files in galaxy ftp server can't be started

Question: files in galaxy ftp server can't be started

3.0 years ago by

xiaohe • 10

United States

xiaohe • 10 wrote:

My files were uploaded to the galaxy ftp server successfully but none of them could be started (status message:"Failed: Internal Server Error (500)") ? Any suggestions? Thanks.

galaxy • 897 views

ADD COMMENT • link •

modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by xiaohe • 10

Hello - where are you using Galaxy? Jen

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

In Chicago area from my home. Thanks

ADD REPLY • link written 3.0 years ago by xiaohe • 10

Sorry, I'll clarify - we need to know the URL of the public Galaxy (if using one), or if you are using a Galaxy hosted by your work/institution, or your own local Galaxy, or possibly your own cloud Galaxy. This makes a difference in how to help. Thanks!

ADD REPLY • link modified 3.0 years ago • written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

This is the URL I logged in: https://usegalaxy.org/ . Thanks

ADD REPLY • link written 3.0 years ago by xiaohe • 10

OK - thanks. I'll give FTP a test right now on the Main server and will get back to you.

Meanwhile, double check that your access credentials are correct, each individual upload dataset is under 50 GB in size, and there is no internet access limitation from where you are working from.

https://wiki.galaxyproject.org/Support#Loading_data

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

3.0 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Testing was successful for fastq data, fastq.gz (compressed) data, and BAM datasets.

The problem is not with the FTP server, but with usage. Review the help here (and other items in the last comment above): https://wiki.galaxyproject.org/Support#Loading_data

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

Jen, thanks for your help but I still can't start any files, small or large, in the ftp server. All files are smaller than 5G and they are bam files. I have 250G disk quote and only 1.3G have been used. I tested to upload one of my files to galaxy@biomina via the ftp and it worked without any glitch. Is it possible any hidden files take up all my disk quote?

ADD REPLY • link written 3.0 years ago by xiaohe • 10

You account is active and has plenty of room for new data. Although I should clarify there that this first step in FTP upload does not access your account quota, that is only used when moving the dataset into a history in the second step of FTP upload.

We can probably rule out that passive FTP is being used or that the BAM has compression problems if the load at the other Galaxy server was successful.

The issue then steers toward network restrictions. I am not sure where you are working, but certain institutions (and even countries) can impose restrictions on external server access/data transfer. If you have a local admin, check in with them. If using your own network, check in with your ISP provider.

ADD REPLY • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k

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