Hi, I tried to download the data using the sample R script provided, and got the error message 'SSL certificate problem: self signed certificate in certificate chain. Will wait for 0 seconds then retry. Press CTRL+C to quit.' when running the line 'chal_data_table = synTableQuery('select id,name from syn9763946')'. The R script keep trying but can not get through. I am using R version 3.4.1 for Windows under the Windows 7 OS. Thanks!

Created by Lei Shen leixus
Hi Mike, Indeed it is due to the restriction on the computer. I changed to another 'more free' computer and the issue goes away. Thanks! Lei
Hi Lei, The folks on our side believe your issue is due to permissions on your machine or the server you are working on. As a work around I would actually recommend using the synapse R, python or command line client to pull down the vcfs individually after (list all the synIds in the folder of interest and then pull down). Synapse will let you parallelize up to 8 pull downs. The tar ball would be so large that it could have other issues but if you pull down individually synapse will check the .synapseCache and skip anything that is already their. Thus any fails would be easy pick up from where you left off , which is not the case for the tar ball.
Hi Mike, As a work around I have already downloaded some files manually through the web interface. However for the genomic data there are many small vcf files, are you able to create a tarball for each group of vcfs (MuTect2 vcfs, Strelka indel vcfs and Strelka snv vcfs)? Then I can download them manually. Thanks a lot! Lei
Hi Lei, I am forwarding this to some better suited to answer this. They are abroad right now so there may be a delay in addressing it. Regards, mike

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