Too crazy about phylophlan!! Can anyone help me? Crying for~~

[Lu Yang]

Hi,

 

I have spent almost 8 hours in the installation of phylophlan, both version 1 and version 2. I am worn out. So crazy!!!!! I really need someone's help.

Initially I installed version 2, but got error with 

[e] Command '['FastTreeMP']' returned non-zero exit status 1.

[e] program not installed or not present in the system path
    command_line: FastTreeMP
           stdin: None
          stdout: None 

env: {'MANPATH': '$MANPATH:/home/zzhang78/ssu-align-0.1.1/share/man', 'XDG_SESSION_ID': '1173', 'HOSTNAME': 'transwer.cee.utk.edu', 'SELINUX_ROLE_REQUESTED': '', 'TERM': 'xterm-256color', 'SHELL$

But my FastTree is actually existed!

FastTreeMP
Usage for FastTree version 2.1.10 Double precision (No SSE3), OpenMP (56 threads):
  FastTree protein_alignment > tree
  FastTree < protein_alignment > tree
  FastTree -out tree protein_alignment
  FastTree -nt nucleotide_alignment > tree
  FastTree -nt -gtr < nucleotide_alignment > tree
  FastTree < nucleotide_alignment > tree
FastTree accepts alignments in fasta or phylip interleaved formats

Then I turn to version 1, since I think this older version will be much easier to install! But still tons of error!

Here is a description of how I install the software version 1, and the errors I faced. 

# following the procedures on website https://bitbucket.org/nsegata/phylophlan/wiki/Home

python /home/zzhang78/phylophlan/phylophlan.py -u my_genomes

# --erorr
Traceback (most recent call last):

  File "/home/zzhang78/phylophlan/phylophlan.py", line 27, in <module>

    import taxcuration as taxc

ImportError: No module named taxcuration

(base) transwer:input zzhang78$ ../phylophlan.py -h

Traceback (most recent call last):

  File "../phylophlan.py", line 27, in <module>

    import taxcuration as taxc
# ---Fixed way

escaped_home=${HOME//\//\\\/}
sed -i "s/taxcuration\/')/$escaped_home\/phylophlan\/taxcuration\/')/g" $HOME/phylophlan/phylophlan.py

export PATH="$HOME/phylophlan":$PATH
#--> then I think it is ok to run

# ---error

python /home/zzhang78/phylophlan/phylophlan.py -u my_genomes

Traceback (most recent call last):

  File "/home/zzhang78/phylophlan/phylophlan.py", line 27, in <module>

    import taxcuration as taxc

ImportError: No module named taxcuration

# ---Fixed way

cd phylophlan

escaped_home=${HOME//\//\\\/}

sed -i "s/taxcuration\/')/$escaped_home\/phylophlan\/taxcuration\/')/g" $HOME/phylophlan/phylophlan.py

export PATH="$HOME/phylophlan":$PATH

mkdir usearch

export PATH=$PATH:/home/zzhang78/usearch/

python ../phylophlan.py -u example_corynebacteria/

# ---erorr
Extracting data/ppa.seeds.faa ... Traceback (most recent call last):

  File "../phylophlan.py", line 780, in <module>

    init()

  File "../phylophlan.py", line 141, in init

    with closing(tarfile.open( compressed(f)  )) as inp:

  File "/home/zzhang78/miniconda2/lib/python2.7/tarfile.py", line 1673, in open

    return func(name, "r", fileobj, **kwargs)

  File "/home/zzhang78/miniconda2/lib/python2.7/tarfile.py", line 1738, in gzopen

    fileobj = gzip.GzipFile(name, mode, compresslevel, fileobj)

  File "/home/zzhang78/miniconda2/lib/python2.7/gzip.py", line 94, in __init__

    fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')

IOError: [Errno 2] No such file or directory: 'data/ppa.seeds.faa.tar.bz2'

But they are actiually under folder /home/zzhang78/phylophlan/data/在此输入代码...

I really have no idea of how to continue.

Can I have the help???

Really appreciate it!!