Stuck at tree generation step

[Paul Kirchberger]

Hello!

I am trying to run kSNP3 on a set of 20 genomes with the minimum required parameters (input file, output directory, number of kmers). However, the program seems to get stuck after the SNP finding step.

Number_SNPs: 258421
Finished finding SNPs
Mon 16 Nov 2015 14:14:53 MST
rm: TemporaryFilesToDelete: No such file or directory
mv: No match.
Building parsimony tree
TOO FEW SPECIES
grep: RAxML_info.SNPs_all: No such file or directory
grep: RAxML_info.SNPs_all: No such file or directory
grep: RAxML_info.SNPs_all: No such file or directory
Number of most parsimonious trees from SNPs_all: 0
Score of those trees:

There is definitely a directory TemporaryFilesToDelete in the output directory, in fact it is 5GB in size. The program also created several other output files in the directory. Most seem fine, but annotate_list and SNPs_all_matrix.fasta are empty.

The program is installed into a directory other than usr/local, but I changed both the path and the kSNP3 file accordingly, and the programs seems to have no problem finding other executables/files before the tree building step.

Is there something obvious I am missing that would resolve this issue?

thank you very much

[Paul Kirchberger]

I was able to resolve the issue myself - the input files did not have proper tab separated Genome IDs, causing the program to not recognize them - hence the TOO FEW SPECIES warning. I suppose a moderator could delete this topic or leave it for future reference.

[sara silva]

Hi Paul,

I have a similar problem with one of my datasets (it works fine with the others), but I'm working with assembled contigs.
Were you working with finished genomes ?

Thanks
Sara