error running fastStructure

[Norhalida mohamed serdari]

Hi everyone,

I wanted to run population structure analysis using fastStructure. My data file is in .str format which contains 700 samples and 2300 SNPs. So I've formatted my data with first four columns as blank then my sample ID ( column 5), population info (column 6) the rest of the columns is my SNPs data. Then I ran the analysis using default script and it gave me the following message.

[Dida@opgp-sgi fastStructure-1.0]$ python structure.py -K 3 --input=test/germ1 --output=test/germ1output_simple --format=str --full --seed=100

Traceback (most recent call last):

  File "structure.py", line 172, in <module>

    G = parse_str.load(params['inputfile'])

  File "parse_str.pyx", line 10, in parse_str.load (parse_str.c:1468)

    L = loci.shape[1]

IndexError: tuple index out of range

First I would like to know is my input data file correct? 

Then, why it say the tuple index out of range? 

Hope someone can give some advice.

Thanks & Regards,

Dida-

[f.pina...@gmail.com]

Hi Dida,

fastStructure is not very helpfull with error messages.
See if Structure_threader's docs can help:
http://structure-threader.readthedocs.io/en/latest/usage/#faststrucutre-warning

If you format you input file as in the example, things **should** work.

Best,

Francisco

[Norhalida mohamed serdari]

Hi Francisco,

Finally, I figured out what the issue was and now the analysis is running. 

And thanks for the link :)

Regards,

Dida

[f.pina...@gmail.com]

Glad I could help.

Best,

Francisco