Why does makeblastdb raise this exception on linux?
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0
Entering edit mode
10.6 years ago

Hello,

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 helpful.

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,

R

linux makeblastdb exception • 3.3k views
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2
Entering edit mode
10.6 years ago
Michael 55k

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.

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