merenlab
[BUG] anvio installation
Short description of the problem
I get an error for checking if anvio is installed correctly.
anvi'o version
anvio-8
System info
Linux 64, I followed your tutorial https://anvio.org/install/linux/stable/, step by step.
Detailed description of the issue
I`m following https://anvio.org/install/linux/stable/ and things go well to the end of pip install anvio-8.tar.gz. But when I run anvi-self-test --suite mini, it says ImportError: liblzma-51a76f52.so.5.2.4: cannot open shared object file: No such file or directory.
Hello @UniAlberta , Can you share your log file with me so that I can understand the problem?
Hi,
I`m a beginner to Linux and anvio. What do you mean by log file?
On Fri, Jul 26, 2024 at 10:19 AM Metehan Sever @.***> wrote:
Hello @UniAlberta https://github.com/UniAlberta , Can you share your log file with me so that I can understand the problem?
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hey @UniAlberta , Your error is most likely caused by the samtools installation and you can find how to fix it in this section of the document: https://anvio.org/install/linux/stable/#issues-related-to-samtools
Hi,
There was no problem with my samtools. Do I need to update it to 1.9? [image: image.png]
On Fri, Jul 26, 2024 at 1:54 PM Metehan Sever @.***> wrote:
hey @UniAlberta https://github.com/UniAlberta , Your error is most likely caused by the samtools installation and you can find how to fix it in this section of the document: https://anvio.org/install/linux/stable/#issues-related-to-samtools
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Hi again,
It seems that anvio is installed successfully based o this message but I still get an error when checki the installation. [image: image.png]
On Fri, Jul 26, 2024 at 2:54 PM Nafsa Khazaei @.***> wrote:
Hi,
There was no problem with my samtools. Do I need to update it to 1.9? [image: image.png]
On Fri, Jul 26, 2024 at 1:54 PM Metehan Sever @.***> wrote:
hey @UniAlberta https://github.com/UniAlberta , Your error is most likely caused by the samtools installation and you can find how to fix it in this section of the document: https://anvio.org/install/linux/stable/#issues-related-to-samtools
— Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/2312#issuecomment-2253374197, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZVXR3X2BFZWREFHWL564BTZOKSOVAVCNFSM6AAAAABLQZHHLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJTGM3TIMJZG4 . You are receiving this because you were mentioned.Message ID: @.***>
[image: image.png]
On Fri, Jul 26, 2024 at 3:17 PM Nafsa Khazaei @.***> wrote:
Hi again,
It seems that anvio is installed successfully based o this message but I still get an error when checki the installation. [image: image.png]
On Fri, Jul 26, 2024 at 2:54 PM Nafsa Khazaei @.***> wrote:
Hi,
There was no problem with my samtools. Do I need to update it to 1.9? [image: image.png]
On Fri, Jul 26, 2024 at 1:54 PM Metehan Sever @.***> wrote:
hey @UniAlberta https://github.com/UniAlberta , Your error is most likely caused by the samtools installation and you can find how to fix it in this section of the document: https://anvio.org/install/linux/stable/#issues-related-to-samtools
— Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/2312#issuecomment-2253374197, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZVXR3X2BFZWREFHWL564BTZOKSOVAVCNFSM6AAAAABLQZHHLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJTGM3TIMJZG4 . You are receiving this because you were mentioned.Message ID: @.***>
Since the ImportError is happening for the pysam package, I suspect it is rather an issue with the pysam installation.
Please try to re-install pysam like this: https://anvio.org/install/linux/stable/#issues-with-pysam-installation-using-pip
If the self test still doesn't work, let us know.
I tried reinstallation of pysam and again got the same error.
On Mon, Jul 29, 2024, 01:02 Iva Veseli @.***> wrote:
Since the ImportError is happening for the pysam package, I suspect it is rather an issue with the pysam installation.
Please try to re-install pysam like this: https://anvio.org/install/linux/stable/#issues-with-pysam-installation-using-pip
If the self test still doesn't work, let us know.
— Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/2312#issuecomment-2255094403, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZVXR3TAVYVSELALT3OV3WTZOXSIRAVCNFSM6AAAAABLQZHHLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJVGA4TINBQGM . You are receiving this because you were mentioned.Message ID: @.***>
@UniAlberta Recently I tried to produce your error on my Linux system but I couldn't. It worked properly on my computer. I can only suggest to create new environment and use mamba instead of conda.
