Using CAMI format input for metagenome_from_profile.py

[raquellewei]

Hi, I was trying to run metagenome_from_profile.py using a .profile input file as the manual says it accepts either biom format or CAMI format. However, I received this error message "TypeError: my_run/my_profile.profile does not appear to be a BIOM file!" Is there anywhere I should specify that it is a CAMI file explicitly? I took a look at the config file and did not find something suggestive... Any help would be really appreciated. Thank you!

[AlphaSquad]

Hi, unfortunately the simulation from CAMI-format .profile files is not functional yet. It is on my todo list, but I cannot give a date as to when it will be functional, sorry.

[raquellewei]

Hi, Thank you for the clarification. In that case, can you give me a hint on how your .biom file (Like the mini.biom, for example) is generated? Thank you!

[AlphaSquad]

Oh sorry, your answer must have gotten lost in time. It probably is too late, but the BIOM format is generated by (some) 16S profilers such as QIIME