Question: help with fastq-dump
0
gravatar for tsai.141
2.1 years ago by
tsai.1410
tsai.1410 wrote:

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

fastq-dump sratool • 889 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by tsai.1410
1

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

ADD REPLYlink written 2.1 years ago by genomax49k
1
gravatar for piet
2.1 years ago by
piet1.4k
planet earth
piet1.4k wrote:

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.

ADD COMMENTlink written 2.1 years ago by piet1.4k
0
gravatar for tsai.141
2.1 years ago by
tsai.1410
tsai.1410 wrote:

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:~$

ADD COMMENTlink written 2.1 years ago by tsai.1410
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