One thing I can suggest is to try the solutions described here for manually linking the shared library file: https://stackoverflow.com/questions/480764/linux-error-while-loading-shared-libraries-cannot-open-shared-object-file-no-s
Basically, if you can find the liblzma-51a76f52.so.5.2.4 file on your computer, then the fix might be as simple as adding the directory in which that file lives to your LD_LIBRARY_PATH environment variable.
If you cannot find that specific file in any of the locations where shared object (.so) files are usually installed by your package manager, but if you can find a different version of the liblzma .so somewhere, sometimes you can fix this sort of issue by symlinking the version you have to the version pysam is looking for, ie running something like ln -s liblzma-51a76f52.so.X.X.X liblzma-51a76f52.so.5.2.4 in the LD_LIBRARY location. But messing with that sort of thing is risky if you don't know what you are doing, so please have caution.
It might be better to ask the Pysam developers for help with this. You can open an issue on their Github: https://github.com/pysam-developers/pysam/issues
I have python 3.12.2. I see that in the command lines there`s python 3.10. Can this be the source of problem?
On Mon, Jul 29, 2024 at 3:08 AM Iva Veseli @.***> wrote:
One thing I can suggest is to try the solutions described here for manually linking the shared library file: https://stackoverflow.com/questions/480764/linux-error-while-loading-shared-libraries-cannot-open-shared-object-file-no-s
Basically, if you can find the liblzma-51a76f52.so.5.2.4 file on your computer, then the fix might be as simple as adding the directory in which that file lives to your LD_LIBRARY_PATH environment variable.
If you cannot find that specific file in any of the locations where shared object (.so) files are usually installed by your package manager, but if you can find a different version of the liblzma .so somewhere, sometimes you can fix this sort of issue by symlinking the version you have to the version pysam is looking for, ie running something like ln -s liblzma-51a76f52.so.X.X.X liblzma-51a76f52.so.5.2.4 in the LD_LIBRARY location. But messing with that sort of thing is risky if you don't know what you are doing, so please have caution.
It might be better to ask the Pysam developers for help with this. You can open an issue on their Github: https://github.com/pysam-developers/pysam/issues
— Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/2312#issuecomment-2255400141, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZVXR3XKVWDVNARW35OXGVLZOYBBFAVCNFSM6AAAAABLQZHHLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJVGQYDAMJUGE . You are receiving this because you were mentioned.Message ID: @.***>
I also have liblzma.so.5.4.6 which is different from what is said in the error of liblzma-51a76f52.so.5.2.4 not found.
On Mon, Jul 29, 2024 at 12:03 PM Nafsa Khazaei @.***> wrote:
I have python 3.12.2. I see that in the command lines there`s python 3.10. Can this be the source of problem?
On Mon, Jul 29, 2024 at 3:08 AM Iva Veseli @.***> wrote:
One thing I can suggest is to try the solutions described here for manually linking the shared library file: https://stackoverflow.com/questions/480764/linux-error-while-loading-shared-libraries-cannot-open-shared-object-file-no-s
Basically, if you can find the liblzma-51a76f52.so.5.2.4 file on your computer, then the fix might be as simple as adding the directory in which that file lives to your LD_LIBRARY_PATH environment variable.
If you cannot find that specific file in any of the locations where shared object (.so) files are usually installed by your package manager, but if you can find a different version of the liblzma .so somewhere, sometimes you can fix this sort of issue by symlinking the version you have to the version pysam is looking for, ie running something like ln -s liblzma-51a76f52.so.X.X.X liblzma-51a76f52.so.5.2.4 in the LD_LIBRARY location. But messing with that sort of thing is risky if you don't know what you are doing, so please have caution.
It might be better to ask the Pysam developers for help with this. You can open an issue on their Github: https://github.com/pysam-developers/pysam/issues
— Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/2312#issuecomment-2255400141, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZVXR3XKVWDVNARW35OXGVLZOYBBFAVCNFSM6AAAAABLQZHHLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENJVGQYDAMJUGE . You are receiving this because you were mentioned.Message ID: @.***>
You shouldn't have Python 3.12. Please follow the installation instructions word-by-word :)
Sorry, I double checked it now and it is 3.10
On Mon, Jul 29, 2024 at 1:51 PM A. Murat Eren (Meren) < @.***> wrote:
You shouldn't have Python 3.12. Please follow the installation instructions word-by-word :)
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I retried your suggestions but I still get the error.
On Mon, Jul 29, 2024 at 5:04 PM Nafsa Khazaei @.***> wrote:
Sorry, I double checked it now and it is 3.10
On Mon, Jul 29, 2024 at 1:51 PM A. Murat Eren (Meren) < @.***> wrote:
You shouldn't have Python 3.12. Please follow the installation instructions word-by-word :)
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