Hi! I got the following error, don't know what is it about or how to fix it ``` Your workflow job, (submission ID 9691778), has failed to complete. The message is: -packages/toil/leader.py", line 246, in run STDERR: 2019-08-26T03:32:34.216492530Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2019-08-26T03:32:34.216498022Z toil.leader.FailedJobsException ``` thank you!

Created by Martin Guerrero martinguerrero89
Hi @martinguerrero89 This should be fixed. Please let us know if you continue to have difficulties. Brian
cool! let me know what you decide about it! Thanks!
Yes, you are correct. I'm looking into it.
Dear @andrewelamb After some debugging, I discovered an error/variation in the dataset DS389-ensg-gene-expr.csv. Column "Gene" is not what it is supposed to be: ``` expression_matrix[1:10,"Gene"] [1] NA [2] "---" [3] "ENSG00000000003 /// OTTHUMG00000022002" [4] "ENSG00000000005 /// OTTHUMG00000022001" [5] "ENSG00000000419 /// OTTHUMG00000032742" [6] "ENSG00000000457 /// OTTHUMG00000035941" [7] "ENSG00000000460 /// OTTHUMG00000035821" [8] "ENSG00000000938 /// OTTHUMG00000003516" [9] "ENSG00000000971 /// ENSG00000244414 /// OTTHUMG00000035607 /// OTTHUMG00000036276" [10] "ENSG00000000971 /// OTTHUMG00000035607" ``` As you can see, it has NAs and this OTTHUM code and we are supposed to use this as the feautres names to our models but other datasets have different format. Is it possible to solve it? If not I would need to do a lot of research on the datasets and add complex code to get the right input to the model Please let me know, if not, I'll have to try a workaround Thank you! Martin
Great! Thanks, I suspected that that might fail, so I changed it in a new script and failed anyway. I will look deeper into it Thank you Andrew!
@martinguerrero89 You are correct I was looking at the wrong log file. Sorry about that! The actual error you are getting is : Error in expression_matrix[featureMaster$ENSEMBL, ] : subscript out of bounds Calls: -> .f Execution halted
I'm guessing it has to do with something from you guys because after looking for "toil" on the internet (https://github.com/DataBiosphere/toil) it appears to be a pipeline management system that is used by the Synapse workflow https://github.com/Sage-Bionetworks/SynapseWorkflowHook/blob/master/Dockerfile.Toil
That is weird I will look into it.
That is completely weird because I have no python code at all in it. Just R and Tidyverse packages. Also, when I run it in my computer, with the blocked network is still working properly... ``` ## Start from this Docker image FROM rocker/tidyverse:3.6.0 ## Install R packages in Docker image RUN Rscript -e "install.packages('xxx')" #not disclosing so I don't give away information about my method ## Copy files into Docker image COPY finegrained.rdata /finegrained.rdata COPY finegrainedsubmission.R /finegrainedsubmission.R COPY featureMaster.Rdata /featureMaster.Rdata ## Make script executable RUN chmod a+x /finegrainedsubmission.R ## Make Docker container executable ENTRYPOINT ["Rscript", "finegrainedsubmission.R"] ```
@martinguerrero89 It looks like you are still getting an error. Based on the most recent log file it looks like python code in your docker container is trying to access a resource via the web. We are restricting the docker containers web access for this challenge.
hi @martinguerrero89 It looks like Synapse got taken down for maintenance while your submission was processing. I'm re-running it now.

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