Entering edit mode
5.0 years ago
jaqx008
▴
110
Hey everyone, I am trying to download an sra file via the unix command line and below is my efetch command. Many did encountered this error and found solutions from the recommendations. But I havent. I am thinking something is wrong with my efetch usage.
efetch -db sra -format fastq -id SAMD00028077 > Blastula.fastq
I get the following error and all the info for that sample is output into the fastq
Error
400 Bad Request No do_post output returned from 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id=SAMD00028077&rettype=fastq&retmode=text&edirect_os=linux&edirect=11.2&tool=edirect&email=edthompson@magnolia01' Result of do_post http request is $VAR1 = bless( {
'_rc' => 400,
'_protocol' => 'HTTP/1.1',
'_content' => 'ID list is empty! In it there are neither IDs nor accessions. ',
'_msg' => 'Bad Request',
'_request' => bless( {
'_headers' => bless( {
'::std_case' => {
'if-ssl-cert-subject' => 'If-SSL-Cert-Subject'
},
'user-agent' => 'libwww-perl/6.36',
'content-type' => 'application/x-www-form-urlencoded'
}, 'HTTP::Headers' ),
'_method' => 'POST',
'_uri_canonical' => bless( do{\(my $o = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi')}, 'URI::https' ),
'_content' => 'db=sra&id=SAMD00028077&rettype=fastq&retmode=text&edirect_os=linux&edirect=11.2&tool=edirect&email=edthompson@magnolia01',
'_uri' => $VAR1->{'_request'}{'_uri_canonical'}
}, 'HTTP::Request' ),
'_headers' => bless( {
'x-xss-protection' => '1; mode=block',
'client-ssl-cert-subject' => '/C=US/ST=Maryland/L=Bethesda/O=National Library of Medicine/OU=National Center for Biotechnology Information/CN=*.ncbi.nlm.nih.gov',
'server' => 'Finatra',
'strict-transport-security' => 'max-age=31536000; includeSubDomains; preload',
'ncbi-phid' => '322CB55B42D4D2E500002805E9D8639D.1.1.m_2',
'content-type' => 'text/plain; charset=UTF-8',
'client-date' => 'Wed, 24 Apr 2019 15:57:41 GMT',
'::std_case' => {
'client-response-num' => 'Client-Response-Num',
'x-ua-compatible' => 'X-UA-Compatible',
'access-control-allow-origin' => 'Access-Control-Allow-Origin',
'ncbi-sid' => 'NCBI-SID',
'client-ssl-cipher' => 'Client-SSL-Cipher',
'x-ratelimit-remaining' => 'X-RateLimit-Remaining',
'client-ssl-socket-class' => 'Client-SSL-Socket-Class',
'content-security-policy' => 'Content-Security-Policy',
'l5d-success-class' => 'L5d-Success-Class',
'x-ratelimit-limit' => 'X-RateLimit-Limit',
'client-peer' => 'Client-Peer',
'client-transfer-encoding' => 'Client-Transfer-Encoding',
'set-cookie' => 'Set-Cookie',
'client-ssl-cert-issuer' => 'Client-SSL-Cert-Issuer',
'ncbi-phid' => 'NCBI-PHID',
'strict-transport-security' => 'Strict-Transport-Security',
'client-date' => 'Client-Date',
'x-xss-protection' => 'X-XSS-Protection',
'client-ssl-cert-subject' => 'Client-SSL-Cert-Subject'
},
'client-ssl-cert-issuer' => '/C=US/O=DigiCert Inc/OU=www.digicert.com/CN=DigiCert SHA2 High Assurance Server CA',
'vary' => 'Accept-Encoding',
'set-cookie' => 'ncbi_sid=0BF58CE0F7076DE0_99BASID; domain=.nih.gov; path=/; expires=Fri, 24 Apr 2020 15:57:40 GMT',
'client-transfer-encoding' => [
'chunked'
],
'client-peer' => '130.14.29.110:443',
'cache-control' => 'private',
'date' => 'Wed, 24 Apr 2019 15:57:40 GMT',
'x-ratelimit-limit' => '3',
'l5d-success-class' => '1.0',
'content-security-policy' => 'upgrade-insecure-requests',
'client-ssl-socket-class' => 'IO::Socket::SSL',
'x-ratelimit-remaining' => '2',
'client-ssl-cipher' => 'ECDHE-RSA-AES256-GCM-SHA384',
'connection' => 'close',
'ncbi-sid' => '0BF58CE0F7076DE0_99BASID',
'access-control-allow-origin' => '*',
'client-response-num' => 1,
'x-ua-compatible' => 'IE=Edge'
}, 'HTTP::Headers' )
}, 'HTTP::Response' );
if I recal I have spent the last 3 hours trying to install fastq-dump or the sratoolkit but its not been succesful. I use a mac. But I am trying to work on magnolia (cloud) which appears to be a linux system and I have not been able to get fastq-dump on it to perfom the last operation. Help please.
Whenever possible get the fastq files directly from EBI-ENA. SRA-Explorer tool will give you URL's for FTP from EBI-ENA.
For example: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/DRR032/DRR032680/DRR032680.fastq.gz
You could construct them yourself by comparing this URL with the download location above.
I can download it but the thing is I have many of the sra files to download which is the reason why I want to do it on the cloud (server for my school). I was hopping I could download them directly into my folder in the server then work right on the cloud to save me storage and get better speed.
And you can. Just use the ftp URL's from your cloud account so the data gets downloaded directly there. You can search and build a full list with SRA-Explorer in creative ways.
Ok thankss alot. I will do this. I appreciate you for your time and patience.