ERROR: At least 2 columns in the phenotype file should be specified, please check the parameter 'sep.phe'.

[rupesht]

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'.

[YinLiLin]

Please convert the phenotype file into ".txt" format file, or set the argument sep.phe="," then have a try again.

[rupesht]

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.

— Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/rMVP/issues/83#issuecomment-1373099258, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB64KNO56PHZS2WG5QS2QZLWQ6GSDANCNFSM6AAAAAATPYGRDI . You are receiving this because you authored the thread.Message ID: @.***>

[rupesht]

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 : @.***

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 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.

— Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/rMVP/issues/83#issuecomment-1373099258, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB64KNO56PHZS2WG5QS2QZLWQ6GSDANCNFSM6AAAAAATPYGRDI . You are receiving this because you authored the thread.Message ID: @.***>

[YinLiLin]

Please check if there is a file named "mytest.phe" in the work directory.

[rupesht]

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.

— Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/rMVP/issues/83#issuecomment-1374412226, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB64KNMB3C7PZ3ACFOGZEFDWREQRBANCNFSM6AAAAAATPYGRDI . You are receiving this because you authored the thread.Message ID: @.***>

[rupesht]

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.

— Reply to this email directly, view it on GitHub https://github.com/xiaolei-lab/rMVP/issues/83#issuecomment-1374412226, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB64KNMB3C7PZ3ACFOGZEFDWREQRBANCNFSM6AAAAAATPYGRDI . You are receiving this because you authored the thread.Message ID: @.***>