Question: Local Galaxy instance: GTF file from Data Library has 1 line of data and multiple comments of data "Missing metadata"
1
gravatar for isaac.raplee
2.1 years ago by
isaac.raplee10
isaac.raplee10 wrote:

I'm having difficulties uploading a local GTF file into a local instance of galaxy. I'm using the Data Library upload through Shared Data then Add datasets to current folder from path. Once uploaded in to the Data Library I import the file to my history. The file looks like it imports correctly. However, when I look at the file it shows one line of data and the rest of the data is in the comments section. Additionally, the file shows "Required metadata values are missing." when you click the edit option.

Note: This does not happen if I get data from UCSC directly to my history share it in the data library and import it back into history. All data is in the line sections that way and usable.

Does anyone have any insight into what is happening here and how to correct?

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by isaac.raplee10

The error occurred on the main galaxy host for us as well not just the local instance.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by isaac.raplee10

Well that is interesting; disregard my comment on updating then. Which library dataset are you importing? Could you please link it? Also could you please share that history with us (send the link to galaxy-bugs@bx.psu.edu )?

ADD REPLYlink written 2.1 years ago by Martin Čech ♦♦ 4.6k

On usegalaxy.org my PI uploaded via the get data upload file tool and acquired the 1 line multiple comments history. The shared data library data tool was used when we use our local instance of galaxy. Is there a way to provide you the GTF since the file is not uploaded into the data libraries on the main galaxy host?

ADD REPLYlink written 2.1 years ago by isaac.raplee10

I am still unable to reproduce, I tried this on UCSC-obtained gtf file and the whole round of importing into library and then to history works well to me. At this point I suspect that your gtf file in the library is somewhat abnormal. Can you please link it?

ADD REPLYlink written 2.1 years ago by Martin Čech ♦♦ 4.6k

Here is the link to the history. I'll email it to the suggested email as well. Trying to find a way to link the gtf file for you atm. Also, I had no trouble acquiring the data from UCSC to my history --> uploading it into a library --> importing back into history. My trouble came about when I acquired the data from UCSC into my history --> saved the file locally on my node --> loaded the file into the data library --> imported the file to history, or when I uploaded a self curated GTF file into the library and so on. History

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by isaac.raplee10

I downloaded the file from UCSC to my machine, then FTP transferred to Galaxy and import directly into library and then to history -> I think that covers your case.

Thanks for the history. Interestingly enough the number of comments stays the same even if I recalculate the metadata on it, which means the metadata script is not correct. However I was able to run a job on the file and it handled it correctly (ran it on all lines, ignoring the metadata saying they are comments)

ADD REPLYlink written 2.1 years ago by Martin Čech ♦♦ 4.6k

I created an issue for it here: https://github.com/galaxyproject/galaxy/issues/2298

ADD REPLYlink written 2.1 years ago by Martin Čech ♦♦ 4.6k

enter image description here

Thanks for creating an issue Martin. Also, I attempted to run a cufflinks job on an annotation file upload that way and it failed. However, it worked with the same annotation file straight from UCSC.

ADD REPLYlink written 2.1 years ago by isaac.raplee10
1
gravatar for Martin Čech
2.1 years ago by
Martin Čech ♦♦ 4.6k
United States
Martin Čech ♦♦ 4.6k wrote:

it shows one line of data and the rest of the data is in the comments section

Could you please post a printscreen of this?

the file shows "Required metadata values are missing." when you click the edit option.

Metadata is calculated after the import is complete (and you do not see the process). Please try waiting a bit (especially for large files) after the import, before you start using the file so Galaxy has time to prepare it. You can also trigger re-calculating the metadata on the history item in the edit menu. However I would guess that this problem is caused by the one above.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Martin Čech ♦♦ 4.6k

Here I show data imported from the shared data --> data library at GTF_ANAPC1_chr2test.gtf.

139: is the gene annotation uploaded from get data UCSC.

Note: If I dl the UCSC gene annotation file to my local computer and then upload it to the shared data --> data library I get the same error with 1 line and 1,666,000 comments.

enter image description here

ADD REPLYlink modified 2.1 years ago by Martin Čech ♦♦ 4.6k • written 2.1 years ago by isaac.raplee10

Hello - what Galaxy version are you running? 16.01 (the default master) or the development version or ?

Or did this resolve after waiting for the database to fully process the data, as Martin suggested?

Thanks, Jen, Galaxy team

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Jennifer Hillman Jackson25k

hg sum command pulls 15.05 parent: 17124:46a4ef8850b5 Merge release_15.05 to stable branch: stable commit: 1 added, 29301 unknown update: (current)

ADD REPLYlink written 2.1 years ago by isaac.raplee10
1

So this makes your Galaxy one year behind :/

As there is no obvious cause and the Galaxy is pretty old could you please update it to 16.01 or wait a week or so and then update to 16.04?

You will probably need to migrate it from mercurial to git (info on the bottom of this page: https://wiki.galaxyproject.org/Develop/SourceCode )

ADD REPLYlink written 2.1 years ago by Martin Čech ♦♦ 4.6k

I cannot reproduce this behavior locally with the latest Galaxy. What version of Galaxy are you using?

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Martin Čech ♦♦ 4.6k
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