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
2 answers
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 $PATH and never use the installation directory as your current working directory when invoking fastq-dump.
Thank you for your help! It seems indeed, the SRA file was corrupt. Another file works fine! Thanks
tsailab@tsailab-BM1AF-BP1AF-BM6AF:~$ 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:~$
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One thing to check is that your SRA file is not corrupt.
If you continue having an issue get fastq file from here.