cdhitGrouping: Too low cluster threshold for the word length.

[xif033]

Hello Thomas,

I have installed the GitHub version and have some issues with the cdhitGrouping function.
This issue is present when I tried to run the function on my dataset, or when I followed the example:
testPG <- .loadPgExample()
testPG <- cdhitGrouping(testPG)

Here the error message:

Error in cdhitC(options, name, showProgress):
Fatal Error:
%s
Program halted !!

Too low cluster threshold for the word length.
Increase the threshold or the tolerance, or decrease the word length.
Traceback:

1. cdhitGrouping(testPG)
2. cdhitGrouping(testPG)
3. .local(object, ...)
4. precluster(object, kmerSize[1], maxLengthDif, geneChunkSize,
   . cdhitOpts)
5. lapply(seq_len(nChunks), function(i) {
   . if (i != 1 && interactive())
   . cat("\n")
   . cdhit(genes(object, subset = seq.int(chunks$start[i], chunks$end[i])),
   . cdhitOpts, "Preclustering")
   . })
6. lapply(seq_len(nChunks), function(i) {
   . if (i != 1 && interactive())
   . cat("\n")
   . cdhit(genes(object, subset = seq.int(chunks$start[i], chunks$end[i])),
   . cdhitOpts, "Preclustering")
   . })
7. FUN(X[[i]], ...)
8. cdhit(genes(object, subset = seq.int(chunks$start[i], chunks$end[i])),
   . cdhitOpts, "Preclustering")
9. cdhitC(options, name, showProgress)

I would really appreciated some help on this issue! Thank you very much!
Best,
Xin

[abrozzi]

testPG <- .loadPgExample()

testPG <- cdhitGrouping(testPG)
Error in cdhitC(options, name, showProgress) :
Fatal Error:
%s
Program halted !!

Too low cluster threshold for the word length.
Increase the threshold or the tolerance, or decrease the word length.

[abrozzi]

I solved specifying the -c parameter:

-c      sequence identity threshold, default 0.9
 	this is the default cd-hit's "global sequence identity" calculated as:
 	number of identical amino acids in alignment
 	divided by the full length of the shorter sequence

In R:

pg <- cdhitGrouping(pg, cdhitOpts=list(c=.9))

HTH