R-SAIGE on bioconda #272

matuskosut · 2020-11-11T09:26:31Z

I managed to revise Saige dependencies and build conda packages for Saige (https://anaconda.org/bioconda/r-saige), such that it could make installation as easier as possible.

Guide

You will need bioconda and conda-forge channels (added in this order):

conda config --add channels bioconda
conda config --add channels conda-forge

Feel free to try out the new packages and share feedback:

conda create -n saige -c bioconda r-saige=0.44.5
conda activate saige

step1_fitNULLGLMM.R --help
step2_SPAtests.R --help
createSparseGRM.R --help

Available versions

Latest version:

r-saige 0.44.5 (R r-base=3.6.3,r-base=4.0)

conda create -n saige -c conda-forge -c bioconda r-base=4.0 r-saige=0.44.5
conda activate saige

Plaintext dosage files

r-saige 0.35.8.8 (R r-base=3.6.3,r-base=4.0.3)

conda create -n saige -c conda-forge -c bioconda r-base=4.0 r-saige=0.35.8.8
conda activate saige

Other versions previously released

r-saige 0.39 (R r-base=3.5.1, r-base=3.6.1,r-base=4.0)
r-saige 0.42 (R r-base=3.6.1,r-base=4.0)
r-saige 0.42.1 (R r-base=3.6.1,r-base=4.0)
r-saige 0.43.0 (R r-base=3.6.1,r-base=4.0)
r-saige 0.44.0 (R r-base=3.6.3,r-base=4.0)
r-saige 0.44.1 (R r-base=3.6.3,r-base=4.0)
r-saige 0.44.2 (R r-base=3.6.3,r-base=4.0)
r-saige 0.44.5 (R r-base=3.6.3,r-base=4.0)

To create conda environment with specific R version:

conda create -n saige -c conda-forge -c bioconda r-base=3.6.1 r-saige=0.43.0 savvy=1.3.0
conda activate saige

Versions 0.44.0 or older might require savvy=1.3.0. You will need to install them as shown in the example above, if you experience this issue:

... libsavvy.so: cannot open shared object file: No such file or directory
Execution halted

For those installing r-saige with R 3.6.1 I recommend installing lower version of optparse (this doesn't apply for R4.0):

conda install -c conda-forge "r-optparse=1.6.2=r36h6115d3f_1"

Hi @matuskosut thank you very much for sharing these conda packages for saige. I've been attempting to run step1 of saige using the step1_fitNULLGLMM.R with optparse R command line parser package; however, I keep receiving segfault errors: " *** caught segfault *** address 0x19, cause 'memory not mapped' " (saige_error.txt
). This error makes me wonder if it's something to do with my install configuration (i.e. saige is unable to access a necessary memory location). I followed the github instructions to create a conda environment (https://github.com/weizhouUMICH/SAIGE/wiki/Genetic-association-tests-using-SAIGE#installing-saige) and then used your conda r-saige=0.42.1 version with r-base=3.6.1. Any ideas on how to troubleshoot? I'm a newbie when it comes to these errors, so any help would be appreciated. Thank you!

matuskosut · 2020-11-16T16:59:43Z

Hi @hannahpky, thanks for the feedback. Based on the saige_error.txt that you shared it looks like an incompatibility between optparse and r-base version. Could you shared the exact versions of r-optparse and r-base? There is a special hash string that identifies the build number of that version, for example: "r-base 3.6.1 h8900bf8_2". You can get them using these commands in your conda environment:

conda list | grep optparse
conda list | grep r-base

I think that if we manage to pinpoint the matching version of optparse that we could make it work and perhaps also set a requirement in the package such that it could work for others.

EDIT: getting full conda list and conda info could actually help debugging

matuskosut · 2020-11-16T17:54:31Z

@hannahpky could you maybe try to install lower version of optparse? e.g.:

conda install -c conda-forge "r-optparse=1.6.2=r36h6115d3f_1"

hannahpky · 2020-11-16T21:22:11Z

Thanks Matúš - I installed a the lower version of optparse (1.6.2). I no longer receive the following message; however, I am still receiving the same " *** caught segfault *** address 0x19, cause 'memory not mapped'" message.

