Closed johnacurtin closed 1 year ago
@johnacurtin I just ran the following commands:
wget https://github.com/omerwe/polyfun/raw/master/ukb_regions.tsv.g
zcat ukb_regions.tsv.gz | head -3
and obtained the following output:
CHR START END URL_PREFIX
1 1 3000001 https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr1_1_3000001
1 1000001 4000001 https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr1_1000001_4000001
These are the correct addresses. To verify this, you can run the following command:
wget https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr1_1_3000001.gz
So it looks like the file is indeed updated. Can you please provide more details on the problem you're seeing?
Hi, After your reply I decided to try reinstalling polyfun, That got rid of the download error, ukb_regions.tsv.gz now looks ok and the relevant files were downloaded.
However I now have a new error with the reinstall, [WARNING] R[write to console]: Error in (function (XtX, Xty, yty, n, X_colmeans = NA, y_mean = NA, maf = NULL, : susie_suff_stat no longer accepts inputs bhat, shat, R or var_y; these inputs are now accepted by susie_rss instead
Do I need to install a particular version of rsusie (I have r-susier 0.11.92 as that came with the reinstall) or should I load a particular version of R (I have 4.1.0 loaded) Thanks John
From: Omer Weissbrod @.> Sent: 02 May 2023 19:27 To: omerwe/polyfun @.> Cc: John Curtin @.>; Mention @.> Subject: Re: [omerwe/polyfun] Exact path to UKBB LD files on new google cloud space (Issue #158)
@johnacurtinhttps://github.com/johnacurtin I just ran the following commands:
wget https://github.com/omerwe/polyfun/raw/master/ukb_regions.tsv.g
zcat ukb_regions.tsv.gz | head -3
and obtained the following commands:
CHR START END URL_PREFIX
1 1 3000001 https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr1_1_3000001
1 1000001 4000001 https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr1_1000001_4000001
These are the correct addresses. To verify this, you can run the following command:
wget https://broad-alkesgroup-ukbb-ld.s3.amazonaws.com/UKBB_LD/chr1_1_3000001.gz
So it looks like the file is indeed updated. Can you please provide more details on the problem you're seeing?
— Reply to this email directly, view it on GitHubhttps://github.com/omerwe/polyfun/issues/158#issuecomment-1531947884, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMMWHLBMCS22RRJPYRAGOWTXEFGWLANCNFSM6AAAAAAXTD5P7Q. You are receiving this because you were mentioned.Message ID: @.**@.>>
Do I need to install a particular version of rsusie (I have r-susier 0.11.92 as that came with the reinstall) or should I load a particular version of R (I have 4.1.0 loaded)
Can you please activate the conda env (conda activate polyfun
) and then run the following diagnostics in R?
.libPaths()
packageVersion("susieR")
Hi
Thanks for getting back. I normally load like this conda activate polyfun module load apps/gcc/R/4.1.0 in that case I get [2] "/opt/apps/apps/gcc/R/4.1.0/lib64/R/library"
packageVersion("susieR") [1] ‘0.12.35’
When I just do as you suggest ( and do not load R separately) conda activate polyfun I get [1] "/path/.conda/envs/polyfun/lib/R/library" [1] ‘0.11.92’
The installation instruction said we needed to install R, so I assumed I needed to load R. Should I try without loading R and see if that gets rid of the error? John
From: John Blischak @.> Sent: 02 May 2023 21:42 To: omerwe/polyfun @.> Cc: John Curtin @.>; Mention @.> Subject: Re: [omerwe/polyfun] Exact path to UKBB LD files on new google cloud space (Issue #158)
Do I need to install a particular version of rsusie (I have r-susier 0.11.92 as that came with the reinstall) or should I load a particular version of R (I have 4.1.0 loaded)
Can you please activate the conda env (conda activate polyfun) and then run the following diagnostics in R?
.libPaths()
packageVersion("susieR")
— Reply to this email directly, view it on GitHubhttps://github.com/omerwe/polyfun/issues/158#issuecomment-1532121529, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMMWHLFQ4762ZDLZYABJKT3XEFWQNANCNFSM6AAAAAAXTD5P7Q. You are receiving this because you were mentioned.Message ID: @.**@.>>
The installation instruction said we needed to install R, so I assumed I needed to load R. Should I try without loading R and see if that gets rid of the error?
You need to install R yourself only if you are choosing the second option to install everything manually. The first option listed in the README is to install everything via conda (including R)
Thanks very much. I’ve tried it as you suggested and it is working perfectly now. Many thanks
From: John Blischak @.> Sent: 02 May 2023 22:39 To: omerwe/polyfun @.> Cc: John Curtin @.>; Mention @.> Subject: Re: [omerwe/polyfun] Exact path to UKBB LD files on new google cloud space (Issue #158)
The installation instruction said we needed to install R, so I assumed I needed to load R. Should I try without loading R and see if that gets rid of the error?
You need to install R yourself only if you are choosing the second option to install everything manually. The first option listed in the README is to install everything via conda (including R)
— Reply to this email directly, view it on GitHubhttps://github.com/omerwe/polyfun/issues/158#issuecomment-1532188226, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMMWHLB5VIYGU6GIHSDH2BTXEF5HLANCNFSM6AAAAAAXTD5P7Q. You are receiving this because you were mentioned.Message ID: @.**@.>>
Hi, I see there was an issue before https://github.com/omerwe/polyfun/issues/155 where the issue of the exact path to the Exact path to UKBB LD files on new google cloud space was discussed. you mentioned you updated the file ukb_regions.tsv.gz and although the date of the file has changed, the paths within this file are still the same. can you let me know what the new path is so I can update that file myself in my own system,