mothur

Unable to open design file

I do not know what is wrong with my design file. I made it with excel and saved it as tab delimited format. All the files are in the same directory.

Unable to open biofilm. Trying default C:\Mothur\biofilm.
Unable to open C:\Mothur\biofilm. Trying mothur’s executable location C:\Mothur\biofilm.
Unable to open C:\Mothur\biofilm. Trying mothur’s tools location biofilm.
Unable to open biofilm.
Unable to open biofilm
[ERROR]: did not complete amova.

Design file

I wonder if it isn’t actually named biofilm.txt rather than biofilm. It’s also possible it is biofilm, but it’s stored in a different directory. From the directory where you are running mothur, can you type dir and see if you can find this design file?

Pat

Thanks Pat. It is a *.txt file and it is in the same directory of mothur.exe. After the command it read but have the following error.

amova(phylip=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pds.wang.pick.tx.thetayc.1.lt.ave.dist, design=biofilm.txt)
[ERROR]: group 1HTCU1APR23 is not in your design file. Please correct.
[ERROR]: 1HTCU1APR23 is not in your design file, please correct.
[ERROR]: group 1HTCU1JUL16 is not in your design file. Please correct.
[ERROR]: 1HTCU1JUL16 is not in your design file, please correct.
[ERROR]: group 1HTCU1JUN13 is not in your design file. Please correct.
[ERROR]: 1HTCU1JUN13 is not in your design file, please correct.
[ERROR]: group 1HTCU1MAR29 is not in your design file. Please correct.
[ERROR]: 1HTCU1MAR29 is not in your design file, please correct.
[ERROR]: group 1HTCU1MAY15 is not in your design file. Please correct.
[ERROR]: 1HTCU1MAY15 is not in your design file, please correct.
[ERROR]: group 1HTCU2APR23 is not in your design file. Please correct.
[ERROR]: 1HTCU2APR23 is not in your design file, please correct.
[ERROR]: group 1HTCU2JUL16 is not in your design file. Please correct.
[ERROR]: 1HTCU2JUL16 is not in your design file, please correct.
[ERROR]: group 1HTCU2JUN13 is not in your design file. Please correct.
[ERROR]: 1HTCU2JUN13 is not in your design file, please correct.
[ERROR]: group 1HTCU2MAR29 is not in your design file. Please correct.
[ERROR]: 1HTCU2MAR29 is not in your design file, please correct.
[ERROR]: group 1HTCU2MAY15 is not in your design file. Please correct.
[ERROR]: 1HTCU2MAY15 is not in your design file, please correct.
[ERROR]: group 1HTCUMAR29H1 is not in your design file. Please correct.
[ERROR]: 1HTCUMAR29H1 is not in your design file, please correct.
[ERROR]: group 1HTCUMAR29H2 is not in your design file. Please correct.
[ERROR]: 1HTCUMAR29H2 is not in your design file, please correct.
[ERROR]: group 1HTPVC1APR23 is not in your design file. Please correct.
[ERROR]: 1HTPVC1APR23 is not in your design file, please correct.
[ERROR]: group 1HTPVC1JUL16 is not in your design file. Please correct.
[ERROR]: 1HTPVC1JUL16 is not in your design file, please correct.
[ERROR]: group 1HTPVC1JUN13 is not in your design file. Please correct.
[ERROR]: 1HTPVC1JUN13 is not in your design file, please correct.
[ERROR]: group 1HTPVC1MAR29 is not in your design file. Please correct.
[ERROR]: 1HTPVC1MAR29 is not in your design file, please correct.
[ERROR]: group 1HTPVC1MAY15 is not in your design file. Please correct.
[ERROR]: 1HTPVC1MAY15 is not in your design file, please correct.
[ERROR]: group 1HTPVC2APR23 is not in your design file. Please correct.
[ERROR]: 1HTPVC2APR23 is not in your design file, please correct.
[ERROR]: group 1HTPVC2JUL16 is not in your design file. Please correct.
[ERROR]: 1HTPVC2JUL16 is not in your design file, please correct.
[ERROR]: group 1HTPVC2JUN13 is not in your design file. Please correct.
[ERROR]: 1HTPVC2JUN13 is not in your design file, please correct.
[ERROR]: group 1HTPVC2MAR29 is not in your design file. Please correct.