Loading required package: optparse 
Warning message:
package ‘optparse’ was built under R version 3.6.3

I included my conda info and list details to help troubleshoot (
conda_info.txt
conda_list.txt). I'm wondering if I need a different r-base version or some other package version?

matuskosut · 2020-11-16T22:07:59Z

@hannahpky interesting, I would definitely try r-base=4.0 or check other version of saige, e.g. 0.42 is available. I will try to have a closer look on this, any other info about inputs (types, parameters,..) that you could share?

hannahpky · 2020-11-16T23:52:53Z

I tried r-base=4.0 with r-saige=0.42.1, but received the same error. These are the inputs I've been using:

--plinkFile=/vgipiper05/hannah/stuttering/population_analysis/merged/potential_ctrls/selected_controls_taketwo_09092020/ALL_stut_merged_casesmatchedctrls_LDprunednoHLAinv \
--phenoFile=/vgipiper05/hannah/stuttering/population_analysis/merged/potential_ctrls/selected_controls_taketwo_09092020/PHENO.txt \
--phenoCol=STUT \
--covarColList=PC1,PC2,PC3,PC4,PC5,PC6 \
--sampleIDColinphenoFile=IID \
--traitType=binary \
--nThreads=4 \
--LOCO=FALSE \
--outputPrefix=/vgipiper05/hannah/stuttering/population_analysis/merged/potential_ctrls/selected_controls_taketwo_09092020/SAIGE_11162020/Stut_SAIGE_fitNullGLMM```

All the inputs appear to be read-in correctly and then immediately afterward I receive the "*** caught segfault ***
address 0x19, cause 'memory not mapped' " error.

matuskosut · 2020-11-18T08:56:53Z

@hannahpky I have got the new version in, could you try to upgrade or maybe recreate your conda environment such that new version is installed..

conda update r-saige

Esther19960123 · 2020-11-18T10:23:53Z

createSparseGRM.R --help

It works well so I installed saige successfully which I spent two days installing and failed. Thank you a lot

matuskosut · 2020-11-18T10:27:56Z

It works well so I installed saige successfully which I spent two days installing and failed. Thank you a lot

@Esther19960123 Great! Happy to hear that everything is working well 😊 in case you will encounter any bug feel free to open a new issue a tag me in..

hannahpky · 2020-11-19T16:12:56Z

Yep, thanks @matuskosut the new r-saige version seems to be working well! I'm no longer receiving segfault errors :)

weizhou0 · 2020-11-20T21:06:40Z

Hi @matuskosut,

Thank you so much for sharing the bioconda SAIGE!!!

Wei

alecmchiu · 2020-11-23T08:49:54Z

@matuskosut

Works like a charm! Spent several days trying to install this on the cluster that I work on to no avail. However, your bioconda installation was able to get me to all the help messages successfully! Hopefully it runs without a hitch too!

matuskosut · 2020-11-23T09:03:46Z

@alecmchiu awesome! You probably installed 0.42.1 which now seems pretty stable. But as I write this a new release 0.43.0 is being uploaded in case you are interested.

huanghe0220 · 2021-05-11T10:08:13Z

Hi @matuskosut ,I have followed your steps to install saige.
conda create -n saige -c conda-forge -c bioconda r-base=3.6.1 r-saige=0.43.0
conda install -c conda-forge "r-optparse=1.6.2=r36h6115d3f_1"
However, when I came to this step:
step1_fitNULLGLMM.R --help
I received a bug:
Error: package or namespace load failed for ‘SAIGE’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/home/huanghe/miniconda3/lib/R/library/SAIGE/libs/SAIGE.so': libsavvy.so: cannot open shared object file: No such file or directory Execution halted

Do you know how to solve this problem? I have been stuck with this package for 1 week, so any help would be appreciated. Thank you!

matuskosut · 2021-05-11T10:55:35Z

Hi @huanghe0220, thanks for reporting. I updated the guide. There was a bigger change in the new version of savvy library.

