Issue with muscle error

[Yancong Zhang]

Hi PhyloPhlAn group,

I have some issue when running PhyloPhlAn. Could you give me some help?

I installed the latest version of PhyloPhlAn on the dev branch of the repository (https://bitbucket.org/nsegata/phylophlan/branch/dev). Then I tested the example genomes on the downloaded phylophlan folder using the command './phylophlan.py -i -t example_insertion --nproc 10'. But it failed with some error message "[e] Quitting PhyloPhlAn [muscle error]". The muscle version I used is v3.8.31. I couldn't find much more information about this error. Do you have any idea about it? Any suggestion would be appreciated!

Best,

Yancong

[Francesco Asnicar]

Dear Yancong,

Thanks for reporting this. So, you're indeed in the new PhyloPhlAn branch, but the phylophlan.py script is still running the old PhyloPhlAn version. If you're interested in running the latest version you should execute the phylophlan2.py script, otherwise, if you want to run the old version, can you please provide the full output so that I can have a look to what might be the problem?

Many thanks,

Francesco

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[Yancong Zhang]

Hi Francesco,

Thanks so much for your reply! It would be very helpful if we could make the old PhyloPhylAn version works.

I couldn't find any files in the "output/" folder, but there was one newly generated sub-folder named "example_insertion" in the "data/" folder. I attached the files in that sub-folder and whole log file. Hope it could provide some information for your debug. Please let me know if anything else needs to provide.  

Thanks again!

Yancong

On Monday, April 22, 2019 at 5:08:32 AM UTC-4, francescoasnicar wrote:

Dear Yancong,

Thanks for reporting this. So, you're indeed in the new PhyloPhlAn branch, but the phylophlan.py script is still running the old PhyloPhlAn version. If you're interested in running the latest version you should execute the phylophlan2.py script, otherwise, if you want to run the old version, can you please provide the full output so that I can have a look to what might be the problem?

Many thanks,

Francesco

On Tue, Apr 16, 2019 at 6:05 PM Yancong Zhang <zhangy...@gmail.com> wrote:

Hi PhyloPhlAn group,

I have some issue when running PhyloPhlAn. Could you give me some help?

I installed the latest version of PhyloPhlAn on the dev branch of the repository (https://bitbucket.org/nsegata/phylophlan/branch/dev). Then I tested the example genomes on the downloaded phylophlan folder using the command './phylophlan.py -i -t example_insertion --nproc 10'. But it failed with some error message "[e] Quitting PhyloPhlAn [muscle error]". The muscle version I used is v3.8.31. I couldn't find much more information about this error. Do you have any idea about it? Any suggestion would be appreciated!

Best,

Yancong

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[Francesco Asnicar]

Thanks Yancong for the log and the files.

From the files the execution seems to be correct, is muscle installed in your system?

Or, have you specified the --mafft param? In this case, is mafft installed in your system?

Thanks,

Francesco

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[Yancong Zhang]

Hi Francesco,

Yes, I installed MUSCLE v3.8.31 and MAFFT v7.427. I tested them separately and both of them looked works well.

Best,

Yancong