Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #16
    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

    Comment


    • #17
      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! :-)

      Comment


      • #18
        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

        Comment


        • #19
          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.

          Comment


          • #20
            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.

            Comment


            • #21
              I was having the same issue. Specifying the full path worked for me too. Thanks!

              Kevin

              Comment


              • #22
                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.

                Comment


                • #23
                  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.

                  Comment


                  • #24
                    vdb-config --restore-defaults works (I used v2.5.2)

                    Comment

                    Latest Articles

                    Collapse

                    • seqadmin
                      Recent Advances in Sequencing Analysis Tools
                      by seqadmin


                      The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
                      05-06-2024, 07:48 AM
                    • seqadmin
                      Essential Discoveries and Tools in Epitranscriptomics
                      by seqadmin




                      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
                      04-22-2024, 07:01 AM

                    ad_right_rmr

                    Collapse

                    News

                    Collapse

                    Topics Statistics Last Post
                    Started by seqadmin, 05-14-2024, 07:03 AM
                    0 responses
                    17 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 05-10-2024, 06:35 AM
                    0 responses
                    40 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 05-09-2024, 02:46 PM
                    0 responses
                    50 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 05-07-2024, 06:57 AM
                    0 responses
                    41 views
                    0 likes
                    Last Post seqadmin  
                    Working...
                    X