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
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.
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)
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?
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.
Was the expected match a nucleotide-to-nucleotide match (use BLASTN, or Megablast)? Or nucleotide-to-protein match (use BLASTX)?
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!