I think it was...working fine now. Thank you
Hi dear friends
I am trying to use a list of assemblies (one by line) to download some data from ncbi. Example of the list:
GCA_937921735.1
GCA_937897655.1
GCA_902386345.1
GCA_902386385.1
GCA_902386595.1
I am using this command (that I think Genomax suggested a time ago in another post) and this command always worked very fine. However, today I am frustrated because I am getting this message error (in two different conda enviroments).
The command:
cat list_assm | while read -r acc ; do
esearch -db assembly -query $acc </dev/null \
| esummary \
| xtract -pattern DocumentSummary -element FtpPath_GenBank \
| while read -r url ; do
fname=$(echo $url | grep -o 'GCA_.*' | sed 's/$/_genomic.fna.gz/') ;
wget -nc "$url/$fname" ;
done ;
done
The message error:
EMPTY RESULT
LAST ATTEMPT
curl: (22) The requested URL returned error: 500
ERROR: curl command failed ( qua 22 fev 2023 07:07:46 -03 ) with: 22
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi -d retmax=0&usehistory=y&db=assembly&term=GCA_019056805.1&tool=edirect&edirect=16.2&edirect_os=Linux&email=paulosschlogl%40psschlogl
HTTP/1.1 500 Internal Server Error
I know that the data it is there and I can download them manually. So Any of the friends have any tip for solving this?
Thank you a lot by your time.
Paulo
OBS: I will check it out for some error the the e-direct command, however, as I said it never fails before.
1 answer
the url works on my side. A temporary error IMHO.
$ wget -q -O - "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=0&usehistory=y&db=assembly&term=GCA_019056805.1&tool=edirect&edirect=16.2&edirect_os=Linux&email=paulosschlogl%40psschlogl" | xmllint --format -
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD esearch 20060628//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20060628/esearch.dtd">
<eSearchResult>
<Count>1</Count>
<RetMax>0</RetMax>
<RetStart>0</RetStart>
<QueryKey>1</QueryKey>
<WebEnv>MCID_63f5f75de73c2319036cda4b</WebEnv>
<IdList/>
<TranslationSet/>
<TranslationStack>
<TermSet>
<Term>GCA_019056805.1[All Fields]</Term>
<Field>All Fields</Field>
<Count>1</Count>
<Explode>N</Explode>
</TermSet>
<OP>GROUP</OP>
</TranslationStack>
<QueryTranslation>GCA_019056805.1[All Fields]</QueryTranslation>
</eSearchResult>
Friends It seems that it was a temporary error in NCBI database. The code now ir working fine. Thank you.
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