You will need to use savvy=1.3.0 to get the correct match to your saige version. Example:

conda create -n saige -c conda-forge -c bioconda r-base=3.6.1 r-saige=0.43.0 savvy=1.3.0

Or you can add it to your existing environment:

conda install -n saige -c conda-forge -c bioconda savvy=1.3.0

matuskosut · 2021-05-11T13:14:57Z

@weizhou0 @weizhouUMICH does it seem ok to include info about r-saige package in README? I made a Pull request #343 Feel free to comment/change if there is anything off.

huanghe0220 · 2021-05-12T04:54:42Z

@matuskosut Thanks for your reply. I suppose the saige has been installed successfully. But when I came to step 2 with the example dataset, Rscript step2_SPAtests.R --dosageFile=./input/dosage_10markers.txt --dosageFileNrowSkip=1 --dosageFileNcolSkip=6 --dosageFilecolnamesSkip=CHR,SNP,CM,POS,EFFECT_ALLELE,ALT_ALLELE --minMAF=0.0001 --sampleFile=./input/sampleIDindosage.txt --GMMATmodelFile=./output/example.rda --varianceRatioFile=./output/example.varianceRatio.txt --SAIGEOutputFile=./output/example.plainDosage.SAIGE.txt --numLinesOutput=2 --IsOutputAFinCaseCtrl=TRUE
I came into this bug:
Error in getopt_options(object, args) : Error in getopt(spec = spec, opt = args) : long flag "dosageFile" is invalid
If I use my own data, I would bump into another bug in step 1(Rscript step1_fitNULLGLMM.R):
Error in terms.formula(formula, data = data) : invalid model formula in ExtractVars
Do you know why? Looking forward to your reply. Thanks!

Best wishes,
Huang He

matuskosut · 2021-05-12T05:00:28Z

@huanghe0220 is this plain text dosage files being used? If so, you need to use this version r-saige=0.38.8.8.

huanghe0220 · 2021-05-12T05:20:31Z

@matuskosut I think you mean r-saige=0.35.8.8? I couldn't find 0.38.8.8, and installed version 0.35.8.8, but I still got the bug in step 2 with example dataset, and the same bug in step 1 with my own dataset. I got really confused :(

matuskosut · 2021-05-12T05:34:02Z

@huanghe0220 yes, thanks for correcting. I fixed the version typo in the issue text.

I see that your step 2 issue was long flag "dosageFile" is invalid and looking at the source code of 0.35.8.8 --dosageFile is present in step2: https://github.com/weizhouUMICH/SAIGE/blob/0.35.8.8/extdata/step2_SPAtests.R#L10 (it is not present in newer versions)

Could you make an issue for this if you will still have problem? https://github.com/weizhouUMICH/SAIGE/issues/new

huanghe0220 · 2021-05-12T05:37:06Z

@matuskosut Thanks for your reply. I will make an issue.

weizhouUMICH · 2022-01-21T20:40:26Z

Hi @matuskosut,

There seems the query issue for bgen file in the current bioconda version. I wonder whether you used the bgenix version in the /thirdparty folder when you compile SAIGE. If not, that would cause the issue. Thanks!

Wei

matuskosut · 2022-01-25T12:32:12Z

Hi @weizhouUMICH,

Is this related to issue: #393 ? Were you also able to reproduce? Could it be possible to reproduce with some nonsensitive data? since I don't have access to any datasets.

I built bgenix based on same version as in /thirdparty. I was applying the patches that I identified in your repo. I noticed only one that was missing - although I think it is unrelated - but still I rebuilt bgenix and saige and published in conda in case you want to try it. (e.g.: linux-64/r-saige-0.44.6.5-r40h6d4de14_3.tar.bz2 - https://anaconda.org/bioconda/r-saige)

It is possible to also try bgenix separately to isolate the issue: https://anaconda.org/conda-forge/bgenix

weizhou0 · 2022-01-26T02:37:19Z

Hi @matuskosut <https://github.com/matuskosut>, Yes this is related to issue: #393 <#393> ? and another user also observed the same issue using the bioconda version. The code of bgen in the third party actually is not the same as the bgenix library https://anaconda.org/conda-forge/bgenix, because I made some modifications for querying with variant IDs in the gene-based tests. If SAIGE was compiled using the bgen code in the thirdparty folder, it should not have the issue. I just updated the version to 0.45. Would you mind updating the bioconda version? Thanks so much for your help! I'm also trying to learn how to build the bioconda library. :) Thanks, Wei

