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fastq-dump error

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  • fastq-dump error

    When I try to use fastq-dump to convert SRA files to fastq, I get the following error:

    Code:
    > ../../sratoolkit.2.1.2-mac32/fastq-dump --dumpbase SRR121550.sra 
    
    2011-08-03T09:31:05 fastq-dump.2.1.2 err: path incorrect while opening manager within database module - Failed SRR121550
    Written 0 spots
    I have no idea what this means or how to fix it. I tried the 64-bit version too but that didn't work either (I'm running Mac OS 10.6.7). I've gotten fastq-dump to work just fine on a linux machine but for some reason the mac version is giving me this problem. Can anyone shed some light?

  • #2
    Getting the same error, but I'm running the program on a linux cluster. It's worked before with different .sra files, but I am getting the same error with the files from DRX00219.

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    • #3
      I am having the same problem! I used fastq-dump successfully only yesterday, but now I get this error message, even when I use the up arrow to recall the series of commands I used successfully to convert an sra file to fastq yesterday. I am mystified and would truly appreciate some help!

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      • #4
        hi guys... i had also encountered d same error... i tried looking around for solution... but it turned out dat the file was not fully downloaded... so i guess u guys should also chek that...

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        • #5
          Make sure that you are not using an older version of the toolkit than was used to create the sra index. Just download the latest version of the toolkit, compile it on your machine, then give fastq-dump another try. I don't know if this will fix your problem, but it did resolve an issue I was having with fastq-dump a while back.

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          • #6
            I think maybe your .sra file were corrupted
            try to re-download the .sra file and try again

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            • #7
              I having the same problem, me too. I need protocol of fastq-dump. This is simple in NCBI.

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              • #8
                Hi all,I'm using SRA TOOLKIT VERSION 2.3.4 for a 64bit linux system, initially I was able to successfully convert sra to fastq but now I'm getting the following error message:

                2014-06-02T08:58:01 fastq-dump.2.3.4 err: param invalid while constructing file within file system module - content-size in local file 154008449 does not match size of remote file 103584632
                2014-06-02T08:58:14 fastq-dump.2.3.4 err: file descriptor invalid while constructing file within file system module - curl_easy_perform( FileRead, 24.1700 ) failed with curl-error 'CURLE_OPERATION_TIMEDOUT' (28)
                2014-06-02T08:58:14 fastq-dump.2.3.4 err: file descriptor invalid while constructing file within file system module - File TOC not read for .sra header
                2014-06-02T08:58:14 fastq-dump.2.3.4 err: item not found while constructing within virtual database module - the path 'SRR039194' cannot be opened as database or table


                I'm trying to convert SRR039194.sra to fastq.

                kindly help.

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                • #9
                  Have you tried to provide the full path to downloaded SRR039194.sra file when running fastq-dump? I was able to dump the data from that file.

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                  • #10
                    hi i am having the same problem to ....any help

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                    • #11
                      What accession # do you need the data from? You may be able to get the fastq file(s) directly by searching with that accession # at EBI ENA.

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