filtering fragments with small insert size (remaining=501331)
[2026-05-28T20:12:07] Filtering alignments with long gaps (remaining=501331)
[2026-05-28T20:12:08] Filtering fragments with both mates in the same gene (remaining=500655)
[2026-05-28T20:12:08] Filtering fusions arising from hairpin structures (remaining=469942)
[2026-05-28T20:12:09] Filtering reads with a mismatch p-value <=0.01 (remaining=79776)
[2026-05-28T20:12:10] Filtering reads with low entropy (k-mer content >=60%) (remaining=31176)
[2026-05-28T20:12:12] Finding fusions and counting supporting reads (total=28255)
[2026-05-28T20:12:16] Merging adjacent fusion breakpoints (remaining=28034)
[2026-05-28T20:12:16] Filtering multi-mapping fusions by alignment score and read support (remaining=10959)
[2026-05-28T20:12:23] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:12:24] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=10632)
[2026-05-28T20:12:24] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=8557)
[2026-05-28T20:12:24] Filtering fusions with <2 supporting reads (remaining=269)
[2026-05-28T20:12:24] Filtering fusions with an e-value >=0.3 (remaining=115)
[2026-05-28T20:12:24] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=116)
[2026-05-28T20:12:24] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=75)
[2026-05-28T20:12:24] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=75)
[2026-05-28T20:12:25] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=65)
[2026-05-28T20:12:25] Searching for fusions with spliced split reads (remaining=70)
[2026-05-28T20:12:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=60)
[2026-05-28T20:12:27] Filtering read-through fusions with breakpoints near the gene boundary (remaining=58)
[2026-05-28T20:12:27] Searching for fusions with >=4 spliced events (remaining=58)
[2026-05-28T20:12:27] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17)
[2026-05-28T20:12:43] Filtering fusions with anchors <=23nt (remaining=13)
[2026-05-28T20:12:43] Filtering end-to-end fusions with low support (remaining=9)
[2026-05-28T20:12:44] Filtering fusions with no coverage around the breakpoints (remaining=9)
[2026-05-28T20:12:44] Indexing gene sequences 
[2026-05-28T20:12:44] Filtering genes with >=30% identity (remaining=6)
[2026-05-28T20:12:44] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-05-28T20:12:44] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-05-28T20:12:44] Searching for additional isoforms (remaining=1)
[2026-05-28T20:12:44] Assigning confidence scores to events 
[2026-05-28T20:12:45] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:12:45] Writing fusions to file 'ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:12:45] Writing discarded fusions to file 'ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:12:49] Freeing resources
[2026-05-28T20:12:52] Done (elapsed time=00:02:19, CPU time=00:02:18, peak memory=6.07gb)