Re: Tutorial: GTEx v8 MASH models integration with a Coronary Artery Disease GWAS

[Hae Kyung Im]

Dear Lea,

I am forwarding your question to the PrediXcan mailing list where Festus and others can help you.

Haky

On Tue, Feb 8, 2022 at 12:09 PM LEMLER Lea <L.Le...@sms.ed.ac.uk> wrote:

Dear Haky,

 

My supervisor has given me your contact details, I hope you don’t mind me contacting you directly.

 

I am currently trying to run above tutorial but I am struggling with this part:

 

# The following imputes a portion of the imput GWAS.
# The imputation is meant to be split over many executions to improve paralellism
# so you would have to iterate `-chromosome` between [1,22] and `-sub_batch` between [0,_sub_batches],
# ideally in an HPVC environment
python $GWAS_TOOLS/gwas_summary_imputation.py \
-by_region_file $DATA/eur_ld.bed.gz \
-gwas_file $OUTPUT/harmonized_gwas/CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz \
-parquet_genotype $DATA/reference_panel_1000G/chr1.variants.parquet \
-parquet_genotype_metadata $DATA/reference_panel_1000G/variant_metadata.parquet \
-window 100000 \
-parsimony 7 \
-chromosome 1 \
-regularization 0.1 \
-frequency_filter 0.01 \
-sub_batches 10 \
-sub_batch 0 \
--standardise_dosages \
-output $OUTPUT/summary_imputation_1000G/CARDIoGRAM_C4D_CAD_ADDITIVE_chr1_sb0_reg0.1_ff0.01_by_region.txt.gz

I get an error message saying that “AttributeError: 'MultiIndex' object has no attribute 'labels'” if I copy it like this.

Also I do not quite understand what is meant by “# The imputation is meant to be split over many executions to improve parallelism,  so you would have to iterate `-chromosome` between [1,22] and `-sub_batch` between [0,_sub_batches],”.

Could you give me some more explanations how to run this part?

 

Thank you very much & Best Regards,

Lea

 

Lea Lemler

PhD Student

 

L.Le...@sms.ed.ac.uk

 

Colon Cancer Genetics Group,
4th Floor MRC-HGU,
Institute of Genetics and Cancer,
University of Edinburgh,
Crewe Road, Edinburgh  EH4 2XU

 

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--

Hae Kyung Im, PhD - 任慧耕 - 임혜경 - She/her
Assistant Professor, Section of Genetic Medicine
The University of Chicago Medicine & Biological Sciences
Member of Committee on Genetics, Genomics & Systems Biology
Center for Translational Data Science

Computing Environment and Life Sciences Directorate, Argonne National Laboratory
5841 S. Maryland Ave. Chicago, IL 60637, USA| N412
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Email: ha...@uchicago.edu | Twitter: @hakyim
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[Festus]

Hi Lea,

Kindly share the whole lg containing the error message. You can change the -parsimony to 1 so that everything message is logged.

Festus

[Festus]

Hi Lea,

Kindly install the conda environment from here using these commands provided here.

Rerun your analysis.

Festus

[Lea L.]

Hi Festus, 

Thank you. I have installed Miniconda now and tried to create the working environment via file software/conda_env.yaml.

But I get the errors attached. 

I am running 
conda env create -f https://github.com/hakyimlab/MetaXcan/blob/master/software/conda_env.yaml

Thank you for any advice.

Best wishes,

Lea 

[Festus]

Hi Lea,

You need to download that file or copy the contents of the file to a file named conda_env.yaml then run

conda env create -f conda_env.yaml

Festus

[Lea L.]

Hi Festus, 

Ah ok, now I get it, thank you. imlabtools has already the packages (numpy etc.) installed and i dont need to run this part:

conda create -n myenv python=3.6 

source activate myenv       

conda install scipy numpy pandas -y  

conda install -c conda-forge pyarrow -y 

conda install -c bioconda pyliftover -y 

Nevertheless, again I am not able to get further than harmonising input gwas to our reference as described in my first email (following code here: https://github.com/hakyimlab/MetaXcan/wiki/Tutorial%3A-GTEx-v8-MASH-models-integration-with-a-Coronary-Artery-Disease-GWAS).

So I got the file output $OUTPUT/harmonized_gwas/CARDIoGRAM_C4D_CAD_ADDITIVE.txt.gz but running following code (gwas summary imputation) gives the attached error.

Do you have an idea what I could be the reason?

Thank you very much for your help, very appreciated.

Best Regards,

Lea 

[Festus]

Looks like you split your command into two that's why you getting that error.

[Lea L.]

Hi Festus, 

It is working now, thank you very much.

Best Regards,

Lea