Question: error with running in fastSTRUCTURE
gravatar for Ana
3.4 years ago by
Ana180 wrote:

Hi everyone,

I am trying to visualize the expected admixture proportions inferred by fastStructure by using python This is the command that I am running:

python /global/software/faststructure/faststructure_20150319/ -K 5 --input=${GENO} --output=${OUT}

But I get this error message which I could not figure out what is wrong ...!

Traceback (most recent call last):

  File "/global/software/faststructure/faststructure_20150319/", line 162, in <module>

    admixture, population_indices, population_labels = get_admixture_proportions(params)

  File "/global/software/faststructure/faststructure_20150319/", line 60, in get_admixture_proportions

    handle = open('%s.%d.meanQ'%(params['inputfile'],params['K']),'r')

IOError: [Errno 2] No such file or directory: '/home/shsoudi/H_annuus_GWA_2016/faststructure/output_file_random1_10k_RUN2_distruct/random1_10K_genotype.5.meanQ'

Does anyone has any clue to help me out to figure out the solution and run it. I am quite stuck ... I have checked all of the directions and input files. Everything is OK. Any help is really appreciated

ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 3.4 years ago by Ana180

are you sure that this file home/shsoudi/H_annuus_GWA_2016/faststructure/output_file_random1_10k_RUN2_distruct/random1_10K_genotype.5.meanQ

ADD REPLYlink written 3.4 years ago by Medhat8.8k

Yes, I am quite sure. I've checked many times;

4.0K -rw-r-----  1 shsoudi shsoudi  930 Aug 13 14:07 random1_10K_genotype.5.log
476K -rw-r-----  1 shsoudi shsoudi 474K Aug 13 14:07 random1_10K_genotype.5.meanP
 16K -rw-r-----  1 shsoudi shsoudi  16K Aug 13 14:07 random1_10K_genotype.5.meanQ
ADD REPLYlink written 3.4 years ago by Ana180

I'm having the exact same issue. Have you figured out why?

ADD REPLYlink written 8 months ago by rturba070
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