I am using SRA Toolkit to convert .sra files to fastq files but when I am trying to use fastq-dump procedure there occurs a problem. Does anyone have seen such error? What does it mean and how can I overcome this error?
2015-10-19T10:05:00 fastq-dump.2.1.7 err: path incorrect while opening manager within database module - failed /home/mkosinski/WCO/Kasia/SRR1294096.sra
Written 0 spots total
mkosinski@mkosinski-E540:~$ fastq-dump.2.1.7 ~/WCO/Kasia/SRR1294095.sra
2015-10-19T10:05:19 fastq-dump.2.1.7 err: path incorrect while opening manager within database module - failed /home/mkosinski/WCO/Kasia/SRR1294095.sra
Written 0 spots total
mkosinski@mkosinski-E540:~$ fastq-dump.2.1.7 -version
fastq-dump.2.1.7 : 2.1.7
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written
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MarcinKosinski •
OK just to make sure if it works or not, go into the dir where you have your fastq-dump executable and run this:
./fastq-dump <any options you want (split etc)> <absolute path to sra file>
I used sudo apt-get install sra-toolkit to install this kit. How should I know where is my exutable dir :)?
I've checked /usr/bin localization and I have the same error
mkosinski@mkosinski-E540:/usr/bin$ pwd
/usr/bin
mkosinski@mkosinski-E540:/usr/bin$ ls -l *fastq-dump.2.1.7
-rwxr-xr-x 1 root root 93384 cze 15 2012 fastq-dump.2.1.7
mkosinski@mkosinski-E540:/usr/bin$ ./fastq-dump.2.1.7 /home/mkosinski/WCO/Kasia/SRR1294095.sra
2015-10-19T15:13:26 fastq-dump.2.1.7 err: path incorrect while opening manager within database module - failed /home/mkosinski/WCO/Kasia/SRR1294095.sra
Written 0 spots total
OK let's try something different. Fetch this SRA file from here (is a very small sample around 200 MB) and run the fastq-dump again.
It may be that your SRA file is corrupted and you will need to re-download them.
Ok it worked for this file :) Thanks!
mkosinski@mkosinski-E540:~$ fastq-dump.2.1.7 ~/WCO/Kasia/SRR000021.sra
Written 304922 spots for /home/mkosinski/WCO/Kasia/SRR000021.sra
Written 304922 spots total
Even I faced the similar issue. For a quick fix I wrote a python script that downloads any sra file and then it converts it to fastq format.
Here is the link
If you need sra file only, check this out. http://sradownloader.herokuapp.com/
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Hi Marcin,
I'm definitely not an expert but it seems to be a path execution error. Either you put the executable into your path environment variable PATH either you need to run it from the directory you've saved the executable (fastq_dump).
I may be wrong though!
Oh suure, it might be the problem :P
Yeah but when I run
fastq-dump.2.1.7 -versionit looks to workHmmm. Maybe you have two installations of the sratoolkit in your platform. You installed it from source?