[2026-06-08T07:29:23] Launching Arriba 2.4.0
[2026-06-08T07:29:23] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:29:40] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:29:47] Reading chimeric alignments from 'ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1871771)
[2026-06-08T07:30:40] Marking multi-mapping alignments (marked=1556308)
[2026-06-08T07:30:41] Detecting strandedness (no)
[2026-06-08T07:30:41] Annotating alignments 
[2026-06-08T07:30:49] Filtering duplicates (remaining=787941)
[2026-06-08T07:30:51] 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=676841)
[2026-06-08T07:30:51] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=676841)
[2026-06-08T07:30:51] Filtering viral contigs with expression lower than the top 5 (remaining=676841)
[2026-06-08T07:30:52] Filtering viral contigs with less than 5% coverage (remaining=676841)
[2026-06-08T07:30:53] Estimating fragment length (mate gap mean=-57.1187, mate gap stddev=30.7617, read length mean=92.0144)
[2026-06-08T07:30:53] Filtering read-through fragments with a distance <=10000bp (remaining=654481)
[2026-06-08T07:30:53] Filtering inconsistently clipped mates (remaining=634654)
[2026-06-08T07:30:54] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=579474)
[2026-06-08T07:30:54] Filtering fragments with small insert size (remaining=578790)
[2026-06-08T07:30:55] Filtering alignments with long gaps (remaining=578790)
[2026-06-08T07:30:55] Filtering fragments with both mates in the same gene (remaining=578323)
[2026-06-08T07:30:55] Filtering fusions arising from hairpin structures (remaining=542263)
[2026-06-08T07:30:56] Filtering reads with a mismatch p-value <=0.01 (remaining=114231)
[2026-06-08T07:30:57] Filtering reads with low entropy (k-mer content >=60%) (remaining=45675)
[2026-06-08T07:30:58] Finding fusions and counting supporting reads (total=47339)
[2026-06-08T07:31:01] Merging adjacent fusion breakpoints (remaining=46981)
[2026-06-08T07:31:01] Filtering multi-mapping fusions by alignment score and read support (remaining=18956)
[2026-06-08T07:31:08] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:31:09] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=18663)
[2026-06-08T07:31:09] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=13788)
[2026-06-08T07:31:09] Filtering fusions with <2 supporting reads (remaining=328)
[2026-06-08T07:31:09] Filtering fusions with an e-value >=0.3 (remaining=151)
[2026-06-08T07:31:09] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=155)
[2026-06-08T07:31:10] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=126)
[2026-06-08T07:31:10] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=126)
[2026-06-08T07:31:10] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=105)
[2026-06-08T07:31:11] Searching for fusions with spliced split reads (remaining=106)
[2026-06-08T07:31:12] Selecting best breakpoints from genes with multiple breakpoints (remaining=92)
[2026-06-08T07:31:12] Filtering read-through fusions with breakpoints near the gene boundary (remaining=91)
[2026-06-08T07:31:12] Searching for fusions with >=4 spliced events (remaining=91)
[2026-06-08T07:31:12] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15)
[2026-06-08T07:31:37] Filtering fusions with anchors <=23nt (remaining=9)
[2026-06-08T07:31:37] Filtering end-to-end fusions with low support (remaining=8)
[2026-06-08T07:31:37] Filtering fusions with no coverage around the breakpoints (remaining=8)
[2026-06-08T07:31:37] Indexing gene sequences 
[2026-06-08T07:31:37] Filtering genes with >=30% identity (remaining=3)
[2026-06-08T07:31:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-06-08T07:31:37] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-06-08T07:31:38] Searching for additional isoforms (remaining=1)
[2026-06-08T07:31:38] Assigning confidence scores to events 
[2026-06-08T07:31:38] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:31:39] Writing fusions to file 'ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:31:39] Writing discarded fusions to file 'ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:31:44] Freeing resources
[2026-06-08T07:31:48] Done (elapsed time=00:02:25, CPU time=00:02:24, peak memory=6.02gb)