Question about an error using smartpca

[moscato13]

I used the tool for Principal Component Analysis on GWAS using the 70000 genome data as follows .
(I used plink formatted file called .bed, .bim, .fam and total number of samples I used is 72999.)

1. Make par file
   

2. Execute Command line

EIG-6.1.4/bin/smartpca -p test.par

But there was an error like this.

So I'd like to know how to solve this error.

We hope to hear from you soon.

Sincerely

[bumblenick]

Hard to debug remotely but some hints 1) run convertf to make .ind .snp .geno files 2) set population labels as you wish 3) set most of you samples to Ignore and run smartpca to check formats ============ After that works then You have a huge number of samples --- > 70K; you need to run with fastmode: YES and having more samples than snps is dubious. Nick

…

On Wed, Feb 19, 2020 at 1:08 AM moscato13 ***@***.***> wrote: I used the tool for Principal Component Analysis on GWAS using the 70000 genome data as follows . (I used plink formatted file called .bed, .bim, .fam and total number of samples I used is 72999.) 1. Make par file [image: image] <https://user-images.githubusercontent.com/52377866/74806574-a11cb880-5329-11ea-8310-85a685021e83.png> 2. Execute Command line EIG-6.1.4/bin/smartpca -p test.par But there was an error like this. [image: image] <https://user-images.githubusercontent.com/52377866/74806539-9104d900-5329-11ea-96e4-70d917b8a4cc.png> So I'd like to know how to solve this error. We hope to hear from you soon. Sincerely — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#43?email_source=notifications&email_token=AEE77B6YDRHE2YDNXAYTBJDRDTEFXA5CNFSM4KXSR3C2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IOQ5AFQ>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEE77BYMDSYV4YMVHVNSMPTRDTEFXANCNFSM4KXSR3CQ> .

[bumblenick]

Oh. Run convertf with famiynames: NO On Wed, Feb 19, 2020 at 8:54 AM Nick Patterson <[email protected]> wrote:

…

Hard to debug remotely but some hints 1) run convertf to make .ind .snp .geno files 2) set population labels as you wish 3) set most of you samples to Ignore and run smartpca to check formats ============ After that works then You have a huge number of samples --- > 70K; you need to run with fastmode: YES and having more samples than snps is dubious. Nick On Wed, Feb 19, 2020 at 1:08 AM moscato13 ***@***.***> wrote: > I used the tool for Principal Component Analysis on GWAS using the 70000 > genome data as follows . > (I used plink formatted file called .bed, .bim, .fam and total number of > samples I used is 72999.) > > 1. > > Make par file > [image: image] > <https://user-images.githubusercontent.com/52377866/74806574-a11cb880-5329-11ea-8310-85a685021e83.png> > 2. > > Execute Command line > > EIG-6.1.4/bin/smartpca -p test.par > > But there was an error like this. > [image: image] > <https://user-images.githubusercontent.com/52377866/74806539-9104d900-5329-11ea-96e4-70d917b8a4cc.png> > > So I'd like to know how to solve this error. > > We hope to hear from you soon. > > Sincerely > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub > <#43?email_source=notifications&email_token=AEE77B6YDRHE2YDNXAYTBJDRDTEFXA5CNFSM4KXSR3C2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IOQ5AFQ>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AEE77BYMDSYV4YMVHVNSMPTRDTEFXANCNFSM4KXSR3CQ> > . >