esearch problem downloading files
1
0
Entering edit mode
5.2 years ago

Hi all!

Long time...I got pretty bussy learning Pandas to work with dataframes in a decent way , just miss learn more deep python and unix comands....step by step

I try to do manually mapping virus like VIP pipeline just to learn how they do, the case is get stock at this step, on db_instaler.sh stands

 esearch -db nuccore -query "Viruses[Organism] NOT cellular organisms[ORGN] NOT wgs[PROP] NOT gbdiv syn[prop] AND (srcdb_refseq[PROP] OR nuccore genome samespecies[Filter])" | efetch -format fasta > all_virus.fna

Asume the code its for download virus sequences with esearch...Its the first time I install and use this utility

   cd ~
   perl -MNet::FTP -e \
   '$ftp = new Net::FTP("ftp.ncbi.nlm.nih.gov", Passive => 1);
    $ftp->login; $ftp->binary;
     $ftp->get("/entrez/entrezdirect/edirect.tar.gz");'
    gunzip -c edirect.tar.gz | tar xf -
    rm edirect.tar.gz
    export PATH=$PATH:$HOME/edirect
    ./edirect/setup.sh

I open terminal and type the sample above or the one from VIP:

esearch -db protein -query "lycopene cyclase" | efetch -format fasta

and gives me the next asnwer:

You have requested a page which is not open to the public. Your request did not meet the criteria required to grant access to this page. If you believe that you are being denied access to the page in error, send an e-mail problem report to

virus • 1.7k views
ADD COMMENT
0
Entering edit mode

I do something wrong? its like I go to restricted area?

Thanks for the help

ADD REPLY
1
Entering edit mode

esearch -db protein -query "lycopene cyclase" | efetch -format fasta

I get the expected protein sequences. No errors.

ADD REPLY
0
Entering edit mode

Thank genomax, must be st wrong in the installation or in some crazy way they bann me, will try in my other O.S

ADD REPLY
2
Entering edit mode
5.2 years ago

Your edirect is version is outdated.

When that happens it produces an extremely confusing errors where it blabbers about "access criteria" etc but in fact, the tool version does not match the site.

Update your edirect and you'll be fine. Or as I put it in my documenation:

# Perhaps you have a chronic case of Entrez Direct? Update it!
mkdir -p ~/src
curl ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip > ~/src/edirect.zip
unzip -o ~/src/edirect.zip  -d ~/src
echo 'export PATH=~/src/edirect:$PATH' >> ~/.bashrc
source  ~/.bashrc

then see the version:

efetch -version
7.00
ADD COMMENT
0
Entering edit mode

thank you so much! worked with your code.

Thanks

ADD REPLY

Login before adding your answer.

Traffic: 1329 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6