Hi, I want to format the whole nt database with adding the taxid and scientific name via the following script. $file is the split files.

cat $file | while read line
    do 
    if [[ "$line" == ">"* ]]; then
        GI=`echo "$line" | cut -d '>' -f 2 | cut -d ' ' -f 1`
        taxID=`curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=${GI}&rettype=fasta&retmode=xml" | grep TSeq_taxid | cut -d '>' -f 2 | cut -d '<' -f 1`
        orgname_name=`curl -s "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=${GI}&rettype=fasta&retmode=xml" | grep TSeq_orgname | cut -d '>' -f 2 | cut -d '<' -f 1`
        echo ">${GI} scientific_name=${orgname_name}; taxid=${taxID};" >>  t_${file}
    else
        echo "$line" >> t_${file}
    fi
    done

But it is not stable, and always produced some records that returned with no taxid value, like the second one in the following example:

>JQ288447.1 scientific_name=uncultured Geobacter sp.; taxid=186741;
>JQ288458.1 scientific_name=uncultured Geobacter sp.; taxid=;

I tested manually on the failed records and it worked well with returning the correct taxID.

What happened there for those mistakes?

Thank you!!