[ERROR]: 1HTPVC2MAR29 is not in your design file, please correct.
[ERROR]: group 1HTPVC2MAY15 is not in your design file. Please correct.
[ERROR]: 1HTPVC2MAY15 is not in your design file, please correct.
[ERROR]: group 1HTPVCMAR29H1 is not in your design file. Please correct.
[ERROR]: 1HTPVCMAR29H1 is not in your design file, please correct.
[ERROR]: group 1HTPVCMAR29H2 is not in your design file. Please correct.
[ERROR]: 1HTPVCMAR29H2 is not in your design file, please correct.
[ERROR]: group 1RTCU1APR23 is not in your design file. Please correct.
[ERROR]: 1RTCU1APR23 is not in your design file, please correct.
[ERROR]: group 1RTCU1JUL16 is not in your design file. Please correct.
[ERROR]: 1RTCU1JUL16 is not in your design file, please correct.
[ERROR]: group 1RTCU1JUN13 is not in your design file. Please correct.
[ERROR]: 1RTCU1JUN13 is not in your design file, please correct.
[ERROR]: group 1RTCU1MAR29 is not in your design file. Please correct.
[ERROR]: 1RTCU1MAR29 is not in your design file, please correct.
[ERROR]: group 1RTCU1MAY15 is not in your design file. Please correct.
[ERROR]: 1RTCU1MAY15 is not in your design file, please correct.
[ERROR]: group 1RTCU2APR23 is not in your design file. Please correct.
[ERROR]: 1RTCU2APR23 is not in your design file, please correct.
[ERROR]: group 1RTCU2JUL16 is not in your design file. Please correct.
[ERROR]: 1RTCU2JUL16 is not in your design file, please correct.
[ERROR]: group 1RTCU2JUN13 is not in your design file. Please correct.
[ERROR]: 1RTCU2JUN13 is not in your design file, please correct.
[ERROR]: group 1RTCU2MAR29 is not in your design file. Please correct.
[ERROR]: 1RTCU2MAR29 is not in your design file, please correct.
[ERROR]: group 1RTCU2MAY15 is not in your design file. Please correct.
[ERROR]: 1RTCU2MAY15 is not in your design file, please correct.
[ERROR]: group 1RTCUMAR29H1 is not in your design file. Please correct.
[ERROR]: 1RTCUMAR29H1 is not in your design file, please correct.
[ERROR]: group 1RTCUMAR29H2 is not in your design file. Please correct.
[ERROR]: 1RTCUMAR29H2 is not in your design file, please correct.
[ERROR]: group 1RTPVC1APR23 is not in your design file. Please correct.
[ERROR]: 1RTPVC1APR23 is not in your design file, please correct.
[ERROR]: group 1RTPVC1JUL16 is not in your design file. Please correct.
[ERROR]: 1RTPVC1JUL16 is not in your design file, please correct.
[ERROR]: group 1RTPVC1JUN13 is not in your design file. Please correct.
[ERROR]: 1RTPVC1JUN13 is not in your design file, please correct.
[ERROR]: group 1RTPVC1MAR29 is not in your design file. Please correct.
[ERROR]: 1RTPVC1MAR29 is not in your design file, please correct.
[ERROR]: group 1RTPVC1MAY15 is not in your design file. Please correct.
[ERROR]: 1RTPVC1MAY15 is not in your design file, please correct.
[ERROR]: group 1RTPVC2APR23 is not in your design file. Please correct.
[ERROR]: 1RTPVC2APR23 is not in your design file, please correct.
[ERROR]: group 1RTPVC2JUL16 is not in your design file. Please correct.
[ERROR]: 1RTPVC2JUL16 is not in your design file, please correct.
[ERROR]: group 1RTPVC2JUN13 is not in your design file. Please correct.
[ERROR]: 1RTPVC2JUN13 is not in your design file, please correct.
[ERROR]: group 1RTPVC2MAR29 is not in your design file. Please correct.
[ERROR]: 1RTPVC2MAR29 is not in your design file, please correct.
[ERROR]: group 1RTPVC2MAY15 is not in your design file. Please correct.
[ERROR]: 1RTPVC2MAY15 is not in your design file, please correct.
[ERROR]: group 1RTPVCMAR29H1 is not in your design file. Please correct.
[ERROR]: 1RTPVCMAR29H1 is not in your design file, please correct.
[ERROR]: group 1RTPVCMAR29H2 is not in your design file. Please correct.
[ERROR]: 1RTPVCMAR29H2 is not in your design file, please correct.
