CRITICAL ERROR when running humann2 with conda

[Ali]

Hello,

I have installed humann2 with conda. Unfortunately, I am getting the following error "CRITICAL ERROR: Can not call software version for bowtie2" when trying to run a test using demo files however I am sure that bowtie2 is installed.

Any suggestion to solve the problem is appreciated!

Many thanks in advance,
Ali

[Lauren McIver]

Hi Ali - I think by default conda uses wheels instead of installing from source. HUMAnN2 must be installed from source for it to be able to also install its dependencies (bowtie2/diamond). If you uninstall HUMAnN2 in conda and reinstall it from source, I think it should fix the error you are seeing with it not being able to find its dependency bowtie2. See the note in the requirements section of the HUMAnN2 main page for the flags to add to your install command to force install from source: http://huttenhower.sph.harvard.edu/humann2#markdown-header-getting-started-with-humann2 . If you have a newer version of pip "$ pip install humann2 --no-binary :all:" should install from source.

Thanks,

Lauren

[Ali]

Hi Lauren,

Many thanks for the prompt reply. Unfortunately, I am still getting the same error! 

As you suggested, I uninstalled the humann2 with conda and reinstalled from the source (I tried both pip and installing from source methods). As far as I can see all the dependencies are installed however I still get the following error " CRITICAL ERROR: Can not call software version for bowtie2"

Before installing humann2 with anaconda I have tried both pip and brew for installation however I was getting the following error: "the database file for MetaPhlAn does not exist at" which I couldn't resolve it by placing the database in the same file as the metaphlan2 executable. Therefore I decided to uninstall humann2 and metaphlan2 and all their dependencies and tried to install them this time via anaconda. 

I can not figured how to deal with these errors and I would really appreciate your comments and suggestions for getting humann2 into work.

Many thanks in advance,

Ali

[Lauren McIver]

Hi Ali - Is it possible you might have a couple different bowtie2 versions installed and humann2 is picking up an older version? You could try running humann2 with the option to set the location of the bowtie2 executable to use "--bowtie2 <directory containing bowtie2>". I think the error you were seeing about the MetaPhlAn2 database file is because currently humann2 is only compatible with MetaPhlAn2 version <= 2.6.0. In the next release of humann2 it will be compatible with the latest MetaPhlAn2 release. Please let me know if you continue to have issues debugging your install so I can help you get setup.

Thanks,

Lauren

[Ali]

Hi Lauren,

Many thanks for the info. I could fixed the errors I was getting before. However, I couldn't find MetaPhlAn2 version <= 2.6.0 could you please provide a link to the older version of metaphlan2? or is there a way to install the new version and avoid getting the error I was getting with the database? 

Many thanks in advance,

Ali

[Lauren McIver]

Hi Ali, If you have the latest MetaPhlAn2 version installed, when running HUMAnN2 add the option --metaphlan-options='--mpa_pkl databases/mpa_v20_m200.pkl --bowtie2db databases/mpa_v20_m200' providing the full path to the MetaphlAn2 databases. This way you will reset the default MetaPhlAn2 database locations in HUMAnN2 to the locations used with the latest MetaPhlAn2. The next release of HUMAnN2 will be compatible by default with the new default locations of the MetaPhlAn2 database.

Thanks,

Lauren