help with fastq-dump

Question

[tsai.141]

I installed sratoolkit in my ubuntu. I can run fastq-sump --help alright, I guess the program is installed correctly. However when I ran fastq-dump and the path for the sra file, I keep getting this meg. I drag the file to the terminal window, so there shouldn't be typo(s) in the path. Any suggestion will be highly appreciated. thank you

tsailab@tsailab-BM1AF-BP1AF-BM6AF:~/sratoolkit.2.6.3-ubuntu64/bin$ fastq-dump '/home/tsailab/SRR949525.sra' 2016-05-29T08:49:34 fastq-dump.2.1.7 err: path incorrect while opening manager within database module - failed /home/tsailab/SRR949525.sra Written 0 spots total

[GenoMax]

One thing to check is that your SRA file is not corrupt.
If you continue having an issue get fastq file from here.

Answer 1

[piet]

Maybe you have installed more than one version of fastq-dump. What is the outcome of

fastq-dump -V

The error message indicates, that you are running 'fastq-dump.2.1.7', while you presumably have 'fastq-dump.2.6.3' in '~/sratoolkit.2.6.3-ubuntu64/bin'. I would really recommend to add '~/sratoolkit.2.6.3-ubuntu64/bin' to your $PATH and never use the installation directory as your current working directory when invoking fastq-dump.

Answer 2

[tsai.141]

Thank you for your help! It seems indeed, the SRA file was corrupt. Another file works fine! Thanks

tsailab@tsailab-BM1AF-BP1AF-BM6AF:~$ fastq-dump -V

fastq-dump : 2.1.7

tsailab@tsailab-BM1AF-BP1AF-BM6AF:~$ fastq-dump /home/tsailab/SRR949534.sra Written 27730678 spots for /home/tsailab/SRR949534.sra Written 27730678 spots total tsailab@tsailab-BM1AF-BP1AF-BM6AF:~$ fastq-dump '/media/tsailab/6A8067C48067957B/Alg34/SRR949533.sra' Written 18684112 spots for /media/tsailab/6A8067C48067957B/Alg34/SRR949533.sra Written 18684112 spots total tsailab@tsailab-BM1AF-BP1AF-BM6AF:~$