[ERROR]: group 2HTCU1APR23 is not in your design file. Please correct.
[ERROR]: 2HTCU1APR23 is not in your design file, please correct.
[ERROR]: group 2HTCU1JUL16 is not in your design file. Please correct.
[ERROR]: 2HTCU1JUL16 is not in your design file, please correct.
[ERROR]: group 2HTCU1JUN13 is not in your design file. Please correct.
[ERROR]: 2HTCU1JUN13 is not in your design file, please correct.
[ERROR]: group 2HTCU1MAR29 is not in your design file. Please correct.
[ERROR]: 2HTCU1MAR29 is not in your design file, please correct.
[ERROR]: group 2HTCU1MAY15 is not in your design file. Please correct.
[ERROR]: 2HTCU1MAY15 is not in your design file, please correct.
[ERROR]: group 2HTCU2APR23 is not in your design file. Please correct.
[ERROR]: 2HTCU2APR23 is not in your design file, please correct.
[ERROR]: group 2HTCU2JUL16 is not in your design file. Please correct.
[ERROR]: 2HTCU2JUL16 is not in your design file, please correct.
[ERROR]: group 2HTCU2JUN13 is not in your design file. Please correct.
[ERROR]: 2HTCU2JUN13 is not in your design file, please correct.
[ERROR]: group 2HTCU2MAR29 is not in your design file. Please correct.
[ERROR]: 2HTCU2MAR29 is not in your design file, please correct.
[ERROR]: group 2HTCU2MAY15 is not in your design file. Please correct.
[ERROR]: 2HTCU2MAY15 is not in your design file, please correct.
[ERROR]: group 2HTCUMAR29H1 is not in your design file. Please correct.
[ERROR]: 2HTCUMAR29H1 is not in your design file, please correct.
[ERROR]: group 2HTCUMAR29H2 is not in your design file. Please correct.
[ERROR]: 2HTCUMAR29H2 is not in your design file, please correct.
[ERROR]: group 2HTPVC1APR23 is not in your design file. Please correct.
[ERROR]: 2HTPVC1APR23 is not in your design file, please correct.
[ERROR]: group 2HTPVC1JUL16 is not in your design file. Please correct.
[ERROR]: 2HTPVC1JUL16 is not in your design file, please correct.
[ERROR]: group 2HTPVC1JUN13 is not in your design file. Please correct.
[ERROR]: 2HTPVC1JUN13 is not in your design file, please correct.
[ERROR]: group 2HTPVC1MAR29 is not in your design file. Please correct.
[ERROR]: 2HTPVC1MAR29 is not in your design file, please correct.
[ERROR]: group 2HTPVC1MAY15 is not in your design file. Please correct.
[ERROR]: 2HTPVC1MAY15 is not in your design file, please correct.
[ERROR]: group 2HTPVC2APR23 is not in your design file. Please correct.
[ERROR]: 2HTPVC2APR23 is not in your design file, please correct.
[ERROR]: group 2HTPVC2JUL16 is not in your design file. Please correct.
[ERROR]: 2HTPVC2JUL16 is not in your design file, please correct.
[ERROR]: group 2HTPVC2JUN13 is not in your design file. Please correct.
[ERROR]: 2HTPVC2JUN13 is not in your design file, please correct.
[ERROR]: group 2HTPVC2MAR29 is not in your design file. Please correct.
[ERROR]: 2HTPVC2MAR29 is not in your design file, please correct.
[ERROR]: group 2HTPVC2MAY15 is not in your design file. Please correct.
[ERROR]: 2HTPVC2MAY15 is not in your design file, please correct.
[ERROR]: group 2HTPVCMAR29H1 is not in your design file. Please correct.
[ERROR]: 2HTPVCMAR29H1 is not in your design file, please correct.
[ERROR]: group 2HTPVCMAR29H2 is not in your design file. Please correct.
[ERROR]: 2HTPVCMAR29H2 is not in your design file, please correct.
[ERROR]: group 2RTCU1APR23 is not in your design file. Please correct.
[ERROR]: 2RTCU1APR23 is not in your design file, please correct.
[ERROR]: group 2RTCU1JUL16 is not in your design file. Please correct.
[ERROR]: 2RTCU1JUL16 is not in your design file, please correct.
[ERROR]: group 2RTCU1JUN13 is not in your design file. Please correct.
[ERROR]: 2RTCU1JUN13 is not in your design file, please correct.
[ERROR]: group 2RTCU1MAR29 is not in your design file. Please correct.
[ERROR]: 2RTCU1MAR29 is not in your design file, please correct.
