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

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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?

Maybe a little bit late, but I think this may be yet another case of UTF-8 versus ISO-latin finding a way to annoy:

I had the same problem with a different query using blastn, but the offending value was -db. I found out that it was an encoding problem with the "-" part of the command. I.e. if you are copy-pasting the commands from Mac or a pdf or so what looks like "%f" or "-" to us may be not. Try typing all the command instead of copy-pasting.

Blastdbcmd - Too Many Positional Arguments <1>, The , 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� Question: Blastdbcmd - Too Many Positional Arguments <1>, The Offending Value: %F - Windows. 0. 6.7 years ago by. paulhschoi • 0. paulhschoi • 0 wrote:

Your problem is not with the -outfmt argument. It is that -entry_batch requires a file name. Also, you don't need to specify -outfmt '%f' since Fasta format is the default output.

Here is the command line that you want:

blastdbcmd.exe -db databaseBLAST -entry 'all' -out test_query.txt

Paul

blastdbcmd - Too many positional arguments <1 , Maybe a little bit late, but I think this may be yet another case of UTF-8 versus ISO -latin finding a way to annoy: I had the same problem with a� Error: Too many positional arguments (1), the offending value Problem is a copy & past from the BLAST documentation, all dashes ('–') need to be replaced by hand at the command line. Replace / re-type all '–' with '-' blastn -db nt -query nt.fsa -out results.out

Pure guess : remove the quotes, double the % or more probably both.

%f is the default according to the documentation.

Problem calling `blast` on windows � Issue #13 � drostlab/orthologr , but I got this error message:Error: Too many positional arguments (1), the offending value: –db. Is the local db is correctly created? could you� Error: Too many positional arguments (1), the offending value: files\NCBI\blast-2.7.1+\refseq_rna.00' Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: files\NCBI\blast-2.7.1+\refseq_rna.00'

in my case it was a very difficult to spot look-alike for "-" after copy-pasting part of a command. Make sure the minus-signs are real minus signs!

Blastn error: positional arguments ? [Archive], Long and Assignment in line 1 are interpreted by the Bash shell as too many positional arguments, 2 instead of 1. Instead enclose the whole� The first blastdbcmd invocation produces 2 entries per sequence (GI and taxonomy ID), the awk command selects from the output of that command those sequences which have a taxonomy ID of 9606 (human) and prints its GIs, and finally the second blastdbcmd invocation uses those GIs to print the sequence data for the human sequences in the nr database.

command line, Error: Too many positional arguments (1), the offending value: qseqid Error: ( CArgException::eSynopsis) Too many positional arguments (1), the offending� My point is that it contains many local-scope variables that would have to be passed to the extracted function, which could look like: def mysum(x1, x2, x3, x4, x5, x6, x7, x8, x9): x = x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9 return x The problem is that pylint would trigger a warning about too many arguments.

Problem calling `blast` on windows - orthologr, A positional argument is one that doesn't follow something like -foo or --bar . That is, the variable that it should internally map to depends on it's� Error: Too many positional arguments (1), the offending value: nr.AAXJ.fa Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: nr.AAXJ.fa Thank you, any help would be appreciated, Lisa. EDIT: I should also mention I have over 1500 databases.

blast command line, blastdbcmd -db databaseBLAST -entry_batch -outfmt "%f" -out test_query.txt. the following error pops up: Error: Too many positional arguments <1>, the� My point is that it contains many local-scope variables that would have to be passed to the extracted function, which could look like: def mysum(x1, x2, x3, x4, x5, x6, x7, x8, x9): x = x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9 return x The problem is that pylint would trigger a warning about too many arguments.