A small subset of samples running in sample directory

[ghost]

Hello,

I have been having an issue while running parsnp. Sometimes parsnp only includes a very limited number samples in the sample_directory. It normally is under 10 samples.

I run them like this:
parsnp -g Enterobacter_aerogenes_KCTC_2190.gb -r Enterobacter_aerogenes_KCTC_2190.fna -d sample_directory -p 20 -o output_directory/

I have 26 contig files and I downloaded 150 scaffolds of the same bacterial genome. However, I'm unable to include all of the 176 samples together. I've only been able to get 100 samples to run together. I have been able to get all them to work with smaller sample numbers therefore I do not think it is the file itself.

Any tips?

Thanks
Samantha