…

On Tue, Jan 25, 2022 at 7:32 AM Matúš Košút ***@***.***> wrote: Hi @weizhouUMICH <https://github.com/weizhouUMICH>, Is this related to issue: #393 <#393> ? Were you also able to reproduce? Could it be possible to reproduce with some nonsensitive data? since I don't have access to any datasets. I built bgenix based on same version as in /thirdparty. I was applying the patches that I identified in your repo. I noticed only one that was missing - although I think it is unrelated - but still I rebuilt bgenix and saige and published in conda in case you want to try it. It is possible to also try bgenix separately to isolate the issue: https://anaconda.org/conda-forge/bgenix — Reply to this email directly, view it on GitHub <#272 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/APJSQMU5AHHOQQD56H2OK7DUX2J5XANCNFSM4TRYDF5Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were mentioned.Message ID: ***@***.***>

matuskosut · 2022-01-26T05:57:35Z

Hi @weizhouUMICH (@weizhou0 ),

One thing to explain is the principle from conda-forge and bioconda - the package should contain only one tool/library which is also implied by the rule that there should not be multiple licenses packaged together. So each package has to be built separately and stated clearly as dependency. Hence we have to build bgenix from separate repo.
Maybe you could have a look? This is the branch for 1.1.4 version that is used for R-SAIGE:

https://github.com/huntdatacenter/rbgen/tree/build-v1.1.4

Let me know in case you spot any difference. I was aware of some of your earlier changes and passed the patches into that branch, plus I was also patching waf to run with python3. Since this problem appeared only now, I think it still might be some other cause.

In the meantime conda package for 0.45 was released, check here: https://anaconda.org/bioconda/r-saige

weizhouUMICH · 2022-03-16T03:40:36Z

Hi @matuskosut,

We have just released a new version 1.0.0. It no longer depends on the bgen library.

It has computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/

Thanks!
Wei

This was referenced Nov 13, 2020

Allow to use external savvy headers #204

Merged

external headers should not use path relative to code #273

Merged

do not run configure when installing within conda build #274

Merged

This was referenced Nov 17, 2020

R-saige fix build bioconda/bioconda-recipes#25397

Merged

Cleanup precompiled object files #276

Merged

matuskosut mentioned this issue Nov 18, 2020

step4 installation new error #270

Closed

matuskosut mentioned this issue Nov 20, 2020

Getting SAIGE-Gene Step 2 to go faster? #277

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matuskosut changed the title ~~Saige on bioconda~~ R-SAIGE on bioconda Nov 20, 2020

weizhouUMICH mentioned this issue Nov 21, 2020

Compilation failure #278

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matuskosut mentioned this issue Dec 3, 2020

Could you provide the newest version of .tar.gz file for local R package installation? #285

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This was referenced Apr 12, 2021

Segmentation fault (core dumped) #324

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Problems with installation: Fortran compiler broken and not cc1 #329

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xchangchop mentioned this issue Apr 14, 2021

error when running X chromosome #326

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matuskosut mentioned this issue May 8, 2021

Conda environment steps - update #340

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matuskosut mentioned this issue May 11, 2021

add r-saige conda installation into readme #343

Merged

complexgenome mentioned this issue May 14, 2021

installation issues: ERROR: configuration failed for package ‘SAIGE’ #347

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Amelia-uoft mentioned this issue Aug 11, 2021

Error in SAIGE on bioconda #364

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XiangyuYe mentioned this issue Jan 18, 2022

Abnormal output of SAIGE step 2 with "idstoIncludeFile" parameter #393

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weizhouUMICH closed this as completed Mar 16, 2022

pstuart66 mentioned this issue Mar 3, 2025

Current bioconda version OK for BGEN input? saigegit/SAIGE#162

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R-SAIGE on bioconda #272

R-SAIGE on bioconda #272

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R-SAIGE on bioconda #272

R-SAIGE on bioconda #272

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matuskosut commented Nov 11, 2020 • edited Loading

Guide

Available versions

Plaintext dosage files

Other versions previously released

Related

hannahpky commented Nov 16, 2020

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