Cannot find bcftools

[Megan Folkerts]

Hi,

I'm getting the following error when trying to run samplemarkers.py:

Traceback (most recent call last):

  File "/home/mfolkerts/miniconda3/envs/metaphlan2/bin/ooSubprocess.py", line 246, in wrapper

    return f(*args, **kwargs)

  File "/home/mfolkerts/miniconda3/envs/metaphlan2/bin/sample2markers.py", line 414, in run_sample

    bcftools_exe=args['bcftools_exe'])

  File "/home/mfolkerts/miniconda3/envs/metaphlan2/bin/sample2markers.py", line 333, in sam2markers

    stderr=error_pipe)

  File "/home/mfolkerts/miniconda3/envs/metaphlan2/bin/ooSubprocess.py", line 105, in chain

    'in the executable path!'%prog)

ooSubprocess.ooSubprocessException: Error: cannot find the program /home/mfolkerts/miniconda3/envs/metaphlan2/bin/bcftools_0.1.19 in the executable path!

This is the line of code I'm running:

sample2markers.py --ifn_samples *.sam.bz2 --input_type sam --output_dir samplemarkersout/ --nprocs 12 --bcftools_exe /home/mfolkerts/miniconda3/envs/metaphlan2/bin/bcftools_0.1.19 

I'm giving it the absolute file path of the bcftools executable (as per the suggestion of previous threads), but I'm still getting the above error. This also seems to be the correct version of bcftools, again as per previous threads.

I re-installed metaphlan to make sure that I'm running the latest version, and repeated the command, but it didn't solve the issue. 

Any help would be appreciated.

[Aitor Blanco-Miguez]

Hi Megan,

Thank you for reporting this issue. Could you tell me which version of MetaPhlAn2 are you running? Did you install it through conda?

Best,

Aitor 

[Megan Folkerts]

Yes I installed through conda. I'm running Metaphlan 2.9.

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Megan Folkerts, MS
Research Associate II
Center for Emerging Pathogens and Technologies
TGen North
Flagstaff, Arizona
928-226-6375

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[Aitor Blanco-Miguez]

Hi again,
We reported some problems with bftools in the last conda version of Metaphlan2. We will fix the problem asap. In the meanwhile, I recommend you to remove the Metaphlan2's conda installation and install the last metaphlan version from the bitbucket repository: https://bitbucket.org/biobakery/metaphlan2/src/2.9/

Best,
Aitor

[Megan Folkerts]

I will try that. Thanks!

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