Error with count.seqs() command

Commands in mothur
1

Hi all,
I am a high school sophomore doing some research using mothur. I have looked at the MiSeq SOP and 454 SOP. I’ve figured out most of the commands as well as their purpose and function. However, I have encountered an error that is “inconsistent” for a lack of a better term when I try to execute the count.seqs() command.
Example 1:
mothur > count.seqs(name=current, group=current)
Using 550_depth.good.groups as input file for the group parameter.
Using 550_depth.good.names as input file for the name parameter.
Using 8 processors.
[ERROR]: processes reported processing 131135 sequences, but group file indicates you have 131269 sequences. Could you have a file mismatch?
It took 3 secs to create a table for 131135 sequences.
Total number of sequences: 131135
Output File Names:
550_depth.good.count_table

Above, even though there’s an error reporting a file mismatch, the output file is still created. However, in other cases when I have the error, an output file is not created.
Example 2:
mothur > count.seqs(name=current, group=current)
Using 300_depth.good.groups as input file for the group parameter.
Using 300_depth.good.names as input file for the name parameter.

Using 8 processors.
[ERROR]: processes reported processing 125187 sequences, but group file indicates you have 125313 sequences. Either you have a file mismatch or a process failed to complete the task assigned to it.

I would highly appreciate any suggestions or helpful advice. Thank you!

2

Wow - a high school sophomore - impressive!

These errors typically happen because one of the previous steps excluded either the name or group file. The first thing to try is to remove all of the files that were created after running make.contigs and then start over at screen.seqs. Give this a shot and let us know how it goes. Also, you generally want all of your samples together in the same file. From the examples you provided it looks like you might have them separated?

Pat

3

Hi Dr. Schloss,

Thanks for the quick reply! I actually didn’t start out with the make.contigs command. I used the extremely helpful SOPs on the mothur wiki as guidelines for how to process and analyze some of my own data samples, but I didn’t follow them step by step. I’ve actually figured out the problem was that I set the number of processors used to 4 in the preceding steps(before count.seqs). Once I set the number of processors to 1, the count.seqs() command was able to create an output file!

Thanks for your help and advice,

Michael