Trouble with SRA toolkit fastq-dump

[ALB_1]

Hi there, I am trying to use fastq-dump on an sra file downloaded from NCBI GEO and keep getting the error message:

err: name not found while resolving tree within virtual file system module - failed to open 'SRRfilenamehere'
Written 0 spots total

I downloaded the correct version and have used this toolkit successfully on other computers. Could it be an installation issue? Thank you!

[GenoMax]

See post#6 in this thread. I assume you are using the newest (v.2.3.2) sratoolkit.

[ALB_1]

Thanks for the suggestion.

I am using the latest version 2.3.2. I ran the perl script as suggested and wasn't prompted with any questions as your post from the March thread suggested. The script ran and then read "Configuration is correct"

I'm by no means a bioinformatics expert, but I thought downloading the SRA toolkit and running fastq-dump should be straightforward.

[GenoMax]

Thanks for the suggestion.

I am using the latest version 2.3.2. I ran the perl script as suggested and wasn't prompted with any questions as your post from the March thread suggested. The script ran and then read "Configuration is correct"

I'm by no means a bioinformatics expert, but I thought downloading the SRA toolkit and running fastq-dump should be straightforward.

What OS are you doing this on?

If this is on unix then look at the ".ncbi" directory in your $HOME. There should be a preferences file in it that should have several lines. If it doesn't then that means the script did not work correctly. This setup only has to be done once per user but if it does not work correctly the first time (it does not explicitly tell you if it does not) then you will see the error you reported.

SRA is switching to reference based compression for .sra files. If the sra file you are looking to expand is one of the newer ones then you have to run the perl script or the java jar to setup a location for storage of the reference files that are downloaded from SRA on the fly.

[oaklander141]

I'm having the exact same issue right now.

I don't have a preferences file in the /bin/ncbi directory

[GenoMax]

On Windows you should do the following (once):

Run the "sratoolkit.jar" file located in "sratoolkit.2.3.2-4-win64\bin" directory. This file should be identified as "executable jar", if you have java installed.

As a part of the installation, the program will ask you to identify a location to store reference files downloaded from NCBI/SRA. The default location is "c:\users\your_windows_user_name\ncbi\public". Make changes (if needed) and allow the program to complete the configuration.

Once the configuration is complete you should see a configuration file ("user-settings.mkfg") created in c:\users\your_windows_user_name\.ncbi". NOTE: The config files in "bin\ncbi" directory are part of the installer.

Now you should be able to open a command window and run "Provide_PATH_TO\fastq-dump SRR#.sra". Program will automatically determine if the SRA file is based on reference compression and will download the necessary reference files from NCBI/SRA (and store them in the location chosen above).

[Susanna5]

I'm having the exact same issue right now.

I don't have a preferences file in the /bin/ncbi directory

Same here. If running on unix, I get the following procedure:

> perl configuration-assistant.perl
==========================================
Welcome to the SRA Toolkit Configuration Script.
SRA toolkit documentation:

http://www.ncbi.nlm.nih.gov/Traces/sra/std

==========================================

cwd = '/data/home/svdven/sratoolkit.2.3.2-centos_linux64/bin'

checking for fastq-dump (local build)... no
checking for fastq-dump (./fastq-dump: found)... yes
checking for sam-dump (local build)... no
checking for sam-dump (./sam-dump: found)... yes
checking for vdb-config (local build)... no
checking for vdb-config (./vdb-config: found)... yes

Reading configuration
refseq/servers: not found
refseq/volumes: not found
refseq/paths: not found

repository: found
repository/site: not found

repository/remote: found
repository/remote/protected/CGI/resolver-cgi: 'http://www.ncbi.nlm.nih.gov/Trace s/names/names.cgi'
repository/remote/main/NCBI/apps/refseq/volumes/refseq: 'refseq'
repository/remote/main/NCBI/apps/wgs/volumes/fuseWGS: 'wgs'
repository/remote/main/NCBI/apps/sra/volumes/fuse1000: 'sra-instant/reads/ByRun/ sra'
repository/remote/main/NCBI/disabled: not found
repository/remote/main/NCBI/root: 'http://ftp-trace.ncbi.nlm.nih.gov/sra'
repository/user: found
repository/user/main/public/apps/refseq/volumes/refseq: 'refseq'
repository/user/main/public/root: '/data/home//svdven/ncbi/public': don't exist
repository/user/main/public/cache-enabled: 'true'
repository/user/main/public/apps/sra/volumes/sraFlat: 'sra'
repository/user/main/public/apps/wgs/volumes/wgsFlat: 'wgs'

Configuration is incorrect
Your configuration is incomplete. Would you like to fix it? [Y/n] Y

Fixing configuration

Would you like to enable Remote Internet access to NCBI(recommented)? [Y/n] Y
'repository/remote/main/NCBI/disabled' => 'no': updated


Checking configuration
refseq/servers: not found
refseq/volumes: not found
refseq/paths: not found

repository: found
repository/site: not found

repository/remote: found
repository/remote/protected/CGI/resolver-cgi: 'http://www.ncbi.nlm.nih.gov/Traces/names/names.cgi'
repository/remote/main/NCBI/apps/refseq/volumes/refseq: 'refseq'
repository/remote/main/NCBI/apps/wgs/volumes/fuseWGS: 'wgs'
repository/remote/main/NCBI/apps/sra/volumes/fuse1000: 'sra-instant/reads/ByRun/sra'
repository/remote/main/NCBI/disabled: 'no'
repository/remote/main/NCBI/root: 'http://ftp-trace.ncbi.nlm.nih.gov/sra'
repository/user: found
repository/user/main/public/apps/refseq/volumes/refseq: 'refseq'
repository/user/main/public/root: '/data/home//svdven/ncbi/public': don't exist
repository/user/main/public/cache-enabled: 'true'
repository/user/main/public/apps/sra/volumes/sraFlat: 'sra'
repository/user/main/public/apps/wgs/volumes/wgsFlat: 'wgs'

Configuration is correct

Then checking the directory of ncbi, I don't see any preferences. I'm following the guide on the toolkit as I'm new to this. Any help would be appreciated as I'd like to get started on the downloading of data from the SRA, and keep getting caught in this sort of problems.

