Getting a curl: (22) The requested URL returned error: 500 ERROR

Question

[schlogl]

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.

Answer 1

[Pierre Lindenbaum]

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>

[schlogl]

I think it was...working fine now. Thank you

[schlogl]

Friends It seems that it was a temporary error in NCBI database. The code now ir working fine. Thank you.