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SEQanswers June Challenge Has Begun!

The competition has begun! We're giving away a $50 Amazon gift card to the member who answers the most questions on our site during the month. We want to encourage our community members to share their knowledge and help each other out by answering questions related to sequencing technologies, genomics, and bioinformatics. The competition is open to all members of the site, and the winner will be announced at the beginning of July. Best of luck!

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  • esearch stuck

    Hi,
    I am using esearch (part of the edirect tools) and it seems that it gets stuck without feedback. I am using version 12.0
    Any suggestions?
    Thank you all

  • #2
    Break your search into smaller chunks. Make sure you are signed-up for and are using NCBI_API_KEY.

    Comment


    • #3
      I did not realize edirect needs a key at command line. As an example, I am using this command:
      $ esearch -db pubmed -query "Roe B" | efetch -format docum

      On different note, While setting up edirect on cygwin, the setup.sh complained about "too many arguments on line 85" before declaring "installation was successful".
      I am not sure this is linked to my problem.

      Thanks

      Comment


      • #4
        Do you get something back with just first part? An API key is only needed if you are going to run multiple entrezdirect commands over a period of time.

        Code:
        esearch -db pubmed -query "Roe B"
        Second part has a typo. Option should be "docsum`.

        Comment


        • #5
          I get nothing back. It just keeps running until I interrupt it.

          Comment


          • #6
            You likely have a broken install then. Is entrezdirect supported on cygwin? If you have Windows 10 then you should use WSL instead.

            Comment


            • #7
              They mentioned to download "cygwin" for windows users. I am trying to find what other emulators I can use.
              Thank you for your time Genomax

              Comment

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