SOP tutorial crash

mothur bugs
1

Have been working through the SOP tutorial.

chimera.uchime crashes, however, as shown below.

Would be most grateful for your advice.

William

mothur > chimera.uchime(fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.fasta, name=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.names, group=GQY1XT001.shhh.good.groups, processors=8)


uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.

Checking sequences from GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.fasta …
sh: ./uchime: No such file or directory
sh: ./uchime: No such file or directory
sh: ./uchime: No such file or directory
sh: ./uchime: No such file or directory
sh: ./uchime: No such file or directory
sh: ./uchime: No such file or directory
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera75790.tempF003D142
sh: ./uchime: No such file or directory
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera75788.tempF003D006
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera75787.tempF003D004
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera75792.tempF003D146
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera75791.tempF003D144
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimeraF003D000
sh: ./uchime: No such file or directory
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera75789.tempF003D008
[ERROR]: Could not open GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera75786.tempF003D002

2

In version 1.22 we released the uchime executable with mothur’s executable. To be able to run the chimera.uchime command, the uchime executable must be in the same location as mothur’s executable.

3

Thanks. I have checked and both executables are in the same folder.

William

4

So the problem persists even though the executable is in the same location as mothur’s executable? Did you build the mothur executable from source or did you download it? Do you have the same problem if you use only 1 processor?

5

Yes, the problem persists although the executable is in the same location as mothur’s executable.

I downloaded the executable (1.22.0, Mac 64-bit).

Same problem if only one processor used.

Thank you for your help,

William

6

Hi,
I have the same issue. I think it is because the “call” for uchime in 1.22.1 uses
./uchime
rather than just
uchime
so it looks for it in the local folder in which mothur is called rather than in the path.
The temporary fix is to put a copy of uchime in the local folder. (I have verified this). This is, of course undesirable. I think it is a quick fix in the mothur software.

Thanks, Mothur!

7

Thanks for your help in finding the problem! It will be resolved in our next release.

8

Many thanks to both of you for your help.

William

9

Hi,

I am running Mothur 1.22.2 (compiled from source code) on a linux machine (Ubuntu 10.04 LTS).
Also with me this problem still persists.
Both the Mothur and Uchime executables are in the same directory. The output is in italics below. What would you suggest to avoid this, or should I rather use the chimera.slayer command? Also with one processor the same problem remains showing up.

_mothur > chimera.uchime(fasta=current,name=current,group=current,processors=4)

Using G09LI9X03.shhh.trim.unique.good.filter.unique.precluster.fasta as input file for the fasta parameter.
Using G09LI9X03.shhh.good.groups as input file for the group parameter.
Using G09LI9X03.shhh.trim.unique.good.filter.unique.precluster.names as input file for the name parameter.

uchime by Robert C. Edgar
http://drive5.com/uchime
This code is donated to the public domain.

Checking sequences from G09LI9X03.shhh.trim.unique.good.filter.unique.precluster.fasta …
sh: ./uchime: not found
[ERROR]: Could not open G09LI9X03.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera9679.tempMID-13.Bac530f
sh: ./uchime: not found
[ERROR]: Could not open G09LI9X03.shhh.trim.unique.good.filter.unique.precluster.uchime.chimeraMID-1.Bac530f
sh: ./uchime: not found
[ERROR]: Could not open G09LI9X03.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera9681.tempMID-6.Bac530f
sh: ./uchime: not found
[ERROR]: Could not open G09LI9X03.shhh.trim.unique.good.filter.unique.precluster.uchime.chimera9680.tempMID-3.Bac530f_

10

This issue will be fixed in version 1.23.0, but in the meantime I would recommend gaidos’ workaround.

11

Is there a timetable, when you plan to release next version? There are some very good improvements and I’m looking forward to it.

12

Unfortunately, it may not be until the New Year - sorry. We’re working on one last feature that we’d like to get in to this release.

13

I didn’t have any problem with Mothur version 1.22, but now I have the same problem with version 1.23. What might have caused this?

14

Could you post the error you are getting?

15

This is the error I get

Checking sequences from /home/noo.final.fasta …
[ERROR]: Could not open /home/noo.final.uchime.chimera0

16

Could you send your full logfile to mothur.bugs@gmail.com?