Problem running phenotype generation

[hangphan]

Hi Richard, I've just tried running the phenotype generation script using the examples you provided in the manual and got the following error.

Do you think you could help pointing out where/how I could get zlib installed? I tried several ways (e.g. using install.packages("Rcompression", repos = "http://www.omegahat.net/R ") or tried the link http://www.gzip.org/zlib/ ) but it does not work. Installing this package using "install.packages('zlib')" gave me the following error

Your help will be highly appreciated. Many thanks Hang

[Richard-Packer]

Hi Hang,

I've not encountered this specific error before. Have you tried reinstalling data.table? The other option would be to decompress the gz files in the R package folder if it is an issue with loading the built in gz files.

Best, Richard

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From: Hang Phan @.> Sent: 12 April 2023 17:18 To: Richard-Packer/DeepPheWAS @.> Cc: Subscribed @.***> Subject: [Richard-Packer/DeepPheWAS] Problem running phenotype generation (Issue #1)

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Hi Richard, I've just tried running the phenotype generation script using the examples you provided in the manual and got the following error. [image]https://user-images.githubusercontent.com/7782225/231519047-fb666857-7a56-4b0c-8682-a7ba236cab84.png

Do you think you could help pointing out where/how I could get zlib installed? I tried several ways (e.g. using install.packages("Rcompression", repos = "http://www.omegahat.net/R ") or tried the link http://www.gzip.org/zlib/ ) but it does not work. Installing this package using "install.packages('zlib')" gave me the following error [image]https://user-images.githubusercontent.com/7782225/231519680-4bfe4eac-f9b4-47d1-9d0f-95f2ffae3f1d.png

Your help will be highly appreciated. Many thanks Hang

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[hangphan]

Hi, I managed to resolve the problem by installing the 2 R packages that has the zlib library prior to installing data.table. I'm trying to run the script to generate the dataset to input to the DeepPHEWAS as below

$package_folder/extdata/scripts/phenotype_generation/01_minimum_data.R \ --data_file $package_folder/extdata/worked_example/ukb_data.csv.gz \ --save_loc $phewas_folder/data/min_tab_test.gz

Could you please let me know how long this step would take using this test dataset that you provided? Many thanks Hang

[Richard-Packer]

Hi Hang,

All the examples should run in seconds to minutes.

Richard

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From: Hang Phan @.> Sent: 17 April 2023 17:09 To: Richard-Packer/DeepPheWAS @.> Cc: Packer, Richard J. (Dr.) @.>; Comment @.> Subject: Re: [Richard-Packer/DeepPheWAS] Problem running phenotype generation (Issue #1)

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Hi, I managed to resolve the problem by installing the 2 R packages that has the zlib library prior to installing data.table. I'm trying to run the script to generate the dataset to input to the DeepPHEWAS as below

$package_folder/extdata/scripts/phenotype_generation/01_minimum_data.R --data_file $package_folder/extdata/worked_example/ukb_data.csv.gz --save_loc $phewas_folder/data/min_tab_test.gz

Could you please let me know how long this step would take using this test dataset that you provided? Many thanks Hang

— Reply to this email directly, view it on GitHubhttps://github.com/Richard-Packer/DeepPheWAS/issues/1#issuecomment-1511672632, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AH5PHRBBJYXJZRDYRZZFZHTXBVTJ7ANCNFSM6AAAAAAW35AKGU. You are receiving this because you commented.Message ID: @.***>

[hangphan]

That's really weird. I tried running the above command and it just stalled. Is it possible to provide the output of the command I listed above? The min_tab_test.gz file?

Do you notice anything obviously wrong with that one above? Many thanks. Hang

[hangphan]

By the way, my test bash script is like this. It would be great to hear what you think about this. Many thanks. Hang

package_folder=/opt/conda/lib/R/library/DeepPheWAS/
phewas_folder=/home/jovyan/testDeepPheWAS/
$package_folder/extdata/scripts/phenotype_generation/01_minimum_data.R \
--data_file $package_folder/extdata/worked_example/ukb_data.csv.gz \
--save_loc $phewas_folder/data/min_tab_test.gz
$package_folder/extdata/scripts/phenotype_generation/02_data_preparation.R \
--save_location $phewas_folder/data/ \
--min_data $phewas_folder/data/min_tab_test.gz \
--hesin_diag $package_folder/extdata/worked_example/HES_Diag.csv.gz \
--HESIN $package_folder/extdata/worked_example/hesin.csv.gz \
--death_cause $package_folder/extdata/worked_example/death.csv.gz \
--death $package_folder/extdata/worked_example/death_date.csv.gz \
--king_coef $package_folder/extdata/worked_example/KING_coef.csv.gz \
--GPC $package_folder/extdata/worked_example/GPC.csv.gz