checkm tree_qa throws AttributeError about checkm

[donovan-h-parks]

Hello Dieter,

It looks like you are running CheckM correctly. Perhaps this is a bug that we have not encountered. I noticed that you are running a lot of genomes through CheckM (3600!). Can you try running just a few genomes (say, 2 or 3) to see if the problem persists? If so, it should be easier to determine what is happening.

Cheers,
Donovan

[aistBMRG]

Hi Donovan,

Thank you for the quick response. Yes, I used many bins ... I guess I was not expecting any trouble due to the number of bins.

I tried your suggestion of running with less bins/genomes (I used 2) and now it completed without error. Not sure what is happening or at what point (how many genomes) the process gives the error ...

At this point I will run in smaller batches and remove some bins.

Thanks again !!!

Dieter.

[donovan-h-parks]

The number of bins shouldn't matter. My guess is one of the bins is problematic. If you can identify which bin it is, I can determine why it is causing a problem.

[aistBMRG]

Ok, I will run a loop and then see which one fails. Btw, I just tested a subset of 504 and no issues ...

[donovan-h-parks]

I am assuming this can be closed as there has been no follow-up in over a month.