Hi,

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/metaphlan2.py 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/metaphlan2.py", line 1565, in <module>
    metaphlan2()
  File "/home/user/metaphlan2/metaphlan2.py", line 1496, in metaphlan2
    maybe_generate_biom_file(tree, pars, outpred)
  File "/home/user/metaphlan2/metaphlan2.py", line 1344, in maybe_generate_biom_file
    input_is_dense       = True
  File "/usr/lib64/python3.5/site-packages/biom/table.py", line 508, in __init__
    errcheck(self)
  File "/usr/lib64/python3.5/site-packages/biom/err.py", 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!