Question: Why does makeblastdb raise this exception on linux?
gravatar for ronaldnieuwenhuis
4.1 years ago by
European Union
ronaldnieuwenhuis0 wrote:


I am trying to make a blast database of several fasta files.
When I use makeblastdb (on linux) however, I am getting an exception which is not very helpfull.

My command:

$ makeblastdb -in stu_ref_SolTub_3_chrPltd.fa stu_ref_SolTub_3_chrUn.fa NC_000964.faa rn_alt_Rn_Celera_chr1.fa rn_alt_Rn_Celera_chr2.fa rn_alt_Rn_Celera_chr3.fa rn_alt_Rn_Celera_chr4.fa rn_alt_Rn_Celera_chr5.fa rn_alt_Rn_Celera_chr6.fa rn_alt_Rn_Celera_chr7.fa rn_alt_Rn_Celera_chr8.fa rn_alt_Rn_Celera_chr9.fa rn_alt_Rn_Celera_chr10.fa rn_alt_Rn_Celera_chr11.fa rn_alt_Rn_Celera_chr12.fa rn_alt_Rn_Celera_chr13.fa rn_alt_Rn_Celera_chr14.fa rn_alt_Rn_Celera_chr15.fa rn_alt_Rn_Celera_chr16.fa rn_alt_Rn_Celera_chr17.fa rn_alt_Rn_Celera_chr18.fa rn_alt_Rn_Celera_chr19.fa rn_alt_Rn_Celera_chr20.fa rn_alt_Rn_Celera_chrUn.fa rn_alt_Rn_Celera_chrX.fa rn_ref_Rnor_6_chrMT.fa rn_ref_Rnor_6_chrY.fa zm_ref_B73_RefGen_v3_chr1.fa zm_ref_B73_RefGen_v3_chr2.fa zm_ref_B73_RefGen_v3_chr3.fa zm_ref_B73_RefGen_v3_chr4.fa zm_ref_B73_RefGen_v3_chr5.fa zm_ref_B73_RefGen_v3_chr6.fa zm_ref_B73_RefGen_v3_chr7.fa zm_ref_B73_RefGen_v3_chr8.fa zm_ref_B73_RefGen_v3_chr9.fa zm_ref_B73_RefGen_v3_chr10.fa zm_ref_B73_RefGen_v3_chrMT.fa zm_ref_B73_RefGen_v3_chrPltd.fa zm_ref_B73_RefGen_v3_chrUn.fa -dbtype nucl -out filterDatabase

The exception:

Error: (CArgException::eSynopsis) Too many positional arguments (1), the offending value: stu_ref_SolTub_3_chrUn.fa
Error: (CArgException::eSynopsis) Application's initialization failed

Do I feed too many arguments? If this is the case what is the limit?

Yours sincerely,



linux exception makeblastdb • 1.6k views
ADD COMMENTlink modified 4.1 years ago by Michael Dondrup44k • written 4.1 years ago by ronaldnieuwenhuis0
gravatar for Michael Dondrup
4.1 years ago by
Bergen, Norway
Michael Dondrup44k wrote:

Edit: Argh!

Of course makeblastdb supports multiple input files as a list like so:

makeblastdb -in "file1.faa file2.faa" -dbtype prot -out mydb


makeblastdb supports only a single input file. You need to either concatenate the files before running it or use blastdb_aliastool to join all databases. 

ADD COMMENTlink modified 3.9 years ago • written 4.1 years ago by Michael Dondrup44k
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