metaphlan2.py [Errno 2] No such file or directory

Question

[Giffredo]

Hi, I installed metaphlan2 with all his dependencies. I used:

$ hg clone https://bitbucket.org/biobakery/metaphlan2

I don't understand the error..

$ metaphlan2.py 17NA211_L001_R1_001.fastq --input_type fastq > profiled_metagenome.txt

Downloading MetaPhlAn2 database Please note due to the size this might take a few minutes

File /data/DNA/Web/giorgio/metaphlan2/databases/mpa_v20_m200.tar already present!

File /data/DNA/Web/giorgio/metaphlan2/databases/mpa_v20_m200.md5 already present! Traceback (most recent call last):   File "/data/DNA/Web/giorgio/metaphlan2/metaphlan2.py", line 1560, in <module>
    metaphlan2()   File "/data/DNA/Web/giorgio/metaphlan2/metaphlan2.py", line 1340, in metaphlan2
    pars['nproc'])   File "/data/DNA/Web/giorgio/metaphlan2/metaphlan2.py", line 823, in check_and_install_database
    bowtie2_build, nproc)   File "/data/DNA/Web/giorgio/metaphlan2/metaphlan2.py", line 795, in download_unpack_tar
    stderr=subp.STDOUT)   File "/usr/lib/python2.7/subprocess.py", line 567, in check_output
    process = Popen(stdout=PIPE, *popenargs, **kwargs)   File "/usr/lib/python2.7/subprocess.py", line 711, in __init__
    errread, errwrite)   File "/usr/lib/python2.7/subprocess.py", line 1343, in _execute_child
    raise child_exception OSError: [Errno 2] No such file or directory

[Giffredo]

thanks, bowtie2 was not installed... know it gives me another error:

metaphlan2.py 17NA211_L001_R1_001.fastq --input_type fastq > profiled_metagenome.txt

Warning! Biom python library not detected! Exporting to biom format will not work! No MetaPhlAn BowTie2 database found [--bowtie2db option]! (or wrong path provided). Expecting location ${mpa_dir}/db_v20/map_v20_m200

biom is installed.. ..

[Istvan Albert]

If it says it is not installed it means that it cannot see it the way it thinks it should be there. You should post this on the developer's website since it is them that the most knowledgeable and ought to assist you with it.

In general, like I said these are the simplest problems to troubleshoot - if it says it is not there then stop thinking about "but it is there" No it is not there as far as the program is concerned - why? it is some sort of setup problem specific to your computer.

[Fatima]

These links might help:

https://bitbucket.org/nsegata/metaphlan/issues/9/bowtie2-error

https://groups.google.com/forum/m/#!topic/metaphlan-users/5_Ey2MGROa8

https://groups.google.com/forum/m/#!topic/metaphlan-users/5ltD8X8Xitc

[leneborma]

To get rid of this error you can try using os.listdir() function to check that at least python sees the file exists or not.

Answer 1

[Istvan Albert]

This is the simplest but also often the most infuriating of all errors a program can raise.

A file is missing. But which one ... alas, the program does not speak to that.

Trace the error message through the source, if you have the same version as the source that seems to indicate that bowtie2 is not installed correctly

https://bitbucket.org/biobakery/metaphlan2/src/d8ab9ca4244c09a7a4995042a99fbba1e3598ac0/metaphlan2.py?at=default&fileviewer=file-view-default#metaphlan2.py-795