Question: Blast+ db problem
0
gravatar for Xylanaser
4.1 years ago by
Xylanaser60
Poland - Warsaw - SGGW/WULS
Xylanaser60 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 • 1.8k views
ADD COMMENTlink modified 19 months ago by RamRS26k • written 4.1 years ago by Xylanaser60
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 19 months ago by RamRS26k • written 4.1 years ago by genomax80k
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