Error:Could not open individual file
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2.7 years ago
kk.mahsa ▴ 140

When I ran the following command to Fst calculation

vcftools --gzvcf All_samples.vcf.gz --weir-fst-pop Pop1_list.txt --weir-fst-pop Pop2_list.txt --fst-window-size 50000 --fst-window-step 25000 --out pop1_pop2_50_25.windowed.weir.txt

I get this error

 Error:Could not open individual file: Pop1_list.txt

format of Pop1_list.txt is one individual per line like

ind1
ind2
ind3

what is wrong?

Fst VCF vcftools • 1.2k views
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2.7 years ago

please provide further information on your current working directory and the directory in which Pop1_list.txt is located.

VCFtools is pseudo-deprecated, by the way.

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Thank you for response; Current working directory located in the one external harddisk that contain only pop1_list.txt and also pop2_list.txt files. The inputted vcf file locate in another folder.

Did you mean the information I gave or do you need other information to help me?

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If these files are in different folders, then your command, as run, will produce an error. Can you please look up 'absolute' and 'relative' paths?

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I put all the input files in one folder and tried running vcftools with absolute and relative paths and unfortunately, still the problem is not solved. Is it possible that my individual files were not prepared properly?But in every file, there should not be people related to a population, each individual per line?

i have 16 samples that 10 samples belong to pop1 and 6 to pop2. I created two text files containing 10 and 6 lines, respectively.

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