I just tested .bam upload using FTP (with the client FileZilla) and all
went fine. Just to confirm, you are using the public Main Galaxy server
Many of our services were down for several
hours yesterday for maintenance related reasons - if you upload
overlapped with that all (9am-6pm EST US), you will want to do the
upload again now.
In my test, I did not set the datatype when I moved the file into a
history, but the file was named with a ".bam" extension. In another
history, I happened to have a .bam file that had a metadata detection as
you describe, and when I reset, the datatype was resolved. So, given
these tests done right now - I think everything is OK on the server.
First, when you uploaded the file via FTP - this was confirmed to be
successful? This is reported by the client tools (and command-line if
using that method). Double check, as this is important. Interrupted
transfers can be resumed (next time) - leave the file in the holding
area, connect to the server first, then start the resume. If you are not
sure of the status, maybe try again and track this, it is an important
first step. Personally, I would name the file with a ".bam" extension if
doing over, as this is the datatype (anyway, not just Galaxy).
Second, let me show you how to reset metadata since that may also solve
the issue. When the message to reset metadata comes up in an expanded
dataset, this is a link. Click on it, and in the center panel the Edit
Attributes form will come up. On the first, default page, near the
bottom, will be a button to "detect metadata". Click on this and let the
If neither of these work, then you probably need to examine the contents
of the .bam file to make sure it is really .bam (and only .bam).
SAMTools on the line command is a good, simple choice for this. Are you
able to run tools on the file? Converting to sam format will change the
indexed format to one that is in plain text, if you find something off
that you want to examine.
You could also check with the source to see if they are aware of any
problems. And not to make this overly confusing, but a transfer problem
from the source to your computer could have occurred, corrupting the
file. The option to upload via URL is possible if the source has the
file available that way. The screencast linked from here shows all
Please review and let us know if you continue to have problems,
On 12/4/13 8:15 AM, Lu, Yuan (MU-Student) wrote:
Dear Sir or Madam,
Recently I was trying to use Galaxy for my data analysis but ran into
I used galaxy server at PSU.
I tried load local .bam file directly to galaxy, I also tried FTP, but
both ways resulted into the same outcome.
The .bam files I was using are pure .bam files with no index.
1.After I load them, the file was recognized as .txt file, and it is
"empty" (But it did take long time to upload to FTP ~1GB), in the
annotation window, it shows "The uploaded binary file contains
2. I tried to convert the file to .bam format, it returns "An error
occurred setting the metadata for this dataset. You may be able to set
it manually or retry auto-detection."
Could you help me for this, I just uploaded a small file to the FTP,
just in case you need it for a test.
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
To search Galaxy mailing lists use the unified search at: