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Alan-Collins / CRISPR_comparison_toolkit

Tools to analyze the differences and similarities between CRISPR arrays
GNU General Public License v3.0
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BLAST Database error: Error: Not a valid version 4 database. #5

Open MeganMarieMartinez opened 2 weeks ago

MeganMarieMartinez commented 2 weeks ago

Hi,

While trying to run spacerblast with the attached database , I get "BLAST Database error: Error: Not a valid version 4 database." I successfully created the database using makeblastdb and included the -parse_seqids option, so I'm unsure how to troubleshoot this.

Thank you!

spacerblast_phage_db.zip

Alan-Collins commented 2 weeks ago

Hi Megan,

Did you create the BLAST db using a different version of BLAST than the one you are using with CCTK? The BLAST db you shared is version 5. That error message suggests that you have an older version of BLAST in your CCTK environment which is unable to read the version 5 database.

If that's the case then either updating the BLAST in your CCTK environment or creating the db with the BLAST in your CCTK environment should fix the issue.

MeganMarieMartinez commented 1 week ago

Hi,

That ended up being the issue— I remade the BLAST db using the BLAST in my CCTK environment. However, I am now running into another issue, where when I try to do the basic spacerblast command, instead of stdout output, it writes out

"Warning: [blastn] lcl|Query_5228 unknown_CRISPR_type(1D)_11: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options"

Does this invalid query sequence completely prevent the rest of the blast from running? I tried sending the output to a file using -o, but when I do I keep getting error:

"ERROR: Seed region must be specified as a range of start:stop with no spaces. i.e., 0-base integer start coordinate, a ":" character, and a 0-base stop coordinate. See the documentation for details."

Even when I add the -E flag, I still get this error.

I appreciate your help! Megan