Dear Challenge Organizers, I submitted predictions to Sub challenge 1 and received the following validation error: "1_ppi_anonym_v2.txt include wrong geneID in subchallenge 1" We are using the given challenge data as is and have not introduced any spurious gene IDs. The submission files have been named and formatted as per the challenge rules. Is there anyway of getting more information about this error. Kind regards, Suhas Srinivasan

Created by Suhas Srinivasan suhassrinivasan
Hi Dr. Guan, Thank you for the script. But my submission was accepted. Hi Li, I guess there was an error in the validation process and it has been fixed. That is why the pipeline was not progressing for sometime in the night. Also, it might help to remove trailing white spaces at the end of the gene list in each line. Kind regards, Suhas Srinivasan
i changed the files to take in directly submission files (zip files ) and check the following: i think it is really ridiculous that we have wait for hours to see if it is valid. last night i stayed up waited for 7 hours and it is still not up for validation!!! which totally ruined my work today....... http://guanlab.ccmb.med.umich.edu/yuanfang/sanity_check.tar 1. if cluster size is ok, 3-100 2. if repeated genes. 3. if non-existing genes appears. 4. if zip file contains wrongly named files. 5. wrong seperations (reported as wrong genes) i think i have covered everything. i actually used much less functions when i submit.... but i cannot check very well, since my submission was correct... it runs like: perl sanity_check_sc1.pl sc1.zip perl sanity_check_sc2.pl sc2.zip e.g. this is what i run perl sanity_check_sc1.pl ../submission_sc1/2016_8_16/i_support_trump.zip perl sanity_check_sc2.pl ../submission_sc2/2016_8_16/nicebug.zip if it is successful it prints success, other wise it reports the above errors. there i some temp files that i named with my id. so that it won't overlap with any files that one needs to use.
Hi Yuanfang, I am asking more information about wrong gene id error from the organizers. You are absolutely welcome to release the checking code.
hi, dong, i think it does pick up the tab issues and report a whole line is invalid. i can modify it to check both really quickly, if that can help you. let me know if you (or someone else) needs that. ideally yes, i agree with you it should be provided by the organizers, but their code is typically very difficult to use and runs forever....
@gyuanfan Hi Yuanfang, thanks for you code. Unfortunately we can only use it to check the format such as tab-seprator, not the wrong gene id error. I also had this problem in subchallenge2. In theory as long as each gene id < 21115 then it is legal. Could @daniel.marbach help to explain a bit?
suhas, you can use my code to detect your error: http://guanlab.ccmb.med.umich.edu/yuanfang/sanity_check_single.pl // please acknowledge me in your final write-up if this helps you to detect the error. yuanfang

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