ERROR: At least 2 columns in the phenotype file should be specified, please check the parameter 'sep.phe'. #83
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Please convert the phenotype file into ".txt" format file, or set the argument |
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Thank you for your suggestions i will tryout and let you know if any
difficulties arise.
…On Fri, Jan 6, 2023, 12:29 PM Lilin Yin ***@***.***> wrote:
Please convert the phenotype file into ".txt" format file, or set the
argument sep.phe="," then have a try again.
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Dear Xiaolei-Lab/Rmvp Team,
I am getting a new error now, as I used the suggested text. file. Kindly
suggest what I should do.
Preparation for GENOTYPE data is done within 2m42s
200 common individuals between phenotype and genotype.
Preparation for PHENOTYPE data is Done within 0s
Imputing...out is NULL, impute inplace.
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|Impute Genotype File is done!
MVP data prepration accomplished successfully!Browse[1]> pheno <-
read.table("mytest.phe", header = TRUE)Error during wrapup: cannot
open the connection
Error: no more error handlers available (recursive errors?); invoking
'abort' restart
Browse[1]>
*(Postdoctoral Researcher) *
*Ph.D.** Plant BioScience*
School of Applied Biosciences
College of Agriculture and Life Sciences
Kyungpook National University[image: KNU logo에 대한 이미지 검색결과]
80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea
E-mail : ***@***.***
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…On Fri, Jan 6, 2023 at 12:29 PM Lilin Yin ***@***.***> wrote:
Please convert the phenotype file into ".txt" format file, or set the
argument sep.phe="," then have a try again.
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Please check if there is a file named "mytest.phe" in the work directory. |
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When i restart R, now getting following error,
MVP.Data(filePhe = "Pheno_r.txt", fileVCF = "rice_qc_out_vcf.vcf" , out = "mvp")Preparing data for MVP...
Reading file...Error in vcf_parser_map(vcf_file = vcf_file, out = out) :
ERROR: Wrong VCF file, no line begin with "#CHROM".>
MVP.Data(filePhe = "Pheno_r.txt", fileVCF = "rice_qc_out_gws.vcf"
, out = "mvp")
*(Postdoctoral Researcher) *
*Ph.D.** Plant BioScience*
School of Applied Biosciences
College of Agriculture and Life Sciences
Kyungpook National University[image: KNU logo에 대한 이미지 검색결과]
80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea
E-mail : ***@***.***
<https://scholar.google.com/citations?user=kupmg_UAAAAJ&hl=en>
<https://www.researchgate.net/profile/Rupesh_Tayade>
<https://www.linkedin.com/in/dr-rupesh-tayade-b519aa22/>
<https://twitter.com/Rupeshtayade> <https://orcid.org/my-orcid>
<https://twitter.com/Rupeshtayade>
…On Sat, Jan 7, 2023 at 5:13 PM Lilin Yin ***@***.***> wrote:
Please check if there is a file named "mytest.phe" in the work directory.
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I resolved the previous issue but while running, it aborted the process,
showing the following error that R encountered a fatal error. Please help
out how to deal with it.
[image: image.png]
*(Postdoctoral Researcher) *
*Ph.D.** Plant BioScience*
School of Applied Biosciences
College of Agriculture and Life Sciences
Kyungpook National University[image: KNU logo에 대한 이미지 검색결과]
80 Daehakro, Bukgu, Daegu, 41566, Republic of Korea
E-mail : ***@***.***
<https://scholar.google.com/citations?user=kupmg_UAAAAJ&hl=en>
<https://www.researchgate.net/profile/Rupesh_Tayade>
<https://www.linkedin.com/in/dr-rupesh-tayade-b519aa22/>
<https://twitter.com/Rupeshtayade> <https://orcid.org/my-orcid>
<https://twitter.com/Rupeshtayade>
…On Sat, Jan 7, 2023 at 5:13 PM Lilin Yin ***@***.***> wrote:
Please check if there is a file named "mytest.phe" in the work directory.
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I am getting the following error while running the rMVP (GWAS), kindly suggest how to proceed further and resolve it.
Preparation for GENOTYPE data is done within 4m48s Error in MVP.Data.Pheno(pheno_file = filePhe, out = out, header = TRUE, : ERROR: At least 2 columns in the phenotype file should be specified, please check the parameter 'sep.phe'.
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