Question: metaphlan2 --biom option error
gravatar for christina
11 months ago by
New Zealand
christina0 wrote:


I am trying to use the --biom option for running a metaphlan2 run with the intermediate bowtie2.bz2 files from a previous run.

Command to run metaphlan2:

python /home/user/metaphlan2/ sample.bowtie2.bz2 --nproc 12 --input_type bowt
ie2out --biom sample.biom > sample_profile.txt

It works fine for creating the profile.txt files, but I am getting the following error with the --biom flag:

Traceback (most recent call last):
  File "/home/user/metaphlan2/", line 1565, in <module>
  File "/home/user/metaphlan2/", line 1496, in metaphlan2
    maybe_generate_biom_file(tree, pars, outpred)
  File "/home/user/metaphlan2/", line 1344, in maybe_generate_biom_file
    input_is_dense       = True
  File "/usr/lib64/python3.5/site-packages/biom/", line 508, in __init__
  File "/usr/lib64/python3.5/site-packages/biom/", line 472, in errcheck
    raise ret
biom.exception.TableException: Size of observation metadata differs from matrix size!

It only creates the sample_profile.txt, but no biomfile.

Any idea on why I am getting this error?

Thanks for your help!

ADD COMMENTlink written 11 months ago by christina0
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