[ERROR]: group 2RTCU1MAY15 is not in your design file. Please correct.
[ERROR]: 2RTCU1MAY15 is not in your design file, please correct.
[ERROR]: group 2RTCU2APR23 is not in your design file. Please correct.
[ERROR]: 2RTCU2APR23 is not in your design file, please correct.
[ERROR]: group 2RTCU2JUL16 is not in your design file. Please correct.
[ERROR]: 2RTCU2JUL16 is not in your design file, please correct.
[ERROR]: group 2RTCU2JUN13 is not in your design file. Please correct.
[ERROR]: 2RTCU2JUN13 is not in your design file, please correct.
[ERROR]: group 2RTCU2MAR29 is not in your design file. Please correct.
[ERROR]: 2RTCU2MAR29 is not in your design file, please correct.
[ERROR]: group 2RTCU2MAY15 is not in your design file. Please correct.
[ERROR]: 2RTCU2MAY15 is not in your design file, please correct.
[ERROR]: group 2RTCUMAR29H1 is not in your design file. Please correct.
[ERROR]: 2RTCUMAR29H1 is not in your design file, please correct.
[ERROR]: group 2RTCUMAR29H2 is not in your design file. Please correct.
[ERROR]: 2RTCUMAR29H2 is not in your design file, please correct.
[ERROR]: group 2RTPVC1APR23 is not in your design file. Please correct.
[ERROR]: 2RTPVC1APR23 is not in your design file, please correct.
[ERROR]: group 2RTPVC1JUL16 is not in your design file. Please correct.
[ERROR]: 2RTPVC1JUL16 is not in your design file, please correct.
[ERROR]: group 2RTPVC1JUN13 is not in your design file. Please correct.
[ERROR]: 2RTPVC1JUN13 is not in your design file, please correct.
[ERROR]: group 2RTPVC1MAR29 is not in your design file. Please correct.
[ERROR]: 2RTPVC1MAR29 is not in your design file, please correct.
[ERROR]: group 2RTPVC1MAY15 is not in your design file. Please correct.
[ERROR]: 2RTPVC1MAY15 is not in your design file, please correct.
[ERROR]: group 2RTPVC2APR23 is not in your design file. Please correct.
[ERROR]: 2RTPVC2APR23 is not in your design file, please correct.
[ERROR]: group 2RTPVC2JUL16 is not in your design file. Please correct.
[ERROR]: 2RTPVC2JUL16 is not in your design file, please correct.
[ERROR]: group 2RTPVC2JUN13 is not in your design file. Please correct.
[ERROR]: 2RTPVC2JUN13 is not in your design file, please correct.
[ERROR]: group 2RTPVC2MAR29 is not in your design file. Please correct.
[ERROR]: 2RTPVC2MAR29 is not in your design file, please correct.
[ERROR]: group 2RTPVC2MAY15 is not in your design file. Please correct.
[ERROR]: 2RTPVC2MAY15 is not in your design file, please correct.
[ERROR]: group 2RTPVCMAR29H1 is not in your design file. Please correct.
[ERROR]: 2RTPVCMAR29H1 is not in your design file, please correct.
[ERROR]: group 2RTPVCMAR29H2 is not in your design file. Please correct.
[ERROR]: 2RTPVCMAR29H2 is not in your design file, please correct.
[ERROR]: group CNTLFC2Y1 is not in your design file. Please correct.
[ERROR]: CNTLFC2Y1 is not in your design file, please correct.
[ERROR]: group CNTLFC2Y2 is not in your design file. Please correct.
[ERROR]: CNTLFC2Y2 is not in your design file, please correct.
[ERROR]: group DW1JUN12 is not in your design file. Please correct.
[ERROR]: DW1JUN12 is not in your design file, please correct.
[ERROR]: group DW2JUN12 is not in your design file. Please correct.
[ERROR]: DW2JUN12 is not in your design file, please correct.
[ERROR]: group DW3SEP12 is not in your design file. Please correct.
[ERROR]: DW3SEP12 is not in your design file, please correct.
[ERROR]: group LP1B1 is not in your design file. Please correct.
[ERROR]: LP1B1 is not in your design file, please correct.
[ERROR]: group LP1B2 is not in your design file. Please correct.
[ERROR]: LP1B2 is not in your design file, please correct.
[ERROR]: group LP1T1 is not in your design file. Please correct.
[ERROR]: LP1T1 is not in your design file, please correct.
