Question: Problems connecting to NCBI using NCBI edirect
0
gravatar for ttom
5 months ago by
ttom200
ttom200 wrote:

Hello All,

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

python taxon_check.py 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 eutils.ncbi.nlm.nih.gov:443 (Connection timed

out) No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=txid9606%5BOrganism%3Aexp%5D&retmax=0&usehistory=y&edirect_os=linux&edirect=8.50&tool=edirect&email=tinu@node1.server.ch'

However when I do wget "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=taxonomy&term=txid9606%5BOrganism%3Aexp%5D&retmax=0&usehistory=y&edirect_os=linux&edirect=8.50&tool=edirect&email=tinu@node1.server.ch"

<eSearchResult>
<Count>3</Count>
<RetMax>0</RetMax>
<RetStart>0</RetStart>
<QueryKey>1</QueryKey>
<WebEnv>
NCID_1_251456449_130.14.18.34_9001_1524747720_1001819887_0MetA0_S_MegaStore
</WebEnv>
<IdList/>
<TranslationSet/>
<TranslationStack>
<TermSet>
<Term>txid9606[Organism:exp]</Term>
<Field>Organism</Field>
<Count>3</Count>
<Explode>N</Explode>
</TermSet>
<OP>GROUP</OP>
</TranslationStack>
<QueryTranslation>txid9606[Organism:exp]</QueryTranslation>
</eSearchResult>

Any help would be much appreciated.

Thanks

esearch edirect ncbi • 241 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by ttom200
1

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 5 months ago by genomax57k

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

ADD REPLYlink written 5 months ago by Sishuo Wang140
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