Trouble with blastdbcmd skipping entries

[fastqfanatic0761]

I'm having a bit of a strange problem with blastdbcmd. Whenever I try to query a transcript, I keep encountering this message: Error: [blastdbcmd] Skipped TRANSCRIPT/4865

I'm not sure if this is due to a formatting issue in my database or if there's something off with the way the header is labeled. Has anyone else experienced this? I'd really appreciate any tips or advice on how to troubleshoot or resolve these skipped entries

 

[st3@k to_go]

I'm having a bit of a strange problem with blastdbcmd. Whenever I try to query a transcript, I keep encountering this message: Error: [blastdbcmd] Skipped TRANSCRIPT/4865

I'm not sure if this is due to a formatting issue in my database or if there's something off with the way the header is labeled. Has anyone else experienced this? I'd really appreciate any tips or advice on how to troubleshoot or resolve these skipped entries

try to double check that your query TRANSCRIPT/4865 exactly matches how the ID appears in the database sequence header. Case sensitivity, extra spaces, or different delimiters (something like |, _) can cause this

 

[Josef_10]

I'm having a bit of a strange problem with blastdbcmd. Whenever I try to query a transcript, I keep encountering this message: Error: [blastdbcmd] Skipped TRANSCRIPT/4865

I'm not sure if this is due to a formatting issue in my database or if there's something off with the way the header is labeled. Has anyone else experienced this? I'd really appreciate any tips or advice on how to troubleshoot or resolve these skipped entries

I agree with @st3@k to_go. The Skipped error usually happens due to a mismatch between your query and the header format in the BLAST database.

For example, if your database headers are >TRANSCRIPT/4865, but you're querying TRANSCRIPT/4865, blastdbcmd won't find it. Try including the ">" or any other special characters. If the header has multiple identifiers, you might need to use the full header. You can also use "blastdbcmd -info -db [your_db_name]" to get some details about the database and see what kind of IDs it's expecting.