Problems with version 4.9.0 about pr2database

[vaulot]

Dear René

I localized the first three errors and fixed them. in the latest release 4.9.1.

Concerning the last error, this is due to the fact the text files are in UNIX format so there is just a LF character at the end of each line. What you should do use Notepad++ or similar to convert the end of lines characters for both fasta and . I have explained this in the wiki, here (see at the end):

Please let me know if this works for you now.

Cheers. Daniel

[rgroben]

Dear Daniel,

thank you for the quick response and your help! There were however a few more errors that popped up when I tried to use v. 4.9.1. I fixed them in my version of the files but want to mention them here as well so that they can be "officially" corrected (see below). Also, after some problems in the beginning, I realized that the format in which to save the files in Notepad++ is very important. mothur is very sensitive regarding correct text file types. Saving it as a *.txt file (the default setting in Notepad++) adds specific formatting information to the file which will stop mothur from properly recognizing it as e.g. a *.tax file anymore.

But in the end everything worked well and I could classify my sequences with the latest version of PR2.

Errors in file “pr2_version_4.9.1_mothur.fasta”
KJ995958.1.1684_U contains a space between > and KJ995958.1.1684_U; delete space

Errors in file “pr2_version_4.9.1_mothur.tax”
LC002840.1.1722_U contains a hard break in its taxonomic classification; delete hard space
KJ995958.1.1684_U contains a space before KJ995958.1.1684_U; delete space

The Wiki explanation for “Converting files from UNIX to Windows format” should to be amended with this following instruction at “4. Save the files”:
Save files using “Save as” and change “Save as type” from “Normal text file (.txt)” to “All types (.*)”.

Best wishes and thanks to everyone involved in the creation of PR2 for your great work,

René

[vaulot]

Dear René

Thanks very much for your feed back. This is very important for PR2 so that we can have a really clean database.
For Notepad++ I just open the file and save it without modifying anything. I think saving as txt does not change anything in the file itself but it add the "txt" extension which then you have to add in the mothur command. But I will add this in the wiki.
I have fixed the two remaining errors and just done a new release 4.9.2.