nsegata-phylophlan error

[Amit Gupta]

Hello

I have installed Phylophlan and all the dependencies and tried to run on example dataset but getting some error. 

Command:Run

./phylophlan.py -u example_corynebacteria/

Error message

All alignments performed!

All alignments already computed!

Aligning finished in 227 secs (2047 total time).

All alignments merged into data/example_corynebacteria//aln.fna!

Start building the tree with FastTree ... 

Traceback (most recent call last):

  File "./phylophlan.py", line 805, in <module>

    fasttree(projn,pars['integrate'])

  File "./phylophlan.py", line 552, in fasttree

    stdout = open(outt,"w") )

IOError: [Errno 2] No such file or directory: 'output/example_corynebacteria//example_corynebacteria/.tree.nwk'

Thanks in advance!

Amit

[Francesco Asnicar]

Dear Amit,

thanks for using PhyloPhlAn. I guess that your error is due to an extra "/" character in the project name input:

./phylophlan.py -u example_corynebacteria/

it should be like this:

./phylophlan.py -u example_corynebacteria

Many thanks,

Francesco

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[Amit Gupta]

Thank you Sir for quick response. 

I have now corrected as you mentioned. But again its showing some error regarding duplicate keys. This I running on Mac. Additionally, I have also read other same error post from group. Now I am trying to do same in Ubuntu might be that will help.

Error message:

Traceback (most recent call last):

  File "./phylophlan.py", line 803, in <module>

    aln_merge(projn,pars['integrate'])

  File "./phylophlan.py", line 505, in aln_merge

    faas = SeqIO.to_dict( faas )

  File "/Library/Python/2.7/site-packages/biopython-1.64-py2.7-macosx-10.10-intel.egg/Bio/SeqIO/__init__.py", line 720, in to_dict

    raise ValueError("Duplicate key '%s'" % key)

ValueError: Duplicate key '644738696'

[Francesco Asnicar]

Dear Amit,

two things you can try/check:

1) if not already done, clean the intermediate files from previous executions of PhyloPhlAn, you can do this using the -c option

2) make sure that your inputs don't contain the id reported (644738696), if one of your inputs contain this id, then you should change the ids of your inputs and this can be done with a dev version of PhyloPhlAn (let me know if this is the case and I'll tell you how you can do this)

Also, we never tested PhyloPhlAn under Mac, so running it under a Linux machine might help.

Please, let me know if you still have errors in executing PhyloPhlAn.

Many thanks,

Francesco

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[Amit Gupta]

Thanks a lot for your help.

I have done configuration on Linux (Ubuntu), now its working fine and I am able to get tree file on example dataset. Additionally, I also want to have your opinion on which tree visualization tools would be best for proper annotation like I have tried GraPhlAn, iTOL, etetoolkit etc. or other third party ones? 

Francesco

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amit gupta

[Amit Gupta]

Thanks a lot for your help.

I have done configuration on Linux (Ubuntu), now its working fine and I am able to get tree file on example dataset. Additionally, I also want to have your opinion on which tree visualization tools would be best for proper annotation like I have tried GraPhlAn, iTOL, etetoolkit etc. or other third party ones? 

Sincerely,

Amit

On Tue, Jun 20, 2017 at 11:30 PM, Francesco Asnicar <francesc...@gmail.com> wrote:

Francesco

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amit gupta

[Francesco Asnicar]

Hi Amit,

I'm glad that you managed to get PhyloPhlAn working.

Among the ones you mentioned, you can also consider Krona and ggtree.

I canno tell you which one is the best, because I think that really depends on what you want to display in the tree (some tools can displayed different types of metadata) and which language you're more familiar with (e.g., ggtree requires a little knowledge of R to handle the data).

Many thanks,

Francesco

Francesco

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