sub.sample throwing error

mothur bugs
1

Hi folks,

I’m running mothur 1.39.5 on a Linux Mint workstation. Every time I try to run sub.sample, mothur throws an error and boots me back to the command prompt. Here is the text from the command and what the machine tells me:

mothur > sub.sample(shared=Coral_Microbiome.processed.shared)
Sampling 1132 from each group.
0.03
*** Error in `mothur’: free(): invalid next size (normal): 0x0000000002060d90 ***
Aborted

Any idea what’s going on? For the record, I tried setting the subsample size to lower and higher values, and get the same error.

Thanks,
Jeff M.

2

After messing around with this problem some more, I’ve discovered that it has something to do with file size. Using filter.shared to remove increasing numbers of rare OTUs, I find that if the file size gets small enough I am able to run sub.sample. I was able to sub.sample a file that was 233K in size (with 3061 OTUs) but mothur aborted when I ran a version of the same .shared file that was 288K and had 3825 OTUs. This is nowhere near enough data to overload my memory (64GB RAM). I’m at a loss!

3

I can confirm this behaviour. Could this be another consequence of inflated OTU numbers? However I imagine that subsampling should be able to handle a file that small?
Edit: Would it then make sense to perform remove.rare after clustering the OTUs?

Best

Jonas

4

Thanks for reporting this bug. The error is unrelated to your dataset. In version 1.39, we compiled using c++11 features. The change effected how some systems handle mothur’s threading functions causing unexpected behavior. The 1.40.0 release has been delayed so we can correct this issue.

5

Hello - I’ve encountered this error too, using v 1.39.5. Has anyone found a work around until v 1.40 is released? Is it a problem on all versions of 1.39.5?

Thanks,
Pete