Question: Blast+ db problem
0
gravatar for Xylanaser
3.6 years ago by
Xylanaser20
Poland - Warsaw - SGGW/WULS
Xylanaser20 wrote:

Hello,

I have a problem with blast db. I make it with makeblastdb with:

blastdbcmd -db nr -entry all -outfmt "%g %T" | \
  awk ' { if ($2 == 9606) { print $1 } } ' | \
  blastdbcmd -db refseq_protein -entry_batch - -out human_sequences.txt

from here

(dont know perl!)

and have this now:

psiblast -query query.txt -db db_prot -outfmt "7 qseqid sseqid evalue bitscore qlen gaps nident" -num_iterations 2 - max_target_seqs 20 -gilist human > seq0.txt>
**Error: NCBI C++ Exception:>
    "/build/buildd/ncbi-blast+-2.2.28/c++/src/corelib/ncbifile.cpp", line 4703: Error: ncbi::CMemoryFileMap::CMemoryFileMap() - To be memory mapped the file must exist:**

Can someone help ?

Regards

blast makeblastdb standalone • 1.6k views
ADD COMMENTlink modified 12 months ago by RamRS24k • written 3.6 years ago by Xylanaser20
1

Here is the relevant bit you need to look at.

To be memory mapped the file must exist

One of the files in your command line either does not exist or is not in the local directory from where you are running the command.

ADD REPLYlink modified 12 months ago by RamRS24k • written 3.6 years ago by genomax71k
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