I just tested .bam upload using FTP (with the client FileZilla) and
went fine. Just to confirm, you are using the public Main Galaxy
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
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
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
doing over, as this is the datatype (anyway, not just Galaxy).
Second, let me show you how to reset metadata since that may also
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
If neither of these work, then you probably need to examine the
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
able to run tools on the file? Converting to sam format will change
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
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,