Unable to open design file

Commands in mothur
1

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

Screenshot (2)
Screenshot (2)3200×1800 272 KB

2

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

3

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.
4

Can you post the contents of your design file?

5

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)

6

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.

7

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

8

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