ete2 requirement by humann2_humann1_kegg

[Nathan LI]

Dear Humann experts,

I tried to use the comment 

humann2_humann1_kegg --ikoc humann1/data/koc --igenels humann1/data/genels --o legacy_kegg_idmapping.tsv 

to generate the idmapping file for using kegg database in humann2. However, when I run this code, it warned that 

ete2 is not installed and thus we cannot provide the full taxonomy for the bug, providing only the name

But actually the ete2 has been installed (version 2.3.10) in the computer. I am wondering what the problem is? Does humann2 have specific version requirement on ete2?

Many thanks!

Yours,

Nathan

[Lauren McIver]

Hi Nathan,

I wonder if the problem is with ete2 downloading and installing its database.

Can you try running the following command? Please let me know if you see any error messages.

$ python -c "from ete2 import NCBITaxa; ncbi=NCBITaxa()"

Thank you,

Lauren

[Nathan LI]

Dear Lauren,

Thank you so much for your response! I tried the command from you, and it showed that

python -c "from ete2 import NCBITaxa; ncbi=NCBITaxa()"

Traceback (most recent call last):

  File "<string>", line 1, in <module>

ImportError: No module named ete2

Does it mean I have not installed the ete2 appropriately? I am not familiar with python, so could you tell what I should do in this situation?

Really appreciate it!

Best regards,

Nathan

[Lauren McIver]

Hi Nathan,

It looks like the ete2 install is not found. Did you possibly install it in a location that is not in your $PYTHONPATH? Alternatively, you might try installing it again. If you have pip installed you can run the following:

$ pip install ete2

(Add the option "--user" if you do not have root permissions).

Thank you,

Lauren

 

[Nathan LI]

Hi, Lauren,

Thank you so much for your suggestion! Now this ete2 step works pretty well.

May I consult you one more question: when I tried to ignore the metaphlan2 step using --bypass-prescreen (I want to use the whole chocophlan dataset), the humann2 program did not work and I attached the log file here. If I remove the "--bypass-prescreen", then it runs well. Could you tell me how I could use the completed chocophlan dataset?

Many thanks for your time!

Warm regards,

Nathan

[Lauren McIver]

Hi Nathan,

Thank you for including your log file. It looks like the concat command exceeds the max command line arguments on your platform. I have been unable to replicate this error on Fedora and CentOS. Are you possibly running on a MacOS? I will try MacOS next to replicate and then resolve the error message. 

Also a quick note about running with the full chocophlan database. This will use up a bit of disk space and memory. It will take upwards of 40GB of memory to build the bowtie2 index of the full chocophlan with database files totaling (20GB (concat fasta file) + 41GB (bowtie2 indexes) = 61GB). However, if you are running multiple samples with the full chocophlan database you only need to build this database once. For more information, please see the HUMAnN2 tutorial section on Joint Taxonomic Profile, more specifically the last step in this section includes information on how to provide a prebuilt database.

Thank you,

Lauren

[Nathan LI]

Dear Lauren,

Thank you so much for your response! Yeah, I am using the MacOS for my data analysis. Do you have any suggestions on it?

Since my Mac has 64GB ram, I think it has the ability to use the whole chocophlan database. Thanks for your reminder!

Take care! Have a good day!

Yours,

Nathan

[Nathan LI]

Hi, Lauren,

In addition to my previous question, may I consult you one more question: I am trying to use the legacy KEGG database now. Therefore, as the first step, I plan to use usearch to map my reads to KEGG database (I obtained it from Eric when I used HUMAnN0.99) and generate the m8 results. During this step, I am wondering which evalue do you suggest to use as the cutoff of usearch?

Many thanks for your time!

Yours,

Nathan

[Lauren McIver]

Hello Nathan,

Thank you for the additional information. That is great you have 64GB of memory. I was able to replicate and resolve the MacOS error message you were seeing. From looking into the error it looks like MacOS has a max args which is ~1/10 of that of some linux distributions (Fedora, CentOS, Ubuntu). If you install the new version of humann2 (v0.6.1), the MacOS error should be resolved.

I would suggest using the default e-value in humann2. 

Thank you,

Lauren

  

[Naina kumari]

Hello Humann users

I am also facing the same problem while running the humann2_humann1_kegg command......I followed the steps listed here but I got stuck in this step:-

$ pip install ete2

(base) [bmgu@localhost ~]$ pip install ete2 --user
Collecting ete2
  Using cached https://files.pythonhosted.org/packages/60/50/0287c4a6cd11bd62fe3bcaa859bbbc18b48bb71b92dc027d439451fe10c1/ete2-2.3.10.tar.gz
    ERROR: Command errored out with exit status 1:
     command: /home/bmgu/miniconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-4cb8inkg/ete2/setup.py'"'"'; __file__='"'"'/tmp/pip-install-4cb8inkg/ete2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info
         cwd: /tmp/pip-install-4cb8inkg/ete2/
    Complete output (6 lines):

    Traceback (most recent call last):
      File "<string>", line 1, in <module>

      File "/tmp/pip-install-4cb8inkg/ete2/setup.py", line 90
        print "Installing ETE (A python Environment for Tree Exploration)."
                                                                          ^
    SyntaxError: invalid syntax
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I am not so well versed with python so I dont understand the error, can anyone please help me with this, it would be very helpful to me.

Thanking you

Naina

[Lauren McIver]

Hello Naina, It looks like you might be installing ete2 in a conda python3 environment and ete2 is not python3 compatible. Try installing ete2 with python2 and that should resolve the issue.

Thanks,

Lauren

--
You received this message because you are subscribed to the Google Groups "HUMAnN Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to humann-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/humann-users/dd82dbda-a729-494c-8b94-cbd69d3b816a%40googlegroups.com.