Error in sub.sample

Commands in mothur
1

I’m following the MiSeqSOP Tutorial in Galaxy: (https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html#sequence-alignment)
where I have 39 sequences as the smallest of all my samples determined via count.group.

When I try to perform sub.sample with the following parameters:

  • “Select type of data to subsample” : OTU Shared
  • “shared” : the shared file from Make.shared tool
  • “size” : 39

It creates an empty list with an error indicator in red rather than a green success.

Appreciate your help, thanks!

2

Hi there,

I’m sorry, but I really don’t know anything about the galaxy set up or how it is building mothur’s commands. Normally, sub.sample will subsample down to the number you give it or to the size of the smallest sample. So, if your smallest sample has 39 sequences then you don’t really need to provide a size. But if you want to exclude that sample (it’s pretty small), you might try a larger number to get rid of the small sample.

Pat

3

Thanks for responding. I also got the same error in galaxy. Here is the error log.

TERM environment variable not set.
TERM environment variable not set.
/galaxy-repl/main/jobdir/024/246/24246223/tool_script.sh: line 25: 18059 Done echo ‘sub.sample( shared=input_otu.dat ,size=16411 )’
18060 | sed ‘s/ //g’
18061 Segmentation fault (core dumped) | mothur
18062 | tee mothur.out.log

4

Hi,

I think you both need to follow up with the galaxy developers to see what’s going on at their end. This doesn’t seem to be a mothur problem.

Pat

5

Thank you Pat! I will follow-up with the Galaxy team.

6

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