make.shared error

Commands in mothur
1

Dear All
I have just started using mothur and enjoyed it so far.
The analysis example are of great help.
With my data, i am haveing the following issues:

  1. Tried to run the make.share command,

make.shared(list=002.an.list, group=002.groups, label=0.03)
but it gives me the error : [ERROR]: Could not open 002.an.27F/534R_001.rabund
for all individual samples, but creates output files: 002.an.27F/534R_001.rabund for all individual samples whihc i dont see in my directory. there is the common 002.an.shared file too.

  1. when i try this : > collect.single(shared=002.an.shared, calc=chao-invsimpson, freq=5)
    gives me an error
    [ERROR]: Could not open 002.an.27F/534R_001.rabund

i compared all my file with the example file and they are ok.

Please let me know if i am missing something here. my dist.seqs and cluster commands did not had any issues.

thanks

K

2

Do your group names contain ‘/’ characters? If so, that will cause problems for the OS.

3

You were so right! that was the issue. i have individual files now.
thanks a ton.

K

4

I am facing another issue with “make.shared” command (Mothur version 1.32.1 Mac)

when I run this command : make.shared(list=EX.list, group=EX.groups, label=0.03), in the terminal i can see there are several “rabund” files (160 of them) and one “shared” output file. BUT these files are not present in mothur folder…. There is also an error message as “the number of sequences in list file and group file are conflicting”

a snap shot of the log file is shown below:

mothur > make.shared(list=EX.list, group=EX.groups, label=0.03)
[ERROR]: 1DM1M_00004_00027 is in your groupfile and not your listfile. Please correct.
[ERROR]: 1DM1M_00004_00029 is in your groupfile and not your listfile. Please correct.
[ERROR]: 1DM1M_00004_00075 is in your groupfile and not your listfile. Please correct.
[ERROR]: 1DM1M_00004_00080 is in your groupfile and not your listfile. Please correct.
……
Your group file contains 523197 sequences and list file contains 358935 sequences. Please correct.

Output File Names:
EX.an.shared
EX.an.01.rabund
EX.an.02.rabund
…….

Is there any way to solve this issue.

Thanks for your valuable support

5

You could run:

list.seqs(list=yourListFile) - list sequences in your list file
get.seqs(group=yourGroupFile, accnos=current) - select sequences in list file from your group file

6

Dear Westcott,

Thanks for your valuable support. It solved the problem.