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problem while using sra tool kit

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  • problem while using sra tool kit

    hi, I need to convert my SRA file into fastq format.. for that i download the SRA toolkit from http://trace.ncbi.nlm.nih.gov/Traces...?view=software. I am using fedora 64 bit linux operating system and choose CentOS Linux 64 bit architecture as sra toolkit compressed file.

    I Decompress the downloaded file, and copy the fastq-dump file to system path. Then I Convert SRA to fastq by using the command
    fastq-dump <SRA archive file>

    but I am getting an error like this..

    2012-05-06T19:18:21 fastq-dump.2.1.12 err: column not found while opening table within short read archive module - failed SRR069603.sra
    Written 0 spots total

    =============================================================
    An error occurred during processing.
    A report was generated into the file '/root/ncbi_error_report.xml'.
    If the problem persists, you may consider sending the file
    to '[email protected]' for assistance.
    ==========================================================

    somebody please tell me why it is happening and the solution..it is urgent!!

    thank u!!

  • #2
    Apparently you're not the only person with this issue:

    http://seqanswers.com/forums/showthread.php?t=17508

    Have you actually done what is suggested and sending the error report to NCBI? What is in the error report anyway? It might hold a clue..

    Comment


    • #3
      thank u for the replay,
      well, I am copying the error report which i got...

      <Report>
      <Run>
      <Cwd>/root/Desktop/sratoolkit.2.1.10-centos_linux64</Cwd>
      <CommandLine argc="2">
      <Arg index="0" value="./bin/fastq-dump"/>
      <Arg index="1" value="SRR069603.sra"/>
      </CommandLine>
      <Result rc="RC(rcSRA,rcTable,rcOpening,rcColumn,rcNotFound)"/>
      </Run>
      <Configuration>
      <Files count="2">
      <File name="/root/Desktop/sratoolkit.2.1.10-centos_linux64/bin/ncbi/config.kf
      g"/>
      <File name="/root/Desktop/sratoolkit.2.1.10-centos_linux64/bin/ncbi/vdb-copy.
      kfg"/>
      </Files>
      <refseq state="not found"/>
      <krypto file="not found">/root/.ncbi/.vdbpass</krypto>
      <sra state="not found"/>
      </Configuration>
      <Object path="/root/Desktop/sratoolkit.2.1.10-centos_linux64/SRR069603.sra" type="table" fs_type="archive" size="138873160">
      </Object>
      <SOFTWARE>
      <VDBLibrary vers="2.2.6"/>
      <Build static="true"/>
      <Tool date="Mar 28 2012" name="./bin/fastq-dump" vers="2.1.12">
      <Binary path="/root/Desktop/sratoolkit.2.1.10-centos_linux64/bin/fastq-dump" type="alias" md5="f65c872ed7b695b92e646b3151133675">
      <Alias resolved="fastq-dump.2">
      <Alias resolved="fastq-dump.2.1.12"/>
      </Alias>
      </Binary>
      </Tool>
      </SOFTWARE>
      </Report>

      ...............................is it because i am using fedora instead of CentOS??? please continue replay........ thank u

      Comment


      • #4
        According to
        ftp://ftp-trace.ncbi.nlm.nih.gov/sra...R069/SRR069603

        The file size is 651,975,610

        Fastq-dump reports size="138873160"

        Either you ran out of disk space or file transfer was aborted. Try to download again.

        You can use sra-dbcc command from SRA Toolkit to check if downloaded file is OK.

        Comment


        • #5
          How did you handle this problem?

          Originally posted by vinila86 View Post
          hi, I need to convert my SRA file into fastq format.. for that i download the SRA toolkit from http://trace.ncbi.nlm.nih.gov/Traces...?view=software. I am using fedora 64 bit linux operating system and choose CentOS Linux 64 bit architecture as sra toolkit compressed file.

          I Decompress the downloaded file, and copy the fastq-dump file to system path. Then I Convert SRA to fastq by using the command
          fastq-dump <SRA archive file>

          but I am getting an error like this..

