Question: Entrez Direct problems
0
gravatar for ioanahrom
4 months ago by
ioanahrom0
ioanahrom0 wrote:

Hello I'm stuck here with the E-Direct links. I followed the steps mentioned on the NBI page:

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

I get the confirmation message:

FAILED TO DOWNLOAD:

xtract.UNSUPPORTED.gz (xtract.UNSUPPORTED.gz: No such file or directory)
gzip: xtract.UNSUPPORTED.gz: No such file or directory
Unable to download xtract executable.

FAILED TO DOWNLOAD:

rchive.UNSUPPORTED.gz (rchive.UNSUPPORTED.gz: No such file or directory)
gzip: rchive.UNSUPPORTED.gz: No such file or directory
Unable to download rchive executable.

Entrez Direct has been successfully downloaded and installed.

On the website of the NCBI, the xtract.UNSUPPORTED.gz it doesn't exist so I tried to change it directly from the files which were installed with the E-direct but it still doesn't work. However I don't know if this is the real problem. If I only use the Esearch and efetch command I don't get any result. For example:

esearch -db nucleotide -query "CP002105" | efetch -format fasta

I get this and nothing else:

student@ubuntuM0151:~/edirect$ esearch -db nucleotide -query "CP002105" | efetch -format fasta

  EFETCH - retrieve entries from sequence databases.

  Synopsis: efetch -options [database:]<query> 

  Databases:  SWissprot/SP, PIR, WOrmpep/WP, EMbl, GEnbank/GB, ProDom, ProSite

  Options:
    -a            Search with Accession number
    -f            Fasta format output
    -q            Sequence only output (one line)
    -s <#>        Start at position #
    -e <#>        Stop at position #
    -o            More options and info...

    -D <dir>      Specify database directory
    -H            Display index header data
    -p            Display entrynames in search path
    -r            Print sequence in 'raw' format
    -m            Fetch from mixed mini database
    -M            Mini format output
    -b            Do NOT reverse the order of bytes
                              (SunOS, IRIX do reverse, Alpha not)
    -d <dbfile>   Specify database file (avoid this)
    -i <idxfile>  Specify index file (avoid this)
    -l <divfile>  Specify division lookup table (avoid this)
    -B <database> Specify database (archaic)
    -A            Only return entryname for accession number
    -n <name>     Give the sequence this name
    -x            Don't require query to match entry's name exactly (avoid)
    -w            For Wormpep: also fetch cross-referenced SwissProt entry
    -h            shows this help text


  Environment:
  SWDIR      = SwissProt  directory - database and EMBL index files
  PIRDIR     = PIR        -- " --
  WORMDIR    = Wormpep    -- " --
  EMBLDIR    = EMBL       -- " --
  GBDIR      = Genbank    -- " --
  PRODOMDIR  = ProDom     -- " --
  PROSITEDIR = ProSite    -- " --
  DBDIR      = User's own -- " -- (fasta format)

  SEQDB    database file (default SwissProt)
  SEQDBIDX index file
  DIVTABL  division lookup table

  Ex. setenv DBDIR /pubseq/seqlibs/embl/

  Note that Prodom family consensus seqs can be fetched by PD:_#

  by Erik Sonnhammer (esr@sanger.ac.uk)
  Version 2.1, 
student@ubuntuM0151:~/edirect$

I'm not an expert on this field and I don't know what else can I do. A few months ago it worked perfectly but I had to reinstall the virtual machine and now I get this problems. I also tried the test confirmation script but I get this message:

esearch version:
11.0
xtract version:

Unable to locate xtract executable. Please execute the following:

  ftp-cp ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract.UNSUPPORTED.gz
  gunzip -f xtract.UNSUPPORTED.gz
  chmod +x xtract.UNSUPPORTED

EDirect install status:

Unable to locate xtract executable. Please execute the following:

  ftp-cp ftp.ncbi.nlm.nih.gov /entrez/entrezdirect xtract.UNSUPPORTED.gz
  gunzip -f xtract.UNSUPPORTED.gz
  chmod +x xtract.UNSUPPORTED

I executed all that it says but still nothing.

Can anybody help me? =) Thank you very much

ADD COMMENTlink modified 4 months ago • written 4 months ago by ioanahrom0
1

Check if there's a version of xtract available for your OS. In all probability, there should be one. I use xtract.Darwin (macOS).

The setup.sh should take care of xtract anyway. What OS are you using?

ADD REPLYlink written 4 months ago by RamRS23k

I'm using Linux with a VM from a Windows 10. On the NCBI website I found that it should be xtract.Linux I made the extraction but it still doesn't work. I unzip it and then I execute stup.sh, and it still doesn't find it.

ADD REPLYlink written 4 months ago by ioanahrom0
1

@ioanahrom could you please send me the output of uname -sm from your VM?

ADD REPLYlink written 4 months ago by vkkodali1.1k
root@ubuntuM0151:~# uname -sm
Linux i686
ADD REPLYlink written 4 months ago by ioanahrom0
2

Thank you. You are using a 32-bit machine and, currently, NCBI provides precompiled binaries for 64-bit machines only. You may be able to compile them from the source code (xtract.go and rchive.go, each of which needs to be built together with common.go, and with some third-party libraries on hand).

ADD REPLYlink written 4 months ago by vkkodali1.1k

Solved Thank you very very much :)

ADD REPLYlink written 4 months ago by ioanahrom0
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