Hey Nikos, I have been meaning to test tophat with the LWR but I haven't been able to get to it and I doubt I will before the Galaxy conference. The one more piece of advice I have (in addition to trying this out with galaxy-central) is that in the staging directory there are going to be some files with odd names (tmpXXXX) or something like that, these files should contain the standard error and standard output of the tophat run so they will hopefully provide some insight into what is going wrong.
-John On Fri, Jun 21, 2013 at 8:21 AM, Nikos Sidiropoulos <nikos.sid...@gmail.com> wrote: > Hi John > > Thank you for the reply. > > In the lwr_staging directory all the runs from tophat are kept in (separate > folders for each run) which means that the job failed to finish. > > In the paster.log the most common error is > > HTTPNotFound: No file found with path > lwr_staging/<uniquejobstring>/working/insertions.bed > > That's the case when tophat's output is set at default and the outputs are > under working/tophat_out/. > > If I change this in the wrapper and redirect the output in working/ I get > the following error. > > Traceback (most recent call last): > File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line > 135, in finish_job > client.download_work_dir_output(source_file, > job_wrapper.working_directory, output_file) > File > "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", > line 146, in download_work_dir_output > self.__raw_download_output(name, self.job_id, "work_dir", output) > File > "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", > line 174, in __raw_download_output > output_path=output_path) > File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_ > client/client.py", line 52, in __raw_execute > response = self.transport.execute(url, data=data, input_path=input_path, > output_path=output_path) > File > "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py", > line 26, in execute > with open(output_path, 'wb') as output: > > TypeError: coercing to Unicode: need string or buffer, file found > > or one time I got this > > Groomed 750000 sanger reads into sanger reads. > Based upon quality and sequence, the input data is valid for: solexa, > sanger, illumina > Input ASCII range: 'B'(66) - 'b'(98) > > Input decimal range: 33 - 65 > > In the last two cases, no error was logged in lwr/paster.log > > > Bests, > Nikos > > > 2013/6/18 John Chilton <chil...@msi.umn.edu> >> >> Hey Nikos, >> >> Thanks for the interest in the LWR and frankly I am excited to hear >> that bowtie worked properly. Some of these core NGS tools that require >> implicit indices spanning multiple files are not really addressed by >> the LWR currently, it only knows how to stage files that actually >> appear in the command-line or a config file. I guess if you are just >> using files from the history this is not a problem, but it is >> something to be aware of if you plan to start using .loc files. >> >> My first thought is that the LWR might not support 'from_work_dir' >> outputs in nested subdirectories. I will have to look more closely at >> that. Something that will help me though, is knowing if TopHat >> produced the outputs. >> >> Can you look at the LWR staging directory and tell me if these files >> were created (by default when a job fails, it is not cleaned up this >> is configurable in galaxy-central but not in galaxy-dist right now)? >> Also, does the LWR have any useful logs available? These will likely >> be in paster.log in the LWR directory. >> >> Also, the tip of galaxy-central includes improved error logging and >> exception handling so it is possible it would produce a better error >> message than this admittedly cryptic problem. I know it is not always >> possible to upgrade, but if it is easy it is something worth >> considering doing. >> >> -John >> >> On Tue, Jun 18, 2013 at 8:18 AM, Nikos Sidiropoulos >> <nikos.sid...@gmail.com> wrote: >> > Hi >> > >> > We are running the latest stable distribution on our server. We want >> > tophat2 >> > (along with other tools) to be executed on another machine. >> > >> > LWR is setup based on the online documentation >> > (http://wiki.galaxyproject.org/Admin/Config/LWR, >> > https://lwr.readthedocs.org/en/latest/) >> > >> > Bowtie2 is working as should but it looks like LWR is unable to return >> > the >> > outputs from tophat2. >> > >> > In universe_wsgi.ini the runner is configured like this: >> > [galaxy:tool_runners] >> > bowtie2 = lwr://https://uniquestring@chaos:8913 >> > tophat2 = lwr://https://uniquestring@chaos:8913 >> > >> > When running tophat2 the following error message is returned. >> > >> > Traceback (most recent call last): >> > File "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", >> > line >> > 135, in finish_job >> > client.download_work_dir_output(source_file, >> > job_wrapper.working_directory, output_file) >> > File >> > >> > "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", >> > line 146, in download_work_dir_output >> > self.__raw_download_output(name, self.job_id, "work_dir", output) >> > File >> > >> > "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", >> > line 174, in __raw_download_output >> > output_path=output_path) >> > File >> > >> > "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/client.py", >> > line 52, in __raw_execute >> > response = self.transport.execute(url, data=data, >> > input_path=input_path, >> > output_path=output_path) >> > File >> > >> > "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py", >> > line 21, in execute >> > response = self._url_open(request, data) >> > File >> > >> > "/hermes-storage/galaxy-dist/lib/galaxy/jobs/runners/lwr_client/transport/standard.py", >> > line 12, in _url_open >> > return urllib2.urlopen(request, data) >> > File "/usr/lib/python2.7/urllib2.py", line 127, in urlopen >> > return _opener.open(url, data, timeout) >> > File "/usr/lib/python2.7/urllib2.py", line 407, in open >> > response = meth(req, response) >> > File "/usr/lib/python2.7/urllib2.py", line 520, in http_response >> > 'http', request, response, code, msg, hdrs) >> > File "/usr/lib/python2.7/urllib2.py", line 445, in error >> > return self._call_chain(*args) >> > File "/usr/lib/python2.7/urllib2.py", line 379, in _call_chain >> > result = func(*args) >> > File "/usr/lib/python2.7/urllib2.py", line 528, in http_error_default >> > raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) >> > HTTPError: HTTP Error 500: Internal Server Error >> > >> > >> > We tried to specify tophat's output folder either directly in lwr's >> > working >> > or output directory without success. >> > >> > Is there a solution to this? >> > >> > Bests, >> > Nikos >> > >> > ___________________________________________________________ >> > Please keep all replies on the list by using "reply all" >> > in your mail client. 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