dutchscientist
dutchscientist
https://twitter.com/RoyChaudhuri/status/1375493280951988229 This solves it at the level of generating the input file (thanks Roy!), but is it a functionality useful for Clinker to have included?
No worries, very little time myself. There are no outputs as the program just "hangs", and after 10 minutes or so I gave up. It works well with the previous...
It is absolutely a bug in ParSNP, it shouldn't read the header like that. Unfortunately it does and I don't think ParSNP is getting any maintenance/bugrepairs. Currently I just use...
I never run it with pairwise comparisons; does it work with --no_pairwise? That should tell you whether it is a problem with your input files or with the pairwise comparisons.
That depends on what you use it for. For my work the --no_pairwise is fine, but I am not hardcore population structure ;)
Thanks, Andrew. Will have a look once I have a chance!
By downloading complete genomes only, it seems to become more manageable.
No worries, just wandered into it and thought I'll ask. It's a great tool!
Hi Josh, they won't be in the assembly report, they will be downloaded in multifasta file of the completed genome. For an example of specific files, see https://www.ncbi.nlm.nih.gov/genome/plasmids/159? (Listeria monocytogenes...
Apologies, been very busy, will come back on this, but may take a week or more (deadlines).