SRA FTP Upload Issue

Question

[saamhasan55]

Hi, I have been trying to upload fastq sequence files to SRA via the FTP command line. I am able to create my sub-directory but once I use the put command to initiate the upload, it returns a message saying the file is not a plain file.

Command:

put V350231682_L04_B5GBEEonewRAAAA-501_1.fq

Message:

200 PORT command successful
150 Opening BINARY mode data connection for V350231682_L04_B5GBEEonewRAAAA-501_1.fq
Not a plain file V350231682_L04_B5GBEEonewRAAAA-501_1.fq 226 Transfer complete

Afterwards I can see the file that is uploaded is only a few bytes and is obviously not the complete file. I have tried this with both compressed non-compressed versions. I have been going back and forth with NCBI Support for a while but so far it has yielded no solution. Any suggestions or pointers would be immensely appreciated.

Thanks, Saam

[GenoMax]

I have been going back and forth with NCBI Support for a while but so far it has yielded no solution.

Doubtful if we can help you via a public forum such as this, if NCBI support has not been able to help.

Are you able to upload a smaller test file? If you are behind a firewall/deep packet inspection device at your institution that could also be causing a problem. You could try to do the upload from some other location as a test.

[saamhasan55]

I have disabled firewall during the upload in case that was the issue but did not make a difference. I haven't actually tried uploading a small test file, I will do that to see if it works. Thanks for the suggestion.

[GenoMax]

I have disabled firewall

You may have done that on your local machine but if you are at a university/company, they will more than likely have a network firewall facing the world that you would not be able to disable.

[Jesse]

Also on this topic: if you enable "passive mode" (if your client isn't doing that already) you should be able to avoid needing to have an open port on your end, possibly sidestepping firewall issues.

(Personally I've only seen "not a plain file" when I tried to upload directories, and when it was the active/passive issue I'd get "No control connection for command" errors.)

[lieven.sterck]

since .fq files are just plain ASCII format, try doing the upload in non-binary mode?