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-   -   esearch stuck (http://seqanswers.com/forums/showthread.php?t=90596)

fznajar 08-22-2019 11:58 AM

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

GenoMax 08-22-2019 01:11 PM

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

fznajar 08-22-2019 01:25 PM

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

GenoMax 08-22-2019 01:34 PM

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`.

fznajar 08-22-2019 01:40 PM

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

GenoMax 08-22-2019 01:43 PM

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

fznajar 08-22-2019 02:12 PM

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


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