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dbGaP, error downloading files

Hi,

I'm trying to download some data in dbGaP. I setup the SRA toolkit per the description and began a download. Everything was working great, but I canceled the download (CTRL-C) so I could start a screen session and restart the download. Rather, I wanted to log out of the machine without losing the connection because the download was going to take way longer than anticipated.

Anyway, after canceling the download, I cannot download the data anymore. I'm getting the following errors:

2015-04-09T21:20:23 prefetch.2.4.5: 1) Downloading 'SRR951854'...
2015-04-09T21:20:23 prefetch.2.4.5:  Downloading via http...
2015-04-09T21:20:24 prefetch.2.4.5 int: archive file not found while validating file within network system module - failed to open file for http://gap-download.ncbi.nlm.nih.gov/0D2DBAFB-0B07-435A-87B4-0FDA689B58B6/505853
2015-04-09T21:20:24 prefetch.2.4.5 int: self NULL while reading file within file system module - http://gap-download.ncbi.nlm.nih.gov/0D2DBAFB-0B07-435A-87B4-0FDA689B58B6/505853: Cannot KFileRead
2015-04-09T21:20:24 prefetch.2.4.5: 1) failed to download SRR951854

Does anyone know how to resolve this error? I emailed the SRA "help desk" last week but they have not responded as yet.

I appreciate your help.

dbgap software-error
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updated by Ram Ram • written by Mark Ebbert Mark Ebbert

Have you tried to remove partially transferred files? Does the transfer work for other SRA files besides 'SRR951854'?

• 0 views • link
written by donfreed donfreed

Thank you for the suggestion. It fails for all of the files in my "cart" file. Only one of those even began downloading. I also just tried getting completely new samples in my cart file. They're all failing with a new error:

2015-04-14T19:59:48 prefetch.2.4.5 int: path corrupt while resolving tree within virtual file system module - SRR1103826: VResolverLocal

Makes me wonder if my setup got corrupted. I don't see a way to start from scratch with the vcb-config. Any ideas?

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written by Mark Ebbert Mark Ebbert

can you give us the prefetch command you used?

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written by Ram Ram

Yup, thanks for your help.

prefetch -X 1000G cart_201504091717.krt
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written by Mark Ebbert Mark Ebbert

1 answer

The SRA "help desk" just got back to me. Sounds like there was an issue on their end because they told me to try the download again. I didn't need to change anything on my end. Hope this helps someone else down the road.

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updated by Ram Ram • written by Mark Ebbert Mark Ebbert

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