Question: How to run Solve3.4 on a server alone
gravatar for w-zhennan
6 weeks ago by
China, Beijing
w-zhennan0 wrote:

Hi everyone, When I use Solve3.4 to assembly Bionano data, there was some errors as follow, some one met them before? Could you give me some advice to solve it? Thank you very much!

      Traceback (most recent call last):
  File "/public/agis/ruanjue_group/wangzhennan/software/Solve3.4_06042019a/Pipeline/06042019/", line 49, in <module>
  File "/public/agis/ruanjue_group/wangzhennan/software/Solve3.4_06042019a/Pipeline/06042019/", line 1840, in run
    skiplevel = self.runAllStages(varsP)
  File "/public/agis/ruanjue_group/wangzhennan/software/Solve3.4_06042019a/Pipeline/06042019/", line 2254, in runAllStages
    stageMRG.mergeComplete() #if :
  File "/public/agis/ruanjue_group/wangzhennan/software/Solve3.4_06042019a/Pipeline/06042019/", line 110, in mergeComplete
    merge_log_path = os.path.join(self.varsP.clusterLogDir, 'refine_merge_outfiles.log')
  File "/public/agis/ruanjue_group/wangzhennan/software/anaconda2/lib/python2.7/", line 70, in join
    elif path == '' or path.endswith('/'):
AttributeError: 'NoneType' object has no attribute 'endswith'
assembly software error • 93 views
ADD COMMENTlink modified 6 weeks ago by Joe14k • written 6 weeks ago by w-zhennan0

the path variable is unexpectedly empty, so when it's tried to call .endswith() on what it thought was going to be a string, an error occurred, as its actually None.

That's all we can say from that error. We need to know more information about the program, how you invoked it etc.

Also, this is a Question, not a Tool, which is reserved for announcements of new tools. I've editied for you (and added code markup to make it clearer), but please bear in mind for next time.

ADD REPLYlink written 6 weeks ago by Joe14k

Thank you very much! I know that is an error, because I ran it on a server without sge schedular. So I want to know someone who ran it on a server without sge schedular successfully.

ADD REPLYlink written 6 weeks ago by w-zhennan0

Do you not have a head node you can run a short test on to see if its working and rule out scheduler issues?

ADD REPLYlink written 6 weeks ago by Joe14k

I have encountered the same error. I think it is a bug, because I run with the non cluster mode but the pipeline still try to get parameters from the cluster arguments xml file.

ADD REPLYlink written 4 weeks ago by coly_fu0
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