opain
commented
1 month ago Hi,
Interesting. Thanks for reaching out. Can you send me the contents of the file
resources/data/logs/download_pgscatalog_utils.log
This should show the error message.
Many thanks,
Ollie
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From: samreenzafer @.> Sent: Tuesday, September 3, 2024 12:44:37 PM To: opain/GenoPred @.> Cc: Subscribed @.***> Subject: [opain/GenoPred] Error in downloading PRS file I think. (Issue #116)
Hi I am a first time user of Genopred, and have been able to successfully download genopred.
I am working on an hpc cluster, and while running the test Case, I get the error. I get the same on an interactive nose, as well as login node, and am attaching the run log from the attempt on interactive node.
@.*** ~]$ bsub -P acc_rareADRs -q interactive -n 4 -W 4:00 -R rusage[mem=5000] -Is /bin/bash
<
@. ~]$ cd ~/softwares/GenoPred/GenoPred/pipeline/ @. pipeline]$ module load anaconda3/latest @. pipeline]$ source activate genopred (genopred) @. pipeline]$ conda config --set channel_priority strict (genopred) @. pipeline]$ ml git (genopred) @. pipeline]$ ml proxies (genopred) @.*** pipeline]$ snakemake -j1 --configfile=example_input/config.yaml --use-conda output_all Config file config.yaml is extended by additional config specified via the command line. Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 1 (use --cores to define parallelism) Rules claiming more threads will be scaled down. Job stats: job count
ancestry_inference_i 1 ancestry_reporter 1 download_pgs_external 2 download_pgscatalog_utils 1 format_target_all 1 format_target_i 1 indiv_report_all 1 output_all 1 prep_pgs_external_i 2 sample_report_i 1 score_reporter 1 sumstat_prep_i 1 target_pgs_all 1 total 15
Select jobs to execute...
[Tue Sep 3 12:38:49 2024] rule download_pgscatalog_utils: output: resources/software/pgscatalog_utils/download_pgscatalog_utils.done log: resources/data/logs/download_pgscatalog_utils.log jobid: 15 benchmark: resources/data/benchmarks/download_pgscatalog_utils.txt reason: Missing output files: resources/software/pgscatalog_utils/download_pgscatalog_utils.done resources: tmpdir=/tmp
Activating conda environment: .snakemake/conda/a1ca3d0129086fba197335c750a581c8_ [Tue Sep 3 12:39:02 2024] Error in rule download_pgscatalog_utils: jobid: 15 output: resources/software/pgscatalog_utils/download_pgscatalog_utils.done log: resources/data/logs/download_pgscatalogutils.log (check log file(s) for error details) conda-env: /xxx/softwares/GenoPred/GenoPred/pipeline/.snakemake/conda/a1ca3d0129086fba197335c750a581c8 shell:
{
rm -r -f resources/software/pgscatalog_utils; git clone https://github.com/PGScatalog/pgscatalog_utils.git resources/software/pgscatalog_utils; cd resources/software/pgscatalog_utils; git reset --hard 6da7eb0e157ba4e73f941233ee8d8ae4fb5e3926; poetry install; poetry build; pip3 install --user dist/*.whl; download_scorefiles -h > download_pgscatalog_utils.done
} > resources/data/logs/download_pgscatalog_utils.log 2>&1
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)Removing output files of failed job download_pgscatalog_utils since they might be corrupted: resources/software/pgscatalog_utils/download_pgscatalog_utils.done Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-09-03T123839.147454.snakemake.log
Can you help me figure out what could be going wrong?
Thank you.
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samreenzafer
Hi I am a first time user of Genopred, and have been able to successfully download genopred.
I am working on an hpc cluster, and while running the test Case, I get the error. I get the same on an interactive nose, as well as login node, and am attaching the run log from the attempt on interactive node.
Can you help me figure out what could be going wrong?
Thank you.