P.s. I also did the java option.. java -jar sratoolkit.jar

[GenoMax]

Susanna5:

In your $HOME (directory you land-in after logging in) there should be a directory called ".ncbi". (NOTE: The "." you will not see this directory unless you use "ls -a" option).

You could try to delete that directory and try to re-run the perl script again.

I do not want to make this complicated but is your $HOME directory located on a partition that is mounted using "NFS" (it appears to be). If you do not know what this is then do not worry. You can check this with your system admin/someone who may know.

We had determined (working with SRA support) that the perl script/java option did not properly work when the $HOME was mounted via NFS (at least that was the only logical explanation). At this time the only option seems to copy (or edit) a working config file into the ".ncbi" directory and adjust paths accordingly. SRA warns you not to edit the file manually so I hesitate to post a version here.

If your $HOME is located on local disks then the configure script works properly.

[Susanna5]

Susanna5:

In your $HOME (directory you land-in after logging in) there should be a directory called ".ncbi". (NOTE: The "." you will not see this directory unless you use "ls -a" option).

You could try to delete that directory and try to re-run the perl script again.

I do not want to make this complicated but is your $HOME directory located on a partition that is mounted using "NFS" (it appears to be). If you do not know what this is then do not worry. You can check this with your system admin/someone who may know.

We had determined (working with SRA support) that the perl script/java option did not properly work when the $HOME was mounted via NFS (at least that was the only logical explanation). At this time the only option seems to copy (or edit) a working config file into the ".ncbi" directory and adjust paths accordingly. SRA warns you not to edit the file manually so I hesitate to post a version here.

If your $HOME is located on local disks then the configure script works properly.

Thanks very much for responding, and so quickly! Your suspicion is correct, my HOME is mounted via NFS. So, if I understand this correctly, there is no way to download data from the SRA for my situation? I am running windows actually, but from the SRAtoolkit guide, I understood that it was only for linux and Amazon Cloud. I'm a bit confused about your other comment over windows, but perhaps that is with NCBI Decryption Tools?

[GenoMax]

Thanks very much for responding, and so quickly! Your suspicion is correct, my HOME is mounted via NFS. So, if I understand this correctly, there is no way to download data from the SRA for my situation? I am running windows actually, but from the SRAtoolkit guide, I understood that it was only for linux and Amazon Cloud. I'm a bit confused about your other comment over windows, but perhaps that is with NCBI Decryption Tools?

There is. Unfortunately the settings file has to be manually modified. You can either email SRA support or I can help off-line.

SRA-tookit is available for windows (http://ftp-trace.ncbi.nlm.nih.gov/sr....2-4-win64.zip) but only for 64-bit. If you have 64-bit windows than get the installer and then follow the directions I posted in #6.

[chenz123]

I had the exact same problem, and apparently the solution is very simple, according to this Czech Wiki site : (https://wiki.metacentrum.cz/wiki/SRA...it_application) you need to execute the fastq-dump command while typing the full path to the SRA file.

for me, it worked like magic.

Cheers.
Chen.

[crazyhottommy]

I had the exact same problem, and apparently the solution is very simple, according to this Czech Wiki site : (https://wiki.metacentrum.cz/wiki/SRA...it_application) you need to execute the fastq-dump command while typing the full path to the SRA file.

for me, it worked like magic.

Cheers.
Chen.

Yes, feed the full path of your sra file to sam-dump resolved my problem also.

[GenoMax]

Yes, feed the full path of your sra file to sam-dump resolved my problem also.

I am curious to know if the SRA file you were interested in employed reference based compression or not?

The original discussion had started with reference to "reference compression based files" which require a one time local storage configuration via the perl script or java file.

[genomeHunter]

Hello,

I am also trying to dump the new reference-based SRA files. It has been driving me nuts, as it is impossible to get to work. Some NBCI staff are very friendly and are trying to help but it all has been fruitless.

Things I have found out till now:

- For some reason, the toolkit is unable to download the refseq so I manually downloaded them from ftp://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/ and put them in "~/ncbi/public/refseq" (the working directory set when using the sratoolkit.jar setup)

- 'test-sra' and 'vdb-validate' can be used for verifying the consistency of SRA files

- fastq-dump works for some files (after manually downloading the refseq files) and does not work for some others with the following ambiguous error message:

VResolverAlgRemoteResolve: name not found while resolving tree within virtual file system module - failed to open

Any ideas?

Cheers
GH

[GenoMax]

Any ideas?

Cheers
GH

Try to run the "configuration-assistant.perl" that is present in the "bin" directory.

While you are running the perl script you will reach a point where the software asks you "Would you like to test SRA files for remote reference dependencies? [y/N]". Choose "Yes" (default answer is No) which will then prompt you to provide an SRA accession number. Try providing the SRA# you are having problems with and see if the script downloads the right reference files.

Try "fastq-dump"ing that SRA file.

There is also a possibility that some SRA files may be corrupt or otherwise problematic (happened with one I was interested in). You may want to ask SRA support to check on the problematic accession #'s.