[ERROR]: group LP1T2 is not in your design file. Please correct.
[ERROR]: LP1T2 is not in your design file, please correct.
[ERROR]: group LP2B1 is not in your design file. Please correct.
[ERROR]: LP2B1 is not in your design file, please correct.
[ERROR]: group LP2B2 is not in your design file. Please correct.
[ERROR]: LP2B2 is not in your design file, please correct.
[ERROR]: group LP2T1 is not in your design file. Please correct.
[ERROR]: LP2T1 is not in your design file, please correct.
[ERROR]: group LP2T2 is not in your design file. Please correct.
[ERROR]: LP2T2 is not in your design file, please correct.
[ERROR]: group LP3B1 is not in your design file. Please correct.
[ERROR]: LP3B1 is not in your design file, please correct.
[ERROR]: group LP3B2 is not in your design file. Please correct.
[ERROR]: LP3B2 is not in your design file, please correct.
[ERROR]: group LP3T1 is not in your design file. Please correct.
[ERROR]: LP3T1 is not in your design file, please correct.
[ERROR]: group LP3T2 is not in your design file. Please correct.
[ERROR]: LP3T2 is not in your design file, please correct.
[ERROR]: group NLP4B1 is not in your design file. Please correct.
[ERROR]: NLP4B1 is not in your design file, please correct.
[ERROR]: group NLP4B2 is not in your design file. Please correct.
[ERROR]: NLP4B2 is not in your design file, please correct.
[ERROR]: group NLP4T1 is not in your design file. Please correct.
[ERROR]: NLP4T1 is not in your design file, please correct.
[ERROR]: group NLP4T2 is not in your design file. Please correct.
[ERROR]: NLP4T2 is not in your design file, please correct.
[ERROR]: group NLP5B1 is not in your design file. Please correct.
[ERROR]: NLP5B1 is not in your design file, please correct.
[ERROR]: group NLP5B2 is not in your design file. Please correct.
[ERROR]: NLP5B2 is not in your design file, please correct.
[ERROR]: group NLP5T1 is not in your design file. Please correct.
[ERROR]: NLP5T1 is not in your design file, please correct.
[ERROR]: group NLP5T2 is not in your design file. Please correct.
[ERROR]: NLP5T2 is not in your design file, please correct.
[ERROR]: group NLP6B1 is not in your design file. Please correct.
[ERROR]: NLP6B1 is not in your design file, please correct.
[ERROR]: group NLP6B2 is not in your design file. Please correct.
[ERROR]: NLP6B2 is not in your design file, please correct.
[ERROR]: group NLP6T1 is not in your design file. Please correct.
[ERROR]: NLP6T1 is not in your design file, please correct.
[ERROR]: group NLP6T2 is not in your design file. Please correct.
[ERROR]: NLP6T2 is not in your design file, please correct.
[ERROR]: group WMLPFC2Y1 is not in your design file. Please correct.
[ERROR]: WMLPFC2Y1 is not in your design file, please correct.
[ERROR]: group WMLPFC2Y2 is not in your design file. Please correct.
[ERROR]: WMLPFC2Y2 is not in your design file, please correct.
[ERROR]: group WMLPFC2Y3 is not in your design file. Please correct.
[ERROR]: WMLPFC2Y3 is not in your design file, please correct.
[ERROR]: group WMLPFC2Y4 is not in your design file. Please correct.
[ERROR]: WMLPFC2Y4 is not in your design file, please correct.

Can you post the contents of your design file?

Here is the *.txt file (created with excel and saved as a tab delimited format).
The file contains my sample names in “group” column and treatment in “material” column.

(Attachment Biofilm.txt is missing)

I copied the biofilm.txt file in the mail but it did not appear in the forum post. The file looks as the screenshot that I posted in my opening post.

Hi,

The attachment doesn’t seem to be posted to the forum. Can you try to post it directly to the forum? Alternatively, can you email it to mothur.bugs@gmail.com and provide a link to this thread with your question?

Thanks,
Pat

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.