Question: Problems connecting to NCBI using NCBI edirect
gravatar for Tinu
4 weeks ago by
Tinu150 wrote:

Hello All,

I am trying to run my program which uses NCBI edirect, somehow not able to connect to NCBI

python tempid.list

    get_taxInfo = "esearch -db taxonomy -query txid%s[Organism:exp] | efetch -format docsum | xtract -pattern DocumentSummary -element TaxId ScientificName Species Subsp" % (taxid)
 output = subprocess.check_output(get_taxInfo, shell=True)
                for res in output.strip().split('\n'):
                        res = res.strip()
                        taxid_pass.write("\t".join(str(i) for i in  [taxid] + res.split('\t')) + "\n")

I get the following error

500 Can't connect to (Connection timed

out) No do_post output returned from ''

However when I do wget ""


Any help would be much appreciated.


esearch edirect ncbi • 109 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Tinu150

Do you have the latest version of eutils installed? If not I suggest you start by upgrading them.

Since you are able to get the wget to work there should no local firewall issues.

ADD REPLYlink written 4 weeks ago by genomax48k

Occasionally there might be something wrong when using it. Try later and hopefully the problem will be solved.

ADD REPLYlink written 4 weeks ago by Sishuo Wang120
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