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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
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.assoc file fails to open. I have tried everything #150

Closed sjmcgeady closed 4 years ago

sjmcgeady commented 5 years ago

Hello I have attached a file that keeps making an error " cannot open base file to read!" but i followed the guidelines and a similar file worked previously. with this file I use the command: Rscript PRSice.R --dir . --prsice PRSice_win64.exe --base AD.PRS.assoc \ --target AD.PRS \ --thread 4 \ --stat BETA \ --binary-target T AD.PRS.assoc.txt

choishingwan commented 5 years ago

Could you please, in the same directory, and using PowerShell (assuming you are on windows), type more AD.PRS.assoc, what'd be the result?

sjmcgeady commented 5 years ago

actually this is the original file screenprint

choishingwan commented 5 years ago

Your header and the file content doesn't match. Are you sure this is the correct file? Also could you please send out the full log?

sjmcgeady commented 5 years ago

Hi sorry for the late response. I did have the wrong file but it still is not working. is the headers still the issue? screenprint

choishingwan commented 5 years ago

I’ll need the log file to know what’s going on -- Dr Shing Wan Choi Postdoctoral Fellow Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC

sjmcgeady commented 5 years ago

Hi Dr Choi, I have been ill the last few weeks. Here is the log file AD.PRS.log

sjmcgeady commented 5 years ago

It should be noted I recieved the Betas and the P values from a paper so the log may not show this

choishingwan commented 5 years ago

That's the log file for PLINK, not for PRSice.

sjmcgeady commented 5 years ago

Sorry for the confusion. I Guess I am still confused about how this works, my PRSice program will not run with the assoc, bit, bam so I do not know how it could create a log file

MingCHEN4 commented 4 years ago

Hello choishingwan,

I also encountered problem of reading asso file, for my case, I tried to use the downloaded PRSice.R file to do quick example PRS calculation first. head 10 lines of the TOY_BASE_GWAS.assoc looks like image

the command was from website: Rscript PRSice.R --dir . --prsice . --base TOY_BASE_GWAS.assoc --target TOY_TARGET_DATA --thread 1 --stat OR --binary-target T

I am sure the current dir include all the downloaded data, but i got error msn saying

sh: 1: .: --base: not found Error: Execution halted

I am not sure where gone wrong, could you give me a hand of this case please?

Thanks in advance! Ming

choishingwan commented 4 years ago

For the —prsice flag, you need to point to the full path of the PRSice.

-- Dr Shing Wan Choi Postdoctoral Fellow Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC

MingCHEN4 commented 4 years ago

For the —prsice flag, you need to point to the full path of the PRSice. … -- Dr Shing Wan Choi Postdoctoral Fellow Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC

Thanks for reply!

Actually I firstly cd to the dir containing all the data downloaded, so I left '.' to indicate current dir. But I still tested new command with every option specifying dir to work with, i.e. Rscript PRSice.R --dir ~/PRSice-2 --prsice ~/PRSice-2 --base ~/PRSice-2/TOY_BASE_GWAS.assoc --target ~/PRSice-2/TOY_TARGET_DATA --thread 1 --stat OR --binary-target T

then i got errors

sh: 1: /home/user/PRSice-2: Permission denied Error: Execution halted

I cannot quite understand the mentioned "Permission" here, I chmod to both the dir and data files with write and execute permission (rwx all added), but the problem was still unsolved.

So how can I check where the problem was? Thanks!

Regards, Ming

choishingwan commented 4 years ago

--prsice need to point to the executable, not the folder. So assuming your folder contains the following:

PRSice_linux (assuming you are on linux) PRSice.R TOY_BASE_GWAS.assoc TOY_TARGET_DATA.fam TOY_TARGET_DATA.bim TOY_TARGET_DATA.bam

You need to do

Rscript PRSice.R --dir . --prsice PRSice_linux --base TOY_BASE_GWAS.assoc --target TOY_TARGET_DATA

You should be able to see all this information on our website prsice.info

From: Ming CHEN notifications@github.com Reply-To: choishingwan/PRSice reply@reply.github.com Date: Tuesday, October 22, 2019 at 1:33 AM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Shing Wan Choi choishingwan@gmail.com, Comment comment@noreply.github.com Subject: Re: [choishingwan/PRSice] .assoc file fails to open. I have tried everything (#150)

For the —prsice flag, you need to point to the full path of the PRSice. … -- Dr Shing Wan Choi Postdoctoral Fellow Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC

Thanks for reply!

Actually I firstly cd to the dir containing all the data downloaded, so I left '.' to indicate current dir. But I still tested new command with every option specifying dir to work with, i.e. Rscript PRSice.R --dir ~/PRSice-2 --prsice ~/PRSice-2 --base ~/PRSice-2/TOY_BASE_GWAS.assoc --target ~/PRSice-2/TOY_TARGET_DATA --thread 1 --stat OR --binary-target T

then i got errors

sh: 1: /home/user/PRSice-2: Permission denied Error: Execution halted

Regards, Ming

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/choishingwan/PRSice/issues/150?email_source=notifications&email_token=AAJTRYULPIUHR6RJJS7PR5TQP2GBHA5CNFSM4IVKKOW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEB4SQFQ#issuecomment-544811030, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAJTRYRGXFJB63WEDEOHZX3QP2GBHANCNFSM4IVKKOWQ.

MingCHEN4 commented 4 years ago

--prsice need to point to the executable, not the folder. So assuming your folder contains the following: PRSice_linux (assuming you are on linux) PRSice.R TOY_BASE_GWAS.assoc TOY_TARGET_DATA.fam TOY_TARGET_DATA.bim TOY_TARGET_DATA.bam You need to do Rscript PRSice.R --dir . --prsice PRSice_linux --base TOY_BASE_GWAS.assoc --target TOY_TARGET_DATA You should be able to see all this information on our website prsice.info From: Ming CHEN notifications@github.com Reply-To: choishingwan/PRSice reply@reply.github.com Date: Tuesday, October 22, 2019 at 1:33 AM To: choishingwan/PRSice PRSice@noreply.github.com Cc: Shing Wan Choi choishingwan@gmail.com, Comment comment@noreply.github.com Subject: Re: [choishingwan/PRSice] .assoc file fails to open. I have tried everything (#150) For the —prsice flag, you need to point to the full path of the PRSice. … -- Dr Shing Wan Choi Postdoctoral Fellow Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC Thanks for reply! Actually I firstly cd to the dir containing all the data downloaded, so I left '.' to indicate current dir. But I still tested new command with every option specifying dir to work with, i.e. Rscript PRSice.R --dir ~/PRSice-2 --prsice ~/PRSice-2 --base ~/PRSice-2/TOY_BASE_GWAS.assoc --target ~/PRSice-2/TOY_TARGET_DATA --thread 1 --stat OR --binary-target T then i got errors sh: 1: /home/user/PRSice-2: Permission denied Error: Execution halted Regards, Ming — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#150?email_source=notifications&email_token=AAJTRYULPIUHR6RJJS7PR5TQP2GBHA5CNFSM4IVKKOW2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEB4SQFQ#issuecomment-544811030>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAJTRYRGXFJB63WEDEOHZX3QP2GBHANCNFSM4IVKKOWQ.

Thanks! It works now!

So I need to specify PRSice_linux to point to the executable.

Nice!

stale[bot] commented 4 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.