Runtime error in MAGScot.R when clustering solutions use identical naming syntax.

[cerebis]

An error occurs in MAGScot.R when the bin to contig file has more than one solution set and the naming syntax for the clusters is identical.

Although this scenario sounds far-fetched, it can occur if you supply different solutions from the same tool. It does not matter if the "Binner" (set names) are unique per solution.

The reported error is:

Error in UseMethod("tbl_vars") :
  no applicable method for 'tbl_vars' applied to an object of class "NULL"

And happens somewhere within:

MAGScoT/MAGScoT.R

Lines 130 to 140 in 0b7b6d1

	binmatch=sapply(seq_along(merge_cand), function(thisbin_id){
	cat("Processing candidate bin ",thisbin_id, " of ", length(merge_cand),"\r")
	thisbin = merge_cand[thisbin_id]
	thisbin_contigs = contig_to_bin_bisco_it %>% filter(bin == thisbin, contig %in% gene_to_contig$contig) %>% pull(contig)
	thisbin_genes = gene_to_contig %>% filter(contig %in% thisbin_contigs)
	if(it>1){thisbin_blacklist = bisco_out %>% filter(bin==thisbin) %>% select(bin_a, bin_b) %>% unlist %>% as.vector()}else{thisbin_blacklist=c()}
	return(contig_to_bin %>% filter(contig %in% thisbin_genes$contig) %>% left_join(thisbin_genes, by="contig") %>%
	distinct_at(.vars=c("bin","gene"), .keep_all=T) %>% group_by(bin) %>% summarize(shared_markers=n()) %>%
	mutate(shared_markers_rel = shared_markers/length(unique(thisbin_genes$gene))) %>% filter(bin != thisbin, !bin %in% thisbin_blacklist, shared_markers_rel >= min_sharing) %>%
	mutate(seed=thisbin, bin_a=ifelse(seed>bin, seed, bin), bin_b=ifelse(seed>bin, bin, seed)) %>% select(seed, bin_a, bin_b, shared_markers, shared_markers_rel))
	}, simplify=F)

The error was resolved when the cluster names for one solution were made distinct by adding a single character to each cluster name.

[mruehlemann]

Hi @cerebis ,
thank you for bringing this to our attention. We will fix this as soon as possible so MAGScoT uses the combination of binner set and cluster name. Until then, you solution to have unique names across the different binning outputs should work just fine!