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  • sciseim
    replied
    vdb-config --restore-defaults works (I used v2.5.2)

    Leave a comment:


  • Rhewter
    replied
    Solve the problem

    Originally posted by ALB_1 View Post
    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!
    Try "fastq-dump --split-files ./library.sra".


    It is works.

    Leave a comment:


  • Richard Finney
    replied
    This is an ongoing case study in why you should just stick with sftp and gzip.

    A camel is a horse designed by a committee and this SRA compression and decryption is a real camel.

    Leave a comment:


  • kmkocot
    replied
    I was having the same issue. Specifying the full path worked for me too. Thanks!

    Kevin

    Leave a comment:


  • Nick
    replied
    Originally posted by genomeHunter View Post
    I think I have finally found the solution!

    Some new SRA files need refseq for dumping. It should be in ~/ncbi/public/refseq (default path). For some reason, my SRA toolkit was unable to download them, so I manually downloaded them from

    ftp://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/

    Try running 'vdb-validate' and 'test-sra +a' to see which sequences you need to download.

    Cheers
    GH

    PS. SRA technical staff are friendly and knowledgable. Contact them if the problem persists! :-)
    This finally worked for me. The home mounted via NFS was not an issue. I also discovered that trying to change the default ncbi directory caused a lot issues, as a ~/ncbi directory was created after adding an encrypted repository. That is also where the refseq files have to go, even if the root is elsewhere. Basically leave the ncbi root in your home directory, and add the refseq files there.

    Leave a comment:


  • tman
    replied
    I had this issue as well and providing the absolute path was not resolving it. In the end I found that the error (virtual file system) had to do with the machine not having web access. Copying the required reference files into: /yourhomedir/ncbi/public/refseq solved it.

    Leave a comment:


  • giorgifm
    replied
    Guys,

    the problem happens when you use a local path for the SRA file. Try using the absolute path! fastq-dump /data/etc/SRR00000.sra should do the trick

    Leave a comment:


  • genomeHunter
    replied
    Solution

    I think I have finally found the solution!

    Some new SRA files need refseq for dumping. It should be in ~/ncbi/public/refseq (default path). For some reason, my SRA toolkit was unable to download them, so I manually downloaded them from

    ftp://ftp-trace.ncbi.nlm.nih.gov/sra/refseq/

    Try running 'vdb-validate' and 'test-sra +a' to see which sequences you need to download.

    Cheers
    GH

    PS. SRA technical staff are friendly and knowledgable. Contact them if the problem persists! :-)

    Leave a comment:


  • genomeHunter
    replied
    Originally posted by GenoMax View Post
    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.
    I have tried everything, in every forum, and in every thread.

    I simply cannot understand why such a presumably simple and tiny application could cause so much headache. It just cannot be solved

    Last thing I tried, without success:

    http://trace.ncbi.nlm.nih.gov/Traces...lkit_doc&f=std

    GH

    Leave a comment:


  • GenoMax
    replied
    Originally posted by genomeHunter View Post

    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.

    Leave a comment:


  • genomeHunter
    replied
    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

    Leave a comment:


  • GenoMax
    replied
    Originally posted by crazyhottommy View Post
    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.

    Leave a comment:


  • crazyhottommy
    replied
    Originally posted by chenz123 View Post
    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.

    Leave a comment:


  • chenz123
    replied
    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.
    Last edited by chenz123; 04-28-2013, 01:52 PM.

    Leave a comment:


  • GenoMax
    replied
    Originally posted by Susanna5 View Post
    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.

    Leave a comment:

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