Strainphlan error

blair.merrick · September 5, 2023, 8:54am

Hi,

Encountering an error when trying to run StrainPhlAn (v.4.0.6).
Previously been able to run a few hundred markers through this, but now getting the following error:

Tue Sep 5 09:49:24 2023: Start StrainPhlAn 4.0.6 execution
Tue Sep 5 09:49:24 2023: Creating temporary directory…
Tue Sep 5 09:49:24 2023: Done.
Tue Sep 5 09:49:24 2023: Filtering markers and samples…
Tue Sep 5 09:49:24 2023: Getting markers from main samples…
Tue Sep 5 09:49:26 2023: [Error] Parallel execution fails: invalid load key, ‘A’.Tue Sep 5 09:49:26 2023: Stop StrainPhlAn execution.

Files all in same folders as previously (when it ran ok).
Tried running it on single core and multiple cores but no difference, and same error whatever the input db_marker file is.

Any ideas what might be causing the issue?

Thanks in advance,
Blair

aitor.blancomiguez · September 22, 2023, 2:27pm

Hi @blair.merrick
Could you paste the exact command you are using?

blair.merrick · September 29, 2023, 9:30am

Hi @aitor.blancomiguez,

Thanks.

Issue seemed to be with a few of the .pkl files within the consensus_markers folder - removing these allowed me to run the command again no problem.

I have noticed that in some of the .pkl file outputs, the list of consensus markers for each SGB does not entirely overlap with the MetaPhlAn output.

e.g. MetaPhlAn has binned into SGB4540_group for Anerostipes hadrus, but consensus markers file for that sample has SGB102029.

Also noticed it for another SGB - SGB14535_group (Collinsella aerofaciens).

Can’t find an example for a non “SGB*_group” - is it therefore just for these “groups”

Thanks,
Blair