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.
Entrez-efetch error. What could be wrong with my efetch usage?
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' );
1 answer
I don't believe that you can use EntrezDirect to fetch sequences from SRA. If you look at help for efetch you will see that only options supported for SRA are following:
sra
native xml EXPERIMENT_PACKAGE_SET XML
runinfo xml SraRunInfo XML
You can do stuff like this:
$ esearch -db sra -query SAMD00028077 | efetch -format runinfo -mode xml
<SraRunInfo>
<Row>
<Run>DRR032680</Run>
<ReleaseDate>2017-09-20 06:08:37</ReleaseDate>
<LoadDate>2017-09-20 07:05:56</LoadDate>
<spots>57063175</spots>
<bases>5763380675</bases>
<spots_with_mates>0</spots_with_mates>
<avgLength>101</avgLength>
<size_MB>3437</size_MB>
<download_path>https://sra-download.ncbi.nlm.nih.gov/traces/dra4/DRR/000031/DRR032680</download_path>
<Experiment>DRX029486</Experiment>
<LibraryName>Bf_blastula_2</LibraryName>
<LibraryStrategy>RNA-Seq</LibraryStrategy>
<LibrarySelection>other</LibrarySelection>
<LibrarySource>TRANSCRIPTOMIC</LibrarySource>
<LibraryLayout>SINGLE</LibraryLayout>
<InsertSize>0</InsertSize>
<InsertDev>0</InsertDev>
<Platform>ILLUMINA</Platform>
<Model>Illumina HiSeq 2000</Model>
<SRAStudy>DRP003810</SRAStudy>
<BioProject>PRJDB3785</BioProject>
<ProjectID>407062</ProjectID>
<Sample>DRS049885</Sample>
<BioSample>SAMD00028077</BioSample>
<SampleType>simple</SampleType>
<TaxID>7739</TaxID>
<ScientificName>Branchiostoma floridae</ScientificName>
<SampleName>SAMD00028077</SampleName>
<Sex>male, female, and mixed</Sex>
<Tumor>no</Tumor>
<CenterName>UT-BS</CenterName>
<Submission>DRA003460</Submission>
<Consent>public</Consent>
<RunHash>00028A5454C28D3B103C3772C0B485A7</RunHash>
<ReadHash>9A87D0D38C636BC9F5D2E527B7FCB677</ReadHash>
</Row>
</SraRunInfo>
I suggest you use Phil Ewel's SRA-Explorer and get the command lines you need to download data from ENA/SRA.
Edit: You could do the following:
$ esearch -db sra -query SAMD00028077 | efetch -format runinfo -mode xml | xtract -pattern SraRunInfo -element download_path
https://sra-download.ncbi.nlm.nih.gov/traces/dra4/DRR/000031/DRR032680
And then use a wget/curl call and save the .sra file. You can then fastq-dump the sequence data.
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.
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