[2026-05-28T20:11:57] Launching Arriba 2.4.0
[2026-05-28T20:11:57] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:12:11] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:12:16] Reading chimeric alignments from 'ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1871771)
[2026-05-28T20:12:54] Marking multi-mapping alignments (marked=1556308)
[2026-05-28T20:12:54] Detecting strandedness (no)
[2026-05-28T20:12:54] Annotating alignments 
[2026-05-28T20:13:02] Filtering duplicates (remaining=787941)
[2026-05-28T20:13:03] 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=676841)
[2026-05-28T20:13:04] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=676841)
[2026-05-28T20:13:04] Filtering viral contigs with expression lower than the top 5 (remaining=676841)
[2026-05-28T20:13:05] Filtering viral contigs with less than 5% coverage (remaining=676841)
[2026-05-28T20:13:06] Estimating fragment length (mate gap mean=-57.1187, mate gap stddev=30.7617, read length mean=92.0144)
[2026-05-28T20:13:06] Filtering read-through fragments with a distance <=10000bp (remaining=654481)
[2026-05-28T20:13:06] Filtering inconsistently clipped mates (remaining=634654)
[2026-05-28T20:13:07] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=579474)
[2026-05-28T20:13:07] Filtering fragments with small insert size (remaining=578790)
[2026-05-28T20:13:08] Filtering alignments with long gaps (remaining=578790)
[2026-05-28T20:13:08] Filtering fragments with both mates in the same gene (remaining=578323)
[2026-05-28T20:13:09] Filtering fusions arising from hairpin structures (remaining=542263)
[2026-05-28T20:13:09] Filtering reads with a mismatch p-value <=0.01 (remaining=114231)
[2026-05-28T20:13:11] Filtering reads with low entropy (k-mer content >=60%) (remaining=45675)
[2026-05-28T20:13:12] Finding fusions and counting supporting reads (total=47339)
[2026-05-28T20:13:14] Merging adjacent fusion breakpoints (remaining=46981)
[2026-05-28T20:13:14] Filtering multi-mapping fusions by alignment score and read support (remaining=18956)
[2026-05-28T20:13:20] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:13:21] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=18663)
[2026-05-28T20:13:21] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=13788)
[2026-05-28T20:13:21] Filtering fusions with <2 supporting reads (remaining=328)
[2026-05-28T20:13:21] Filtering fusions with an e-value >=0.3 (remaining=151)
[2026-05-28T20:13:21] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=155)
[2026-05-28T20:13:22] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=126)
[2026-05-28T20:13:22] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=126)
[2026-05-28T20:13:22] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=105)
[2026-05-28T20:13:23] Searching for fusions with spliced split reads (remaining=106)
[2026-05-28T20:13:23] Selecting best breakpoints from genes with multiple breakpoints (remaining=92)
[2026-05-28T20:13:24] Filtering read-through fusions with breakpoints near the gene boundary (remaining=91)
[2026-05-28T20:13:24] Searching for fusions with >=4 spliced events (remaining=91)
[2026-05-28T20:13:24] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=15)
[2026-05-28T20:13:38] Filtering fusions with anchors <=23nt (remaining=9)
[2026-05-28T20:13:38] Filtering end-to-end fusions with low support (remaining=8)
[2026-05-28T20:13:38] Filtering fusions with no coverage around the breakpoints (remaining=8)
[2026-05-28T20:13:38] Indexing gene sequences 
[2026-05-28T20:13:39] Filtering genes with >=30% identity (remaining=3)
[2026-05-28T20:13:39] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=1)
[2026-05-28T20:13:39] Selecting best breakpoints from genes with multiple breakpoints (remaining=1)
[2026-05-28T20:13:39] Searching for additional isoforms (remaining=1)
[2026-05-28T20:13:39] Assigning confidence scores to events 
[2026-05-28T20:13:40] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:13:40] Writing fusions to file 'ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:13:40] Writing discarded fusions to file 'ColoN_FFPE_L01_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:13:44] Freeing resources
[2026-05-28T20:13:48] Done (elapsed time=00:01:51, CPU time=00:01:50, peak memory=6.02gb)