fastq-dump error: table not found

[lionelguy]

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:

fastq-dump SRR341556.lite.sra -L 5

this returns the following error message (-L 5 is just to have more messages):

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?

[liptrap]

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!