          2012-05-06T19:18:21 fastq-dump.2.1.12 err: column not found while opening table within short read archive module - failed SRR069603.sra
          Written 0 spots total

          =============================================================
          An error occurred during processing.
          A report was generated into the file '/root/ncbi_error_report.xml'.
          If the problem persists, you may consider sending the file
          to '[email protected]' for assistance.
          ==========================================================

          somebody please tell me why it is happening and the solution..it is urgent!!

          thank u!!
          Hi vinila86,

          Recently I have enconter the same problem. I want to know how did you handle this problem finally.

          I have used sra-dbcc to check the file, and the report was as follows:
          ================================
          2012-10-09T04:05:06 sra-dbcc.2.1.6 info: Table 'SRR488770.sra' ok
          ================================
          Thanks.
          Last edited by zeam; 10-08-2012, 08:12 PM. Reason: add some information.

          Comment


          • #6
            I had the same problem. Simply updating the fastq-dump from 2.1.6 to the latest version (2.1.18) solved it.
            Hope this helps.

            Jeff

            Comment


            • #7
              Dear all,
              I have been through all your frustrations:
              - clicking like hell in the SRA archive and running in circles.
              - downloading SRA tools (yes I know my platform!!!) and finding instructions in discrepancy with the outcome
              - trying again - and again - reading the download guide - try again and again and again and after a while thinking that this would have corrected - and then again.
              You do not wish to discuss memory problems, versions, columns, tables etc.
              I have found two backdoors:
              One is when you have found your SRR numbers:
              Then you can download each file individually from your web-browser replacing the digits after SSR in this link:
              http://www.ncbi.nlm.nih.gov/Traces/s...5&format=fastq
              or multible seuences with a link like:
              http://www.ncbi.nlm.nih.gov/Traces/s...5&format=fastq
              The other is more clicking around:
              - Find your study, your link may look like:
              http://trace.ncbi.nlm.nih.gov/Traces...tudy=SRP013698
              - In the experiment to your Right find the clickable “Show RUNs for each experiment” and click.
              - Click one of the SRR numbers
              - DO NOT click download – but click reads instead.
              - Find the “Filtered download” and click.
              - Now select which or all SRR’s you want and select FASTQ – or FASTA if preferred – and download in FASTx.gz starts
              This reply is also meant as thanks to all the great people that brings these data to us and a friendly reminder that all these data could be made much more accessible to common users. Much of the problem is caused ordinary design flaws.
              - best

              Comment


              • #8
                Hi,
                I had a similar problem. You may have to specify the accession directly using the '-A' option. Without this, the accession is taken directly from <path>.

                For example, if this fails:
                /files/fastq-dump SRR234234.sra

                Then try:
                /files/fastq-dump -A SRR234234 SRR234234.sra

                Hope this helps.

                Comment


                • #9
                  still same problem with column not found...

                  I have the same problem with fastq-dump.2.3.2,
                  column not found while opening table within short read archive module
                  tried -A, the perl configuration, the jar, nothing seems to work??


                  I'm doing fastq-dump SRR000712.sra from bash as I've always done?

                  Comment


                  • #10
                    As strange as this may sound have you tried to provide the full file path to the sra file when doing the fastq-dump? Several people have reported that to work for various fastq-dump related issues.

                    /files/fastq-dump /full_path_to/SRR000712.sra

                    Update: I just tried the file myself. Getting the same error.
                    Last edited by GenoMax; 08-28-2013, 04:56 AM.

                    Comment


                    • #11
                      Yeap tried wiht the full path, when I do this the error message changes from file not found to the problem with the columns?

                      Comment


                      • #12
                        Oddly sra-dump seems to work. Try it.

                        These data are from 2008 so who knows what has changed with SRAtoolkit since that time.

                        Comment


                        • #13
                          Sometimes, it's easier to just grab the gzipped fastq file(s) from ENA

                          Comment


                          • #14
                            Although grabbing the gzipped file always works, it also can take hours, as opposed to a few minutes with Aspera.

                            On a separate note, I can't find any useful information about how to use sra-dump. Could somebody give a couple of examples please?

                            Comment

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