Please run Megablast as an option with BLASTN

I am trying to BLAST-n a fasta file that is rather small, but I keep getting an error saying that says" An error occured with this dataset: format tabular. database?"

I have removed all tabs. Anyone have any ideas why this is occurring?
Thanks in advance,
Rob

Welcome, @rob

If you want to post back screenshots of the job details, we can try to help.

Find that view by clicking on the i-info icon inside the error dataset.

Then look at the table summary. Click to open up the datasets and screenshot that. Make sure the datatype format and the first few lines of the files are shown, plus any parameters you set.

Or, you can share the history instead, how to do that is in the banner at this forum. Either is fine to start with. :slight_smile:

Thanks so much for the prompt reply, Jennaj. Here is a screenshot:

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Hi @rob

What you shared is the view from the pencil icon, which are the dataset details of the output.

Please try posting the job details – find that by using the i-info icon.

More about how Galaxy uses icons → FAQ: Different dataset icons and their usage

You can also post back a share link to your history. See the banner at this forum for how to do that, or see here → https://training.galaxyproject.org/training-material/faqs/galaxy/histories_sharing.html

And, I started up a very simple test example in my shared history if you want to compare to it → https://usegalaxy.eu/u/jenj/h/help-megablast

Let us know how this works out, and we can follow up more if you share more about your work. :scientist:

Update

My job failed too! There seems to be a problem with one of the indexes. I’ve reported this to the server admins. They will likely correct this quickly.

Meanwhile, you can try using a different target database for NT.

Errors → NCBI NT (01 Sep 2023)
Works → NCBI NT (22 Jan 2018)

Screen Shot 2024-08-06 at 7.59.16 PM

Thanks for reporting the issue, and I’ll follow up about this once we know what is going on.

Thank you so much, Jenna for you advice. I’m sorry for the delayed response, but I mistakenly thought that I sent this email before, but that has given me time to look at the result. I attempted Megablast using the older nt database you recommended, and it worked. That is awesome! Thank so much for helping me over this hurdle. And then a new one showed up in the result:

The file it produced has no data at all. I know that my test fasta file first sequence will match to Plasmodium bergei, so I’m still at a loss as to what’s wrong with my file even when using the older dataset. Any further advice?

Thanks again for your suggestion.

Rob

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Hi @rob

Hum, one of these could be the reason for the query not finding the target match

  1. The NT database doesn’t include the target. You could check at NCBI to confirm when it was released versus the date we captured our index.

  2. The match parameters are not a fit. You can adjust these on the tool form.

    • You can also switch up how you are accessing Megablast using the BLASTN tool instead → link to the tool at UseGalaxy.eu
    • There are a few flavors of matches (Type of BLAST) plus simple cutoff values plus even more options under Advanced Options. All of these are the original NCBI tools/options.
    • I started up a test using that option here → https://usegalaxy.eu/u/jenj/h/help-megablast
  3. Was the expected match a nucleotide-to-nucleotide match (use BLASTN, or Megablast)? Or nucleotide-to-protein match (use BLASTX)?

  4. Some problem with the fasta query sequence. Check to make sure it is a nucleotide sequence in fasta format. From the peek in your screenshot it seems Ok… but you can check the whole sequence to confirm. The tool NormalizeFasta can help … but BLAST is pretty tolerant of minor differences like inconsistent line wrapping, so I don’t think this is your problem so far.

Ok, let’s see how that alternative tool form works with the indexes, too. I should have mentioned that as an option last week!!

The test worked, and is probably the best way to use Megablast at the public servers anyway. I’m going to consider this resolved. Let us know if you need help setting up your job with the BlastN tool using the Megablast option. Thanks!

Thanks for your help, Jenna.

Rob

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