$ efetch -db nucleotide -id KJ413946.1 -format fasta 501 Protocol scheme 'https' is not supported (LWP::Protocol::https not installed) No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=KJ413946.1&rettype=fasta&retmode=text&edirect_os=linux&edirect=9.90&tool=edirect&email=datta@ttshbio' Result of do_post http request is $VAR1 = bless( { '_content' => 'LWP will support https URLs if the LWP::Protocol::https module is installed. ', '_rc' => 501, '_headers' => bless( { 'client-warning' => 'Internal response', 'client-date' => 'Thu, 27 Sep 2018 06:42:06 GMT', 'content-type' => 'text/plain', '::std_case' => { 'client-warning' => 'Client-Warning', 'client-date' => 'Client-Date' } }, 'HTTP::Headers' ), '_msg' => 'Protocol scheme \'https\' is not supported (LWP::Protocol::https not installed)', '_request' => bless( { '_content' => 'db=nucleotide&id=KJ413946.1&rettype=fasta&retmode=text&edirect_os=linux&edirect=9.90&tool=edirect&email=datta@ttshbio', '_uri' => bless( do{\(my $o = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi')}, 'URI::https' ), '_headers' => bless( { 'user-agent' => 'libwww-perl/6.05', 'content-type' => 'application/x-www-form-urlencoded' }, 'HTTP::Headers' ), '_method' => 'POST' }, 'HTTP::Request' ) }, 'HTTP::Response' );
Installing "perl-LWP-Protocol-https" has solved the problem!
$ sudo yum install perl-LWP-Protocol-https
$ efetch -db nucleotide -id KJ413946.1 -format fasta >KJ413946.1 Escherichia coli strain ECS01 plasmid pNDM-ECS01, complete sequence ATGGCAGAGGAAAGCAAACAGCTAACCAAACGGCAACAAAAAGCCATTGATACAGCGGCGTTAATCCGGC AGGAGCCGCCGCAGGGTGAAGATATGGCATTCACCCACTCCATTCTGTGCCAGGTCGGTTTGCCCCGTTC TAAGGTGGCAGGGCGTGAGTTTATGCGCCGTTCTGGTGATGCCTGGCTCGTCGTACAGGCAGGCTGGATT GATGAAGGCAGTGGCCCGGTAGAGCAGCCTTTACCCTATGGCGCTATGCCGCGACTCACGTTCGCCTGGA TTTCATCGTATGCACTGCGCAACAAAACGCGGGAAATCGCCATCGGCCACAGCGCTAATGAGTTTCTTCA CCTTATGGGGATGGACTCACAGGGAACCCGTCATAAAACGCTGCGTACACAAATGCAGGCGCTGGCCGCG TGTCGTTTGCAGCTGGGCTTTAAGGGCC
$ time for d in $(cat Plasmid.list);do echo $d; efetch -db nucleotide -id $d -format fasta >$d.fasta; done ##takes a bit longer time real 6m47.812s
user 0m43.515s
sys 0m7.811s For extracting multiple records from local NT/NR database with a list of accessions using "blastdbcmd" and make accession as filename
$ time for d in $(cat Plasmid.list);do echo $d; blastdbcmd -db nt -entry $d >$d.fasta; done
real 0m26.736s
user 0m7.004s
sys 0m4.384s
Notice the advantage of having downloaded local databases. It just took 26 secs!!
