Dear Organizers, Yesterday I have submitted to the express lane 2 (submission ID: 9645461). I have received an email with subject: "Error while running submission to MM_Challenge_2_Express_Lane" . The email states "No prediction file generated, please check your log file ". After opening the log it shows "No Logs, or logs exceed size limit of 50kb". Is it possible to have log file with more description within it? That will help me to fix the bug. I am looking forward to your help. Best Regards, Avisek

Created by AVISEK DEYATI avisek.deyati
Dear Tom, Thanks a lot for your reply. This time I have successfully submitted the Docker and the prediction file also created. However I have got the message "Validation error in submission". The prediction file is formatted as per recommendation. I am not what is the error. Can you please help? submission name: syn11286260 submission ID: 9647596 Best Regards, Avisek
Dear Avisek, Apologies for the inconvenience. That unfortunately is your complete log file- it has not been truncated. Feel free to add print statements in your code so you know where in your code is erroring out. Best, Tom
Dear Tom.. Thanks a lot for your reply. Is it possible to send complete log file for my submission submission name: syn11286260 submission ID: 9647243 Best Regards, Avisek
Dear Avisek, Notice how you are reading in `/test-data/dfci.2009_entrezID_TPM_hg19_LBR1.csv`. This file does not exist on the servers right now. Please follow instructions on this [page](https://www.synapse.org/#!Synapse:syn6187098/wiki/449443). Note the filenames on that page are just examples. You will have to read in `/test-data/sc1_Validation_ClinAnnotations.csv` and read in the columns you want to get the correct filenames and access those files. Best, Tom
Dear Thomas, Thanks a lot for your reply. I have fixed that but still getting a new error message while submitting to "MM_Challenge_2_Express_Lane". Looking at the log file it seems like my code is unable to read the test data sets from "/test-data/" directory within Docker. Can you please confirm whether it is the correct directory to access the test data? submission name: syn11264870 submission ID: 9645946 Best Regards, Avisek
Dear Avisek, I have applied a fix for this issue. I will now give you a truncated version of your log file to assist with debugging. I am re-running your submission so that you will get your log file. Please wait until your submission is completely done running to check your log. Ah, in your case, there was nothing to write out to your log file. Docker captures all stout and sterrs. If you know that you write out stout and sterr in your script, it usually means your script wasn't invoked at all. Looking in your container: You should be doing `Rscript yourRscript.R` That will fix your error. Best, Tom

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