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I'm unable to run prospr on a sequence #12

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dante-di opened this issue Feb 28, 2020 · 2 comments
Open

I'm unable to run prospr on a sequence #12

dante-di opened this issue Feb 28, 2020 · 2 comments

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@dante-di
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Hello everyone,
I installed the ProSPr Docker container.

When I try to run ProSPr on a sequence using the command:
docker run -t -v /home/dante/data/:/data prospr/prospr -t --a3mfile /home/dante/data/example1.a3m

I get this error: prospr.py: error: argument command: invalid choice: '/home/dante/data/example1.a3m' (choose from 'run', 'build')

I think I followed the welcome screen directions:
To use prospr on your own sequences: docker run -t -v /path/to/local/data:/data prospr/prospr -t --a3mfile /data/my_file.a3m and place a PSIBLAST database under /data/psiblast and a uniclust database under /data/hhblits. ProSPr will download the database if it is missing (250GB and 25GB respectively).
Note: I was also unable to download the database.

What am I doing wrong?

Thank you very much,
Dante

@Lorenzo360
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Lorenzo360 commented Mar 26, 2020

For me a3m files did not work either. However, you can try to put your sequence in a fasta file and do the following.

mkdir /home/dante/data/example1
cp example1.fasta /home/dante/data/example1/

docker run -it -v /home/Dante/data:/data prospr/prospr build example1

@PedroAbilleira
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I have a somewhat more basic question. I do not know what the folders "/home/dante/data/:/data prospr/prospr" mean. Where are them?

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