Error in reading paf file

[nina-maryn]

Hello! I am trying to use dotPlotly to compare a PacBio long read de novo assembly (produced with PacBio's assembler IPA) to a reference genome to visualize structural variations. I aligned the assembly to the reference using minimap2. The paf file is full and can be read using R pafr read_paf. I was able to get dotPlotly to work beautifully for my other assembly and a test ref-to-ref alignment, so I know the program works on my cluster setup.

Here is the error I'm getting for my assembly that isn't working:
PARAMETERS:
input (-i): N19_1_158_T1_IPAp_minimap2.paf
output (-o): N19_1_158_T1_IPAp_minimap2.plot
minimum query aggregate alignment length (-q): 3e+05
minimum alignment length (-m): 1000
plot size (-p): 12
show horizontal lines (-l): TRUE
number of reference chromosomes to keep (-k): 10
show % identity (-s): TRUE
show % identity for on-target alignments only (-t): TRUE
produce interactive plot (-x): TRUE
reference IDs to keep (-r):
Error in read.table(opt$input_filename, stringsAsFactors = F, fill = T) :
duplicate 'row.names' are not allowed
No traceback available
Error in colnames(alignments)[1:12] = c("queryID", "queryLen", "queryStart", :
object 'alignments' not found
2: stop("duplicate 'row.names' are not allowed")
1: read.table(opt$input_filename, stringsAsFactors = F, fill = T)
Error: object 'alignments' not found
No traceback available
Error: object 'alignments' not found
No traceback available
Error: object 'alignments' not found
No traceback available
Error: object 'queryStartTemp' not found
No traceback available
Warning message:
In rm(queryStartTemp) : object 'queryStartTemp' not found
Error in nrow(alignments) : object 'alignments' not found
Calls: cat -> paste0 -> nrow
No traceback available
Error in unique(alignments$queryID) : object 'alignments' not found
Calls: cat -> paste0 -> unique
3: nrow(alignments)
2: paste0("\nNumber of alignments: ", nrow(alignments), "\n")
1: cat(paste0("\nNumber of alignments: ", nrow(alignments), "\n"))
Error in tapply(alignments$refEnd, alignments$refID, max) :
object 'alignments' not found
3: unique(alignments$queryID)
2: paste0("Number of query sequences: ", length(unique(alignments$queryID)),
"\n")
1: cat(paste0("Number of query sequences: ", length(unique(alignments$queryID)),
"\n"))
Error in tapply(alignments$lenAln, alignments$queryID, sum) :
object 'alignments' not found
1: tapply(alignments$refEnd, alignments$refID, max)
Error: object 'alignments' not found
1: tapply(alignments$lenAln, alignments$queryID, sum)
Error: object 'alignments' not found
No traceback available
Error in tapply(alignments$lenAln, alignments$queryID, sum) :
object 'alignments' not found
No traceback available
Error: object 'alignments' not found
1: tapply(alignments$lenAln, alignments$queryID, sum)
Error in nrow(alignments) : object 'alignments' not found
Calls: cat -> paste0 -> nrow
No traceback available
Error in unique(alignments$queryID) : object 'alignments' not found
Calls: cat -> paste0 -> unique
3: nrow(alignments)
2: paste0("\nAfter filtering... Number of alignments: ", nrow(alignments),
"\n")
1: cat(paste0("\nAfter filtering... Number of alignments: ", nrow(alignments),
"\n"))
Error in factor(alignments$refID, levels = refIDsToKeepOrdered) :
object 'alignments' not found
3: unique(alignments$queryID)
2: paste0("After filtering... Number of query sequences: ", length(unique(alignments$queryID)),
"\n\n")
1: cat(paste0("After filtering... Number of query sequences: ",
length(unique(alignments$queryID)), "\n\n"))
Error: object 'alignments' not found
1: factor(alignments$refID, levels = refIDsToKeepOrdered)
Error in tapply(alignments$refEnd, alignments$refID, max) :
object 'alignments' not found
No traceback available
Error in levels(alignments$refID) : object 'alignments' not found
1: tapply(alignments$refEnd, alignments$refID, max)
Error in factor(alignments$queryID, levels = unique(as.character(alignments$queryID))) :
object 'alignments' not found
1: levels(alignments$refID)
Error in tapply(alignments$lenAln, alignments$queryID, which.max, simplify = F) :
object 'alignments' not found
1: factor(alignments$queryID, levels = unique(as.character(alignments$queryID)))
Error in factor(alignments$queryID, levels = unique(as.character(alignments$queryID))[order(mapply(function(x, :
object 'alignments' not found
1: tapply(alignments$lenAln, alignments$queryID, which.max, simplify = F)
Error in levels(alignments$queryID) : object 'alignments' not found
Calls: sapply -> lapply -> levels
1: factor(alignments$queryID, levels = unique(as.character(alignments$queryID))[order(mapply(function(x,
i) alignments$refStart2[which(i == alignments$queryID)][x],
queryMaxAlnIndex, names(queryMaxAlnIndex)))])
Error in levels(alignments$refID) : object 'alignments' not found
3: levels(alignments$queryID)
2: lapply(X = X, FUN = FUN, ...)
1: sapply((levels(alignments$queryID)), function(x) tapply(alignments$lenAln[which(alignments$queryID ==
x)], alignments$refID[which(alignments$queryID == x)], sum))
Error in factor(alignments$queryID, levels = (levels(alignments$queryID))[order(match(queryID_Ref, :
object 'alignments' not found
1: levels(alignments$refID)
Error in tapply(alignments$queryEnd - alignments$queryStart, alignments$queryID, :
object 'alignments' not found
1: factor(alignments$queryID, levels = (levels(alignments$queryID))[order(match(queryID_Ref,
levels(alignments$refID)))])
Error: object 'queryRevComp' not found
1: tapply(alignments$queryEnd - alignments$queryStart, alignments$queryID,
function(x) sum(x))
Error in tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID, :
object 'alignments' not found
No traceback available
Error in levels(alignments$queryID) : object 'alignments' not found
1: tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID,
alignments$queryID), max)
Error: object 'queryMax' not found
1: levels(alignments$queryID)
Error: object 'queryMax' not found
No traceback available
Error in tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID, :
object 'alignments' not found
No traceback available
Error in levels(alignments$queryID) : object 'alignments' not found
1: tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID,
alignments$queryID), min)
Error: object 'alignments' not found
1: levels(alignments$queryID)
Error: object 'alignments' not found
No traceback available
Error in tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID, :
object 'alignments' not found
No traceback available
Error in levels(alignments$queryID) : object 'alignments' not found
1: tapply(c(alignments$queryEnd, alignments$queryStart), c(alignments$queryID,
alignments$queryID), max)
Error: object 'alignments' not found
1: levels(alignments$queryID)
Error: object 'alignments' not found
No traceback available
Error in levels(alignments$refID) : object 'alignments' not found
No traceback available
Error in tapply(alignments$queryEnd2, alignments$queryID, max) :
object 'alignments' not found
1: levels(alignments$refID)
Error in ggplot(alignments) : object 'alignments' not found
1: tapply(alignments$queryEnd2, alignments$queryID, max)
Error in ggplotly(gp, tooltip = "text") : object 'gp' not found
1: ggplot(alignments)

[ghost]

Hi, did you manage to fix this?

[Maxim-Karpov]

Hi, did you manage to fix this?

You can try adding "row.names=NULL" argument to "alignments = read.table(opt$input_filename, stringsAsFactors = F, fill = T)" in the script file.

[tallnuttrbgv]

Thanks this worked for me too.