Exact path to UKBB LD files on new google cloud space

[johnacurtin]

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,

[omerwe]

@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?

[johnacurtin]

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: @.**@.>>

[jdblischak]

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")

[johnacurtin]

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: @.**@.>>

[jdblischak]

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)

[johnacurtin]

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: @.**@.>>