Blastdbcmd - Too Many Positional Arguments <1>, The Offending Value: %F - Windows
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9.2 years ago
paulhschoi • 0

Hey guys, I'm trying to use blastdbcmd - when I type the following on cmd

blastdbcmd -db databaseBLAST -entry_batch -outfmt "%f" -out test_query.txt

the following error pops up:

Error: Too many positional arguments <1>, the offending value: %f

I typed %f so that it's in Fasta format, and even after spending so much time on the internet to figure out, I still have no idea what to do for this error.. Would you please be able to help me out? Thank you so much in advance.

blast fasta bioinformatics windows • 12k views
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I just got the same problem and the issue was in the name of my folder. There was a white space, blast does not like white spaces, -, + in the files and dir names.

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9.2 years ago
Fwip ▴ 490

Looking at the help, -entry_batch requires a filename after it from which to read each entry. Your command treats -outfmt as the file to be read from, so when it encounters the following "%f" it doesn't know what to do with it.

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