mothur GUIs Windows 32 bit and Linux (Ubuntu 12.10) 64 bit

mothur bugs
1

I have an additional difficulty, I have both the 32 bit Windows GUI and the 64 bit Linux GUI installed. Both work fine until I try using chimera.uchime to detect chimeras. I have tried both checking “self” as the refset and using the silva.gold refence suggested in the Manual/Analysis Examples. In both instances, the program launches but then stops working. Basically it does not finish the job.

The Windows system: Windows 8, 64 bit, running the 32-bit mothurWinGUI, 6 Gb RAM
The Linux system: Ubuntu 12.10, 64 bit, running the 64-bit mothurGUI, 8 Gb RAM

here is the last entry in the logfile:

mothur > chimera.uchime(fasta=Beckerpr.unique.good.filter.unique.precluster.fasta, reference=/home/ansilab/Programs/mothurGUI/mothur/ref/silva.gold.ng.fasta, chimealns=T, dereplicate=T, processors=2)

Using 2 processors.

uchime by Robert C. Edgar
UCLUST downloads
This code is donated to the public domain.

Checking sequences from Beckerpr.unique.good.filter.unique.precluster.fasta …

And here is the last entry on the Output Screen:

Current working directory: /home/ansilab/Programs/mothurGUI/
[H[2J
mothur > chimera.uchime(fasta=Beckerpr.unique.good.filter.unique.precluster.fasta, reference=/home/ansilab/Programs/mothurGUI/mothur/ref/silva.gold.ng.fasta, chimealns=T, dereplicate=T, processors=2)

Using 2 processors.

uchime by Robert C. Edgar
UCLUST downloads
This code is donated to the public domain.

Checking sequences from Beckerpr.unique.good.filter.unique.precluster.fasta …
uchime v4.2.40
by Robert C. Edgar
UCLUST downloads
This code is donated to the public domain.

uchime v4.2.40
by Robert C. Edgar
UCLUST downloads
This code is donated to the public domain.

After that it just stops without providing any output.

In addition, for the Linux 64-bit mothurGUI, everytime it tries to find/write the current files to the screen/logfile it gives the following error(s) on screen. Not sure which refers to what:

Exited with error code 0
Exited with error code -1

and this is what is present in the output window:

Current working directory: /home/ansilab/Programs/mothurGUI/
[H[2J
mothur > chimera.uchime(fasta=Beckerpr.unique.good.filter.unique.precluster.fasta, reference=/home/ansilab/Programs/mothurGUI/mothur/ref/silva.gold.ng.fasta, chimealns=T, dereplicate=T, processors=2)

2

Are you able to run the command with our command line version? I am able to run the command with the GUI and test files? I am wondering if perhaps it is an issue with the fasta file?

3

I am able to run the command line version fine.

All the steps prior to that are fine, so if you are referring to the initial fasta file that I provide, that does not appear to be the issue - as far as I can determine.

The program outputs files but never completes the process. End up with temp files and the output files in the folder. It hangs up there and does not continue the pipeline as it should.

The files present after the process are (this is from the Linux computer):

Beckerpr.unique.good.filter.unique.precluster.uchime.alns19644.temp
Beckerpr.unique.good.filter.unique.precluster.uchime.alns
Beckerpr.unique.good.filter.unique.precluster.uchime.chimeras
Beckerpr.unique.good.filter.unique.precluster.uchime.chimeras19644.temp
Beckerpr.unique.good.filter.unique.precluster.fasta.1.tmp.uchime_formatted
Beckerpr.unique.good.filter.unique.precluster.fasta.0.tmp.uchime_formatted
Beckerpr.unique.good.filter.unique.precluster.fasta.1.tmp


Form the logfile this is all that I have - indirectly indicating that the process has not finished.

mothur > chimera.uchime(fasta=Beckerpr.unique.good.filter.unique.precluster.fasta, reference=/home/ansilab/Programs/mothurGUI/mothur/ref/silva.gold.ng.fasta, chimealns=T, dereplicate=T, processors=2)

Using 2 processors.

uchime by Robert C. Edgar
UCLUST downloads
This code is donated to the public domain.

Checking sequences from Beckerpr.unique.good.filter.unique.precluster.fasta …

It is supposed to continue beyond that point. I will try another of the chimera detection programs to see if the same thing occurs.

4

How long does it go on? The GUI does not output uchime’s screen outputs. It will just output when complete, so if this is a file that takes a while, it may appear to be dying when in fact it is just processing.

5

I left it to run over the weekend (separate weekends) in both instances. So, three to four days. In looking at the system activity, there is nothing going on with the program. It is not running after that point - no RAM or CPU time - is being utilized.

6

As I indicated before, it is supposed to go on to the next step - but doesn’t. It just stops with that last entry. So, the next process should be to find the current directory, and find the current files (as it does each step) but it never continues to that point.

The data set I am using only consists of 74,000 initial sequences - boiled down to 51,000 unique sequences. Everything else up to that point works fine (trim, summary, unique, align, screen, filter).

7

Just to make sure: The next step after the uhime.chimera section is the “remove sequences” step. This requires an accnos file, and I don’t see one being created by uchime.chimera in the file folder. Could this be the problem?

8

Sorry, but I am under a tight deadline to get this up and working, so I was wondering if you had any response to my replies regarding whther the program is working or not, or what I can do to fix this issue?

I tried running chimera.checker over the same dataset using the same pipeline, and the same thing happened.

I was using the Linux (Ubuntu 12.10) OS, with 8 Gb of RAM. The dataset consisted of 71,000 initial sequences, which had been reduced to 51,000 unique sequences. It ran from Friday afternoon until Monday morning, and did not finish but appeared to abort. No CPU or RAM was being utilized by the program, and the files were not completely written to the file.

I am wondering if I am including something wrong?

All steps prior to the chimera checking step work fine.

9

James,

I’m not sure what’s going on but if the command line is working, why not work with that. Also, I’m a bit worried about the number of unique reads you have and that it doesn’t look like you’ve used shhh.flows on your data and that you’re using the reference-based implementation of chimera.uchime. Have you tried just following the 454 SOP?

Pat