so I'm fairly new to using linux and blast - have encountered an error in my work.

I have created a fasta database with the results in this directory path: ~/class/hw/db

I'm currently trying to run a search against my created database against query sequences in a file called seqs.fas.

My code is as follows: blastn -db $db -query seqs.fas -out q1results.txt

However I keep getting this error: Error: Too many positional arguments (1), the offending value: seqs.fas

Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: seqs.fas

I'm not sure what I'm doing wrong here, and would appreciate any advice to fix this, thanks!


I remember having this problem in the past, it was encoding related. Rewriting the -s manually (the dash sign) should fix the issue, please see this.

Problem is a copy & past from the BLAST documentation, all dashes ('–') need to be replaced by hand at the command line.

  • $\begingroup$ Thanks for the comment - I've tried multiple ways to get rid of this, including typing out from hand, copying/pasting, and even copying the '-' that shows up when i type blastn -help, however I'm still getting the same error. Just to be clear, dashes ('-') refer to the 'minus' sign next to 0 right? (I'm a Mac user) $\endgroup$
    – aislinx
    Mar 6 '20 at 14:09
  • $\begingroup$ The only think that I can think of is the $db variable. Does it somehow contain whitespaces or any other character that the shell would not understand? If the tilde sign (~) is part of what $db corresponds to (like in your question), you can try changing it to the exact path of your database. $\endgroup$
    – haci
    Mar 6 '20 at 14:26
  • $\begingroup$ I've just tried blastn -db ~/5030/hw2/db -query seqs.fas -out q1results.txt but that just straight up shows me a BLAST Database rror: no alias or index file found for nucleotide database in search path $\endgroup$
    – aislinx
    Mar 6 '20 at 14:34
  • $\begingroup$ This is another error, I guess you point out to the wrong database path. $\endgroup$
    – haci
    Mar 6 '20 at 15:34
  • $\begingroup$ Just to be clear, when i'm doing -db, to which should I refer to: the directory where I have my database, or the entire DB path? $\endgroup$
    – aislinx
    Mar 6 '20 at 15:35

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