POPMAP ERROR : Populations stacks

[Edgar Caballero]

Hello Stacks community,

I am new using stacks and working with populations genetics.  I would like to ask for some guidelines  to asses an error that I am getting from my analysis

I am try to run the populations command after I performed an denovo_map analysis.

I cleaned my popmap discarding those samples with low coverage (20x<) from the files and the format is :

Sample.1.1 <tab>1 

Sample.1.2 <tab>1 

Sample.2.1 <tab>2 

Sample.2.2 <tab>2

After running my job I get the next error 

  Parsing population map...

Error: Malformed population map -- expected 'SAMPLE \t POP [\t GROUP]'. In file '/scratch/genomics/caballeroeg/populations_ana/p2/popma

p_1.txt', line :

 I have all my samples stored in the same location (-P,--in path) , even those with low coverage , but they are not listed in my popmap file. I am not sure if that affects my analysis or I am committing a sintaxis error. 

I would appreciate your help and advise to come across the situtation and run the population analysis,

Thank you very much for your help, 

 

[Catchen, Julian]

Hi, you likely just have a blank line in the file, which you should remove (the latest version of Stacks ignores these extra lines). It is fine to have extra samples in the output directory that are not in your popmap, this is normal as the program is designed to run with multiple, different popmaps.

.

[Edgar Caballero]

Thanks for your help, it worked !

best,

Edgar