PhyloPhlAn cannot use ASTRID for --tree1

Microbial community profiling PhyloPhlAn
1

This might be an issue of the version of ASTRID, but I couldn’t find the supported versions. I’m using PhyloPhlAn v3.0.3 and ASTRID v2.2.1.

When I try using --tree1 astrid I get the error:

[e] Command '['/local/opt/ASTRID/bazel-bin/src/ASTRID', '-i', 'output_hr/input_hr_concatenated.aln', '-m', 'auto', '-o', '/home/.../input_hr.tre']' returned non-zero exit status 1.

[e] error while executing
    command_line: /local/opt/ASTRID/bazel-bin/src/ASTRID -i output_hr/input_hr_concatenated.aln -m auto -o /home/.../input_hr.tre
           stdin: None
          stdout: None
             env: {...}

When I manually run the failing command I get the ASTRID error Unrecognized argument -m. I suspect PhyloPhlAn meant to use --auto instead of -m auto (?). If so, the solution should be relatively easy.

Thanks in advance!
Miguel.

2

Dear Miguel, thanks a lot for reporting this. It might be due to the fact that I had a very old version of ASTRID in which the param was -m auto and now is --auto. I’ll update the phylophlan_write_config_file script to reflect this. In your case, you can open your config file with your preferred text editor and amend the command line.

Many thanks,
Francesco