Dear organizer, I faced some weird issue since I tested the both test and R1 line and found issues. Fast course line works fine but R1 course line failed. Also, when I submit docker to the R1 Course and Fine two lines, log files always interrupted at 7th data set. However, when I set my code just deal with 7th data set, my model works good and the log files can print the output of my model. My model just contains R code and thus log files help a lot to debug my model. I cannot understand another log file which contains python and describes the error. Could you give me some hint or how to deal with this issue? I appreciate your help. Best, Wennan Chang

Created by wennan chang chang91
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Thank you so much for your help, Andrew! This issue is weird thus I use the below strategy to test the docker system. The problem is that the R program will stop without any error log about my model which is R script. Even I haven't yet to print the prediction result. After I print the data set information and result of each data set, I got below conflicted condition. For R1_Course line, I set the iteration parameter "i" from 1 to the length of input files. The program will stop during the process of data set 7 as below log information. [1] "input/DS468-hugo-gene-expr.csv" [1] "data id :1" [1] "input/DS468-hugo-gene-expr.csv dim is :" [1] 24442 24 [1] "ICTD_round1 DONE!!!" #------------------------------------------------ [1] "input/DS490-hugo-gene-expr.csv" [1] "data id :2" [1] "input/DS490-hugo-gene-expr.csv dim is :" [1] 24442 33 [1] "ICTD_round1 DONE!!!" #------------------------------------------------ [1] "input/DS446395-hugo-gene-expr.csv" [1] "data id :3" [1] "input/DS446395-hugo-gene-expr.csv dim is :" [1] 48434 14 [1] "ICTD_round1 DONE!!!" #------------------------------------------------ [1] "input/DS483-hugo-gene-expr.csv" [1] "data id :4" [1] "input/DS483-hugo-gene-expr.csv dim is :" [1] 24442 14 [1] "ICTD_round1 DONE!!!" #------------------------------------------------ [1] "input/DS488-hugo-gene-expr.csv" [1] "data id :5" [1] "input/DS488-hugo-gene-expr.csv dim is :" [1] 21307 172 [1] "ICTD_round1 DONE!!!" #------------------------------------------------ [1] "input/DS389-hugo-gene-expr.csv" [1] "data id :6" [1] "input/DS389-hugo-gene-expr.csv dim is :" [1] 20623 55 [1] "ICTD_round1 DONE!!!" #------------------------------------------------ [1] "input/DS393-hugo-gene-expr.csv" [1] "data id :7" [1] "input/DS393-hugo-gene-expr.csv dim is :" [1] 31426 13 **!!! The program did not finish but no any log information here.** Then, I try to run my model on each data set separately by setting the iteration parameter "i". However, the program stopped at data set 5 which could be executed as above log information. Below is the log without the error but not yet finish. Also, the R script still not print anything yet. [1]"i=5" [1] "input/DS488-hugo-gene-expr.csv" [1] "data id :5" [1] "input/DS488-hugo-gene-expr.csv dim is :" [1] 21307 172 **!!! The program did not finish but no any log information here.** Thanks again for the github link. I am woking this issue now. Best, Wennan Chang
We are looking into this. My best guess right now is that your prediction files have non-ASCII characters that toil, which we are using, can't handle: See: https://github.com/DataBiosphere/toil/issues/2793 https://github.com/DataBiosphere/toil/issues/427
The message is: -packages/toil/leader.py", line 246, in run STDERR: 2019-09-14T22:01:52.573049649Z raise FailedJobsException(self.config.jobStore, self.toilState.totalFailedJobs, self.jobStore) STDERR: 2019-09-14T22:01:52.573058470Z toil.leader.FailedJobsException The notification email is above. But nothing error information print on the log file. Thanks, advance.

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