sra toolkit error: path incorrect while opening manager within database module

Question

[MarcinKosinski]

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

[Vagelis Ladas]

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!

[MarcinKosinski]

Oh suure, it might be the problem :P

[MarcinKosinski]

Yeah but when I run fastq-dump.2.1.7 -version it looks to work

[Vagelis Ladas]

Hmmm. Maybe you have two installations of the sratoolkit in your platform. You installed it from source?

Answer 1

[Vagelis Ladas]

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>

[MarcinKosinski]

I used sudo apt-get install sra-toolkit to install this kit. How should I know where is my exutable dir :)?

[MarcinKosinski]

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

[Vagelis Ladas]

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.

[MarcinKosinski]

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

Answer 2

[sourabhdattawad]

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/