Unexpected error: CRC check failed

[maegsul]

Hi,

I am testing S-PrediXcan for the first time, using the example dataset and the code:

wget https://s3.amazonaws.com/imlab-open/Data/MetaXcan/sample_data/v0_5/sample_data.tar.gz  

tar -xzvpf sample_data.tar.gz  

./MetaXcan.py \  
--model_db_path data/DGN-WB_0.5.db \  
--covariance data/covariance.DGN-WB_0.5.txt.gz \  
--gwas_folder data/GWAS \  
--gwas_file_pattern ".*gz" \  
--snp_column SNP \  
--effect_allele_column A1 \  
--non_effect_allele_column A2 \  
--beta_column BETA \  
--pvalue_column P \  
--output_file results/test.csv  

After processing the last chromosome, I get this "CRC check failed" error:

.....
INFO - Building beta for chr9.assoc.dosage.gz and data/DGN-WB_0.5.db
INFO - Reading input gwas with special handling: data/GWAS/chr9.assoc.dosage.gz
INFO - Processing input gwas
INFO - Aligning GWAS to models
INFO - Trimming output
INFO - Successfully parsed input gwas in 42.6134901047 seconds
INFO - Started metaxcan process
INFO - Loading model from: data/DGN-WB_0.5.db
INFO - Loading covariance data from: data/covariance.DGN-WB_0.5.txt.gz
INFO - Unexpected error: CRC check failed 0x4ed8f5d6 != 0xc37e2172L

What might be causing this? Thanks in advance!

PS: I am working on a conda python 2.7 environment with below packages & versions:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
blas 2.11 openblas conda-forge
ca-certificates 2019.11.27 0 anaconda
certifi 2019.11.28 py27_0 anaconda
intel-openmp 2019.5 281 anaconda
libblas 3.8.0 11_openblas conda-forge
libcblas 3.8.0 11_openblas conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc-ng 9.2.0 h24d8f2e_1 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.3.0 hdf63c60_0 anaconda
libgomp 9.2.0 h24d8f2e_1 conda-forge
liblapack 3.8.0 11_openblas conda-forge
liblapacke 3.8.0 11_openblas conda-forge
libopenblas 0.3.6 h5a2b251_2 anaconda
libstdcxx-ng 9.2.0 hdf63c60_1 conda-forge
mkl 2019.5 281 anaconda
mkl-service 2.3.0 py27he904b0f_0 anaconda
mkl_fft 1.0.10 py27_0 conda-forge
mkl_random 1.0.4 py27hf2d7682_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
numpy 1.14.2 py27hdbf6ddf_1 anaconda
numpy-base 1.11.3 py27h2f8d375_12 anaconda
openblas 0.2.19 0 anaconda
openmp_impl 4.5 0_gnu conda-forge
openssl 1.1.1 h7b6447c_0 anaconda
pandas 0.24.2 py27he6710b0_0 anaconda
pip 19.3.1 py27_0 conda-forge
python 2.7.15 h5a48372_1009 conda-forge
python-dateutil 2.8.1 py_0 anaconda
pytz 2019.3 py_0 anaconda
readline 8.0 hf8c457e_0 conda-forge
scipy 1.2.1 py27he2b7bc3_0 anaconda
setuptools 44.0.0 py27_0 conda-forge
six 1.13.0 py27_0 anaconda
sqlalchemy 1.3.12 py27h7b6447c_0 anaconda
sqlite 3.30.1 hcee41ef_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
wheel 0.33.6 py27_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge

[Heroico]

Hi there,

It looks like the data download failed. I advice to download again; I just tested it and it worked on my end.

Best,

Alvaro

[maegsul]

Hi Alvaro, it was indeed related to the data download that failed somehow. The issue is solved now, thank you very much!