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kliment-olechnovic / voronota

Voronota is a software tool for analyzing three-dimensional structures of biological macromolecules using the Voronoi diagram of atomic balls.
https://kliment-olechnovic.github.io/voronota/
MIT License
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ronota version 1.20 command 'get-balls-from-atoms-file' exit error: Failed to read line #1

Closed pengzhangzhi closed 1 year ago

pengzhangzhi commented 1 year ago

Hi, I ran into an error Failed to read line when using your tool. The cmd is

cat example/output/graph/model.pdb | utils/SGCN/bin/voronota-linux get-balls-from-atoms-file --radii-file utils/SGCN/metadata/voronota_radii.txt --annotated > example/output/temp/balls

I have set execution permission for voronota using chmod 777. I found the error is caused by the flag --radii-file utils/SGCN/metadata/voronota_radii.txt.

kliment-olechnovic commented 1 year ago

Hello,

This error is not related to the execution permissions. This error occurs because there is nothing to read from the standard input stream. I suggest checking whether the file 'example/output/graph/model.pdb' exists and is not empty.

Cheers, Kliment

pengzhangzhi commented 1 year ago

Thanks! the file 'example/output/graph/model.pdb' exists. I remove the flag --radii-file utils/SGCN/metadata/voronota_radii.txt and run cat example/output/graph/model.pdb | utils/SGCN/bin/voronota-linux get-balls-from-atoms-file --annotated > example/output/temp/balls. It works. But I got another error:

utils/SGCN/bin/sh-featurizer-linux: /lib64/libm.so.6: version `GLIBC_2.27' not found (required by utils/SGCN/bin/sh-featurizer-linux)
utils/SGCN/bin/sh-featurizer-linux: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by utils/SGCN/bin/sh-featurizer-linux)
utils/SGCN/bin/sh-featurizer-linux: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by utils/SGCN/bin/sh-featurizer-linux)
utils/SGCN/bin/sh-featurizer-linux: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by utils/SGCN/bin/sh-featurizer-linux)
utils/SGCN/bin/sh-featurizer-linux: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.22' not found (required by utils/SGCN/bin/sh-featurizer-linux)
kliment-olechnovic commented 1 year ago

Ah, so maybe the 'utils/SGCN/metadata/voronota_radii.txt' was not accessible.

Anyway, the errors that you posted indicate that you perhaps need to recompile the 'utils/SGCN/bin/sh-featurizer-linux' executable on your system. 'sh-featurizer-linux' is not from Voronota, I do not know what it is, sorry.

pengzhangzhi commented 1 year ago

Thank you! Why the 'utils/SGCN/metadata/voronota_radii.txt' was not accessible? the path exists.

kliment-olechnovic commented 1 year ago

Well, you got an error when you specified it, but not when you omitted it. The path you used is relative, so I suggest you may try to use an absolute path (full path) to 'voronota_radii.txt'.

Also, a small disclaimer - as I understood, the issue is with the voronota binaries from "https://github.com/BioinfoMachineLearning/EnQA/tree/main/utils/SGCN/bin" - do not know what version of Voronota they are based on and whether they were modified.

pengzhangzhi commented 1 year ago

Thank you!