[2026-05-28T20:16:13] Launching Arriba 2.4.0
[2026-05-28T20:16:13] Loading assembly from 'ref_genome.fa' 
[2026-05-28T20:16:32] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T20:16:37] Reading chimeric alignments from 'ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=3594837)
[2026-05-28T20:18:07] Marking multi-mapping alignments (marked=2883433)
[2026-05-28T20:18:09] Detecting strandedness (no)
[2026-05-28T20:18:09] Annotating alignments 
[2026-05-28T20:18:32] Filtering duplicates (remaining=1068968)
[2026-05-28T20:18:36] 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=940658)
[2026-05-28T20:18:36] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=940658)
[2026-05-28T20:18:37] Filtering viral contigs with expression lower than the top 5 (remaining=940658)
[2026-05-28T20:18:39] Filtering viral contigs with less than 5% coverage (remaining=940658)
[2026-05-28T20:18:40] Estimating fragment length (mate gap mean=-54.3109, mate gap stddev=27.486, read length mean=90.3816)
[2026-05-28T20:18:40] Filtering read-through fragments with a distance <=10000bp (remaining=928402)
[2026-05-28T20:18:41] Filtering inconsistently clipped mates (remaining=898324)
[2026-05-28T20:18:42] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=789076)
[2026-05-28T20:18:44] Filtering fragments with small insert size (remaining=788003)
[2026-05-28T20:18:44] Filtering alignments with long gaps (remaining=788003)
[2026-05-28T20:18:45] Filtering fragments with both mates in the same gene (remaining=787418)
[2026-05-28T20:18:46] Filtering fusions arising from hairpin structures (remaining=748819)
[2026-05-28T20:18:47] Filtering reads with a mismatch p-value <=0.01 (remaining=146427)
[2026-05-28T20:18:49] Filtering reads with low entropy (k-mer content >=60%) (remaining=65527)
[2026-05-28T20:18:51] Finding fusions and counting supporting reads (total=71335)
[2026-05-28T20:18:57] Merging adjacent fusion breakpoints (remaining=71130)
[2026-05-28T20:18:57] Filtering multi-mapping fusions by alignment score and read support (remaining=25979)
[2026-05-28T20:19:15] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T20:19:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=25396)
[2026-05-28T20:19:18] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=22847)
[2026-05-28T20:19:18] Filtering fusions with <2 supporting reads (remaining=308)
[2026-05-28T20:19:18] Filtering fusions with an e-value >=0.3 (remaining=108)
[2026-05-28T20:19:18] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=108)
[2026-05-28T20:19:20] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=60)
[2026-05-28T20:19:20] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=60)
[2026-05-28T20:19:20] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=58)
[2026-05-28T20:19:23] Searching for fusions with spliced split reads (remaining=60)
[2026-05-28T20:19:26] Selecting best breakpoints from genes with multiple breakpoints (remaining=55)
[2026-05-28T20:19:26] Filtering read-through fusions with breakpoints near the gene boundary (remaining=54)
[2026-05-28T20:19:26] Searching for fusions with >=4 spliced events (remaining=54)
[2026-05-28T20:19:26] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=17)
[2026-05-28T20:19:50] Filtering fusions with anchors <=23nt (remaining=14)
[2026-05-28T20:19:50] Filtering end-to-end fusions with low support (remaining=12)
[2026-05-28T20:19:50] Filtering fusions with no coverage around the breakpoints (remaining=10)
[2026-05-28T20:19:51] Indexing gene sequences 
[2026-05-28T20:19:51] Filtering genes with >=30% identity (remaining=5)
[2026-05-28T20:19:51] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-05-28T20:19:52] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-05-28T20:19:52] Searching for additional isoforms (remaining=0)
[2026-05-28T20:19:53] Assigning confidence scores to events 
[2026-05-28T20:19:54] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T20:19:54] Writing fusions to file 'ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-05-28T20:19:55] Writing discarded fusions to file 'ColoN_FFPE_L07_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-05-28T20:20:04] Freeing resources
[2026-05-28T20:20:15] Done (elapsed time=00:04:02, CPU time=00:04:01, peak memory=7.74gb)