Question: Problems connecting to NCBI using NCBI edirect
gravatar for ttom
22 months ago by
ttom210 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 • 989 views
ADD COMMENTlink modified 22 months ago • written 22 months ago by ttom210

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 22 months ago by genomax78k

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

ADD REPLYlink written 22 months ago by Sishuo Wang190
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