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View Code? Open in Web Editor NEW🦠🧬 Unraveling Viral Genomes from Metagenomes
License: MIT License
🦠🧬 Unraveling Viral Genomes from Metagenomes
License: MIT License
Installing the VOG database fails
mkdir: cannot create directory ‘/tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG’: File exists
[Sat Mar 30 17:51:49 2024]
Error in rule vog_db_download:
jobid: 2
output: /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm
conda-env: /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/conda/233e73b39830a98b818f43b5ca8b38d3_
shell:
curl -Lo /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/vog.hmm.tar.gz http://fileshare.csb.univie.ac.at/vog/latest/vog.hmm.tar.gz
mkdir /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG
tar -xf /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/vog.hmm.tar.gz -C /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG
cat /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG/* > /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm
rm -rf /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/vog.hmm.tar.gz
rm -rf /tmp/10353939/mamba-build/opt/mamba/envs/reneo/lib/python3.10/site-packages/reneo/workflow/../../databases/VOG
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
ERROR: Databases were not setup.
(Note, I have a funky install location, so I've truncated it to start at python3.10)
The HMMs are downloaded and extracted to python3.10/site-packages/databases/VOG/hmm/
:
$ ls python3.10/site-packages/databases/VOG/hmm/ | wc -l
59207
The cat
command is failing:
first, the extraction puts everything into VOG/hmm
and then, you can't cat VOG/hmm/*
as there are too many files:
This is what reneo is trying to do:
cat python3.10/site-packages/reneo/workflow/../../databases/VOG/* > python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm
cat: python3.10/site-packages/reneo/workflow/../../databases/VOG/hmm: Is a directory
This doesn't work
cat python3.10/site-packages/reneo/workflow/../../databases/VOG/hmm/* > python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm
bash: /usr/bin/cat: Argument list too long
but this does:
find python3.10/site-packages/reneo/workflow/../../databases/VOG/ -type f -exec cat {} + > python3.10/site-packages/reneo/workflow/../../databases/AllVOG.hmm
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