[juassis]

unhh, ok!
I'll try the running virtual box!

thanks

[rhall]

I work for PacBio, but not in tech support. If the installation is tied to a machine then go through your FAS for SMRT Analysis install support.

SMRT Analysis is not supported on Red Hat 6.4. You do not have to work on another machine, running virtual box on the Red Hat system will allow you to install a virtual Ubuntu 10.04 system for running SMRT Analysis.
For a discussion of the options, including using amazon AMI see:
http://seqanswers.com/forums/showthr...6421#post96421

[juassis]

rhall,
do you work for pacbio? It has a support contact?

It's impossible work in another machine

Many thanks for your help. =)

[rhall]

Unfortunately this is due to the system - build system mismatch, and SMRT Analysis cannot be easily rebuilt. My only suggestion would be to run a virtual machine using something like virtual box installing a Ubuntu 10.04 system then installing SMRT Analysis on top of that.

[juassis]

wasn´t generated log, I can't even run the smrtpipe.py --help.
sometimes the pipeline functioned.

distribution:

Red Hat Enterprise Linux Server release 6.4 (Santiago).

thanks =)

[rhall]

Also try running with the --debug option

[rhall]

Do you get any output at all? Anything in the ./log/ directory?

What distribution are you running on, this could possibly be a result of a mismatch between the system it is running on and the build system, either Ubuntu 10.04, or Centos 5.6.

[juassis]

Hello,
thank you very much for your help and comments. It was possible to correct several samples
Again some problems. I was able to run the smrtpipe.py command without any errors. However when I tried to run again the SMRTpipe the error message appears:

. /opt/smrtanalysis/etc/setup.sh
$ smrtpipe.py --params=gir_params.xml xml:gir_input.xml

Bus error (core dumped)

--
I did the memory test, and everything is ok.

ulimit -a
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
scheduling priority (-e) 0
file size (blocks, -f) unlimited
pending signals (-i) 4133745
max locked memory (kbytes, -l) 64
max memory size (kbytes, -m) unlimited
open files (-n) 1024
pipe size (512 bytes, -p) 8
POSIX message queues (bytes, -q) 819200
real-time priority (-r) 0
stack size (kbytes, -s) 10240
cpu time (seconds, -t) unlimited
max user processes (-u) 1024
virtual memory (kbytes, -v) unlimited
file locks (-x) unlimited


Filesystem Size Used Avail Use% Mounted on
/dev/sdg 12T 900G 11T 9% /


Many thanks for your help. =)

[rhall]

If the lines are added to the $SEYMOUR_HOME/etc/setup.sh file then SMRT pipe should function correctly after the setup.sh file is sourced.

[juassis]

Hello!
Thanks for the information!
Worked properly! =)

Just one more question,
worked properly in the first analysis, however, when presented new data from another bred came up again this error. I'll have to fix every time I want to examine?

[rhall]

Sorry, second line is:

export LC_ALL=en_US.UTF-8

[rhall]

juassis,
Unfortunately it is a bug due to system location, for a fix, add the following two lines to $SEYMOUR_HOME/etc/setup.sh:

export LANG=en_US.UTF-8
export LANG=en_US.UTF-8

Which sets some environment variables used by python. PacBio is aware of the bug and it should be fixed in the next release.

[juassis]

Hello

I don't understand the error message generated (DeNovo assembly using pacBio data)
with the sample data (e.coli and lambda) is ok.

Then run the command 'smrtpipe.py --params=settings.xml xml:input.xml &>smrtpipe.err' and got an error log message as below:

INFO] 2013-02-20 15:57:08,552 [pbpy.smrtpipe.SmrtDataService writeTo 424] Writing 6 items to DataStore in {'smrt.data.xmlparam': <pbpy.io.MetaAnalysisXml.InputDataUrl object at 0x4295a50>, 'smrt.output.log': '/sto4data-2/zebu4/data/06022013_smrtpipe/teste1_gir/log', 'smrt.data.cmdline': <pbpy.smrtpipe.InputData.CompositeInputData object at 0x42959d0>, 'smrt.output.root': '/sto4data-2/zebu4/data/06022013_smrtpipe/teste1_gir', 'smrt.output.results': '/sto4data-2/zebu4/data/06022013_smrtpipe/teste1_gir/results', 'smrt.output.data': '/sto4data-2/zebu4/data/06022013_smrtpipe/teste1_gir/data'}
[INFO] 2013-02-20 15:57:08,555 [pbpy.smrtpipe.SmrtPipeMain _runTasks 267] Skipping PreWorkflow as it contains zero tasks
[INFO] 2013-02-20 15:57:08,558 [pbpy.smrtpipe.SmrtPipeMain _runTasks 270] Loading 10 tasks into Workflow
[INFO] 2013-02-20 15:57:09,275 [pbpy.smrtpipe.SmrtPipeMain _runTasks 279] Executing workflow Workflow
[INFO] 2013-02-20 15:57:09,649 [pbpy.smrtpipe.engine.SmrtPipeTasks run 622] Running task://Anonymous/P_Fetch/toFofn
[ERROR] 2013-02-20 15:57:14,702 [pbpy.smrtpipe.SmrtPipeMain run 648] time data 'Qua Fev 20 15:57:09 CST 2013' does not match format '%a %b %d %H:%M:%S %Z %Y' Traceback (most recent call last):
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/SmrtPipeMain.py", line 608, in run self._runTasks(pModules)
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/SmrtPipeMain.py", line 281, in _runTasks workflow.execute()
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtPipeWorkflow.py", line 607, in execute self._update(0)
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtPipeWorkflow.py", line 574, in _update self._writeWorkflow()
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtPipeWorkflow.py", line 554, in _writeWorkflow self._graph.toFile(path, format)
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtDAG.py", line 258, in toFile out.write(format2func[format](self))
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtDAG.py", line 255, in <lambda> 'RDF': lambda g: g.toRDF().serialize(),
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtDAG.py", line 208, in toRDF for s, p, o in node.toRDF():
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtDAG.py", line 81, in toRDF Literal(str(self.obj.computeTime))))
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtPipeTasks.py", line 834, in computeTime self._extractComputeTime(regexp)
File "/opt/smrtanalysis-1.4.0/analysis/lib/python2.7/pbpy-0.1-py2.7.egg/pbpy/smrtpipe/engine/SmrtPipeTasks.py", line 821, in _extractComputeTime self._cachedExecTimes[regexp] = datetime.datetime.strptime(match.group(1), LOG_TIME_FORMAT)
File "/opt/smrtanalysis-1.4.0/redist/python2.7/lib/python2.7/_strptime.py", line 325, in _strptime (data_string, format))
ValueError: time data 'Qua Fev 20 15:57:09 CST 2013' does not match format '%a %b %d %H:%M:%S %Z %Y'
[ERROR] 2013-02-20 15:57:14,704 [pbpy.smrtpipe.SmrtPipeMain exit 760] time data 'Qua Fev 20 15:57:09 CST 2013' does not match format '%a %b %d %H:%M:%S %Z %Y'


I need help =)

[sagarutturkar]

I think SMRTanalysis comes bundled with its own python. The error above seems to be referring to a system python2.6 directory though, so are you using the system python?

For clarity you should have started a new thread instead of posting under this one.

Hi,

Thanks for the quick reply. I have created new thread here:

http://seqanswers.com/forums/showthread.php?p=96421#post96421

and updated query with more details. Please reply.

Thanks

[GenoMax]

I think SMRTanalysis comes bundled with its own python. The error above seems to be referring to a system python2.6 directory though, so are you using the system python?

For clarity you should have started a new thread instead of posting under this one.