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