Fwd: [hakyimlab/MetaXcan] ImportError: libathr.so.1: cannot open shared object file: No such file or directory (Issue #139)

[Hae Kyung Im]

forwarding to the predixcanmetaxcan mailing list where you may get help  

Haky

---------- Forwarded message ---------
From: Cuihua Xia <notifi...@github.com>
Date: Sat, Oct 30, 2021 at 10:01 AM
Subject: [hakyimlab/MetaXcan] ImportError: libathr.so.1: cannot open shared object file: No such file or directory (Issue #139)
To: hakyimlab/MetaXcan <Meta...@noreply.github.com>
CC: Subscribed <subsc...@noreply.github.com>

Hello, I have some problems when I run the Predict.py.

Here is my script:
Predict.py --model_db_path ~/test_data/predixcan_sample_data/models/gtex_v8_en/en_Whole_Blood.db --bgen_genotypes ~/test_data/predixcan_sample_data/1000G_hg37_bgen/chr22.bgen --bgen_use_rsid --prediction_output Whole_Blood_test_predict.txt --prediction_summary_output Whole_Blood_test_summary.txt --verbosity 9 --throw

Here is the error:
INFO - Loading samples Traceback (most recent call last): File "/zs32/home/chxia/Softwares/MetaXcan-master/software/Predict.py", line 272, in <module> run(args) File "/zs32/home/chxia/Softwares/MetaXcan-master/software/Predict.py", line 160, in run samples = load_samples(args) File "/zs32/home/chxia/Softwares/MetaXcan-master/software/Predict.py", line 90, in load_samples from metax.genotype import BGENGenotype File "/zs32/home/chxia/Softwares/MetaXcan-master/software/metax/genotype/BGENGenotype.py", line 1, in <module> import bgen_reader File "/zs32/home/chxia/anaconda3/envs/gwasimputation/lib/python3.7/site-packages/bgen_reader/__init__.py", line 26, in <module> from ._metadata import create_metafile File "/zs32/home/chxia/anaconda3/envs/gwasimputation/lib/python3.7/site-packages/bgen_reader/_metadata.py", line 4, in <module> from ._bgen import bgen_file File "/zs32/home/chxia/anaconda3/envs/gwasimputation/lib/python3.7/site-packages/bgen_reader/_bgen.py", line 3, in <module> from ._ffi import ffi, lib ImportError: libathr.so.1: cannot open shared object file: No such file or directory

Could you help me solve this problem?

Thanks!

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[Festus]

Hi

This looks like some of the tools did not install correctly.

Kindly follow this guide to install the conda environment correctly with the required tools.

[Lea L.]

Hi Haky & Festus and Xia, 

I get exactly the same issue with the examples with the bgen files (e.g. Example 2): https://github.com/hakyimlab/MetaXcan/wiki/Individual-level-PrediXcan:-introduction,-tutorials-and-manual 
The examples with the vcf files work without problem.

So I assume it has to do something with the bgen format.

But I am using the imlabtools. I realised that there it only has version 3.0.2 installed instead of the recommended version >= 3.0.3 (https://github.com/hakyimlab/MetaXcan#example-conda-environment-setup) :

bgen_reader               3.0.2 

So installed verision 3.0.3 but still I am getting below error:

PrediXcan]$ python3 $METAXCAN/Predict.py \
> --model_db_path $DATA/models/gtex_v8_en/en_Whole_Blood.db \
> --bgen_genotypes $DATA/1000G_hg37_bgen/chr22.bgen \
> --bgen_use_rsid \
> --prediction_output $RESULTS/bgen_1000G_hg37_en/Whole_Blood__predict.txt \
> --prediction_summary_output $RESULTS/bgen_1000G_hg37_en/Whole_Blood__summary.txt \
> --verbosity 9 \
> --throw

INFO - Loading samples
Traceback (most recent call last):

  File "MetaXcan/software/Predict.py", line 272, in <module>
    run(args)
  File "MetaXcan/software/Predict.py", line 160, in run
    samples = load_samples(args)
  File "MetaXcan/software/Predict.py", line 90, in load_samples
    from metax.genotype import BGENGenotype
  File "/gpfs/igmmfs01/eddie/CCGG-rnaseq/lea/MASH_models/PrediXcan/MetaXcan/software/metax/genotype/BGENGenotype.py", line 1, in <module>
    import bgen_reader
  File "/exports/igmm/eddie/CCGG-rnaseq/lea/MASH_models/conda2022/envs/imlabtools/lib/python3.7/site-packages/bgen_reader/__init__.py", line 26, in <mod                             ule>
    from ._metadata import create_metafile
  File "/exports/igmm/eddie/CCGG-rnaseq/lea/MASH_models/conda2022/envs/imlabtools/lib/python3.7/site-packages/bgen_reader/_metadata.py", line 4, in <mod                             ule>
    from ._bgen import bgen_file
  File "/exports/igmm/eddie/CCGG-rnaseq/lea/MASH_models/conda2022/envs/imlabtools/lib/python3.7/site-packages/bgen_reader/_bgen.py", line 3, in <module>

    from ._ffi import ffi, lib
ImportError: libathr.so.1: cannot open shared object file: No such file or directory

Can anyone help me with this?

Thank you, 

Lea 

[Lea L.]

Dear Haky & Festus, 

Just to update you that I went through my setup again today with two bioinformatician (independently) in my institute and we cannot see any mistake in the way I am doing it.

We tried two ways:

1) Using imlabtools (be aware that it uses bgen_reader=3.0.2) not as specified in your prerequisites as 3.0.3. (https://github.com/hakyimlab/metaxcan#prerequisites)

Also from what I see it is not called bgen_reader from version 3.0.3 instead it is bgen-reader

2) Setting up a new environment and loading all packages manually exactly as specified  (be aware that bgen-reader 3.0.3 needs python 3.6 not 3.5)

I keep getting the error from my last message. This only applies to Example 2 (with bgen file), it does work for the other examples.

Any advice very appreciated as in my institute I contacted all experts and not sure how to continue at this point.

Best Regards,

Lea 

[Hae Kyung Im]

Lea,

if the vcf version works, could you reformat your genotype file? Not ideal but it may be a quick solution.

Haky

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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
Phone:  773.702.3898 | FAX: 773.702.2567
Email: ha...@uchicago.edu | Twitter: @hakyim
http://hakyimlab.org | https://github.com/hakyimlab | https://orcid.org/0000-0003-0333-5685
http://scholar.google.com/citations?user=1QD4sIcAAAAJ
Directions to my office https://tinyurl.com/hki-office

[Lea L.]

Dear Haky, 

Thank you for your reply.

I need to see if my group is happy with that.. Not sure if it could have impact on the quality of my data?!

I have quite a big dataset of 5000 cases.

Lea