Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

              Latest Articles

              Collapse

              • seqadmin
                Strategies for Sequencing Challenging Samples
                by seqadmin


                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                03-22-2024, 06:39 AM
              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Yesterday, 06:37 PM
              0 responses
              10 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              9 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              51 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              67 views
              0 likes
              Last Post seqadmin  
              Working...
              X