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  • fastq-dump error: table not found

    Hi,

    I've been unsuccessfully playing around with the sra toolkit (2.1.9), to extract simple SRA files to fastq. I've tried several recent sra files, but among them:

    Code:
    fastq-dump SRR341556.lite.sra -L 5
    this returns the following error message (-L 5 is just to have more messages):

    Code:
    2012-02-08T09:23:33 fastq-dump.2.1.9 warn: column not found while opening table within short read archive module - column LABEL
    2012-02-08T09:23:33 fastq-dump.2.1.9 warn: column not found while opening table within short read archive module - column LABEL_START
    2012-02-08T09:23:33 fastq-dump.2.1.9 warn: column not found while opening table within short read archive module - column LABEL_LEN
    2012-02-08T09:23:33 fastq-dump.2.1.9 warn: column not found while opening table within short read archive module - column LABEL
    2012-02-08T09:23:33 fastq-dump.2.1.9 warn: column not found while opening table within short read archive module - column LABEL_START
    2012-02-08T09:23:33 fastq-dump.2.1.9 warn: column not found while opening table within short read archive module - column LABEL_LEN
    2012-02-08T09:23:33 fastq-dump.2.1.9 err: table not found while opening table within alignment module module - failed SRR341556.lite.sra
    Written 0 spots total
    I've tried on a Linux 64 bit (compiled from source) and with the macOSX compiled version. Same error.
    Any ideas? Am I doing something wrong?

  • #2
    Hi,

    I'm getting the same error message.

    Details: I'm trying fastq-dump on SRR505888.sra. I'm using the current version (2.1.16) of the SRA toolkit, for Linux compiled from source. I also tried "perl configuration-assistant.perl" as the error message suggests.

    Any insight would be much appreciated. Thanks!

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