Errors:
(1/2) Missing option "--o-filtered-table". ("--output-dir" may also be used)
(2/2) Got unexpected extra argument ( )
/var/spool/slurmd/job20601501/slurm_script: line 14: --o-filtered-table: command not found
Errors that look like this usually happen when you have some kind of formatting issue - in this case, it looks a bit like you might be missing a \ at the end of the second-to-last line of your command, which is then causing your shell to run this command as two separate commands (which doesn't work).
You should double-check that it is exactly the same --- besides the \ characters, you might also have an issue with the single or double quotes on the second-to-last line - an issue there could produce the exact same shell error.
Consult with your slurm sysadmin - they might be using a shell that requires you to quote your command in a different way. The second error message you shared above indicates that there is a problem somewhere with the parsing of the command (by your shell, not QIIME 2). One thing that does jump out at me is the syntax highlighting in the third line - there is something different about the last escape slash at the end.
Yes. I felt something wrong in the slash on the second-to-last line. When I typed it, it was always different with others. And I did not know how to solve it.
Hello @thermokarst, it had the same errors when I used the command "feature-table filter-features". And I have no way to solve the style of the slash on the second-to-last line. Thanks very much.
Sure you do! Option 1: Chat with your sysadmin, ask them about the shell you're using. These errors aren't being caused by QIIME 2 - they are issues with the shell, or program you are using to send commands to QIIME 2. Option 2: