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Question: Missing columns in referenced dataset
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gravatar for gbernard4673
22 months ago by
gbernard4673 • 0
gbernard4673 • 0 wrote:

Dear All,

I hope you are extremely well.

I have used trinity for denovo assembly of my reads and was attempting to use Uniprot to align the reads however under the ID column " missing column in referenced dataset" .

I am unable to run the program. I would appreciate any advice.

Best regards,

rna-seq • 567 views
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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by gbernard4673 • 0
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gravatar for Jennifer Hillman Jackson
22 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

There is probably a format or metadata issue with the input. A few items to check:

  1. The datatype of the dataset (input file) is set and matches the instructions on the tool form for the expected type (some form of tabular data)
  2. The columns in the dataset are set correctly to match the dataset contents
  3. The dataset itself was uploaded into Galaxy correctly - all lines, all columns, no extra spaces between columns, only one tab between columns

Click on the "pencil" icon for a dataset (upper right corner) to reach the Edit Attribute forms where the first two can be reviewed/edited as needed. Tools in the group Text Manipulation can be used to investigate actual content if viewing with the "eye" icon does not reveal a problem. More QA help: https://wiki.galaxyproject.org/Support#Error_from_tools

If you are unable to resolve the issue, can it be reproduced at http://usegalaxy.org (if not working there already)? If yes, please send a shared history link to galaxy-bugs@lists.galaxyproject.org. Please also include a link to this post so we can associate the two.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k

Update: I forgot that this can sometimes occur if the input dataset is still processing. The technical reason for this is that the metadata for the dataset hasn't been set yet and cannot be read by the downstream tool. If this the situation, then 1] waiting for the input data to complete processing (to set column metadata) and 2] bringing up the tool form again (to refresh the metadata it is interpreting) is sometimes the solution to resolving tool form entry problems like this.

ADD REPLY • link written 22 months ago by Jennifer Hillman Jackson ♦ 25k
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