fastStructure input file error

[jtc...@bucknell.edu]

Hi all,

I've been attempting to run fastStructure on a large SNP dataset all day and have successfully built it and ran the test data. But, I keep running into an input file error with my own data via the following:

$ python structure.py -K 6 --input=solanum9/batch_44.structure_Solanum9 --output=solanum9/batch_44.structure_Solanum9output_simple --format=str --full --seed=123
Traceback (most recent call last):
File "structure.py", line 172, in <module>
G = parse_str.load(params['inputfile'])
File "parse_str.pyx", line 7, in parse_str.load (parse_str.c:1334)
handle = open(file+'.str','r')
IOError: [Errno 2] No such file or directory: 'solanum9/batch_44.structure_Solanum9.str'

I'm at a loss as what to do next. Any help you can give would be great

The input file is 603 MB and I assume is too large for the Structure front end to load (perpetually stuck in the final steps of the new project wizard when inputing data).

Thanks,

Jason

[Vikram Chhatre]

Jason -

Try renaming your file by removing the period.

batch_44_structure_Solanum9.str

Also make sure that the formatting requirements are met.  FastStructure format has several empty columns in the beginning.

V

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[Omar Hamarsheh]

I experienced the same problem, I think the point is removing hidden formats added by the txt editor. any suggestion would be greatly appreciated.

thanks

omar

[Vikram Chhatre]

Omar -

The error in the post you replied to is not of that nature.  You need to tell us a bit more about the errors you are getting running fastStructure.

V

--

[Omar Hamarsheh]

Hi Vikram

the error is 

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

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

  File "parse_str.pyx", line 22, in parse_str.load (parse_str.c:1692)

    major = alleles[0]

the input file has been generated from VCF file using PGDspider

thank you

On Monday, January 25, 2016 at 9:13:08 PM UTC-5, Vikram Chhatre wrote:

Omar -

The error in the post you replied to is not of that nature.  You need to tell us a bit more about the errors you are getting running fastStructure.

V

On Mon, Jan 25, 2016 at 8:57 PM, Omar Hamarsheh <ohama...@gmail.com> wrote:

I experienced the same problem, I think the point is removing hidden formats added by the txt editor. any suggestion would be greatly appreciated.

thanks

omar

On Friday, January 8, 2016 at 4:54:42 PM UTC-5, jtc...@bucknell.edu wrote:

Hi all,

I've been attempting to run fastStructure on a large SNP dataset all day and have successfully built it and ran the test data. But, I keep running into an input file error with my own data via the following:

$ python structure.py -K 6 --input=solanum9/batch_44.structure_Solanum9 --output=solanum9/batch_44.structure_Solanum9output_simple --format=str --full --seed=123
Traceback (most recent call last):
  File "structure.py", line 172, in <module>
    G = parse_str.load(params['inputfile'])
  File "parse_str.pyx", line 7, in parse_str.load (parse_str.c:1334)
    handle = open(file+'.str','r')
IOError: [Errno 2] No such file or directory: 'solanum9/batch_44.structure_Solanum9.str'

I'm at a loss as what to do next. Any help you can give would be great

The input file is 603 MB and I assume is too large for the Structure front end to load (perpetually stuck in the final steps of the new project wizard when inputing data).

Thanks,

Jason

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[Vikram Chhatre]

Most likely you have some monomorphic sites left in the data.  Need to remove those before FS will run.

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[Omar Hamarsheh]

thanks Vikram 

any suggestion on how to get them removed...I have huge dataset about 1.2 G

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[Vikram Chhatre]

There is an option in PGD to exclude monomorphic sites. 

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