Question: sra toolkit error: path incorrect while opening manager within database module
0
gravatar for MarcinKosinski
2.8 years ago by
Poland
MarcinKosinski10 wrote:

I am using [SRA Toolkit](http://www.ncbi.nlm.nih.gov/books/NBK158900/) to convert `.sra` files to `fastq` files but when I am trying to use `fastq-dump` procedure there occures 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

 

sratoolkit fastq sra • 3.1k views
ADD COMMENTlink modified 18 months ago by sourabhdattawad0 • written 2.8 years ago by MarcinKosinski10
1
gravatar for Vagelis Ladas
2.8 years ago by
UK, Leicester, University of Leicester
Vagelis Ladas40 wrote:

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!

ADD COMMENTlink written 2.8 years ago by Vagelis Ladas40

Oh suure, it might be the problem :P

ADD REPLYlink written 2.8 years ago by MarcinKosinski10

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

ADD REPLYlink written 2.8 years ago by MarcinKosinski10
1

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

ADD REPLYlink written 2.8 years ago by Vagelis Ladas40
1
gravatar for Vagelis Ladas
2.8 years ago by
UK, Leicester, University of Leicester
Vagelis Ladas40 wrote:

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>

ADD COMMENTlink written 2.8 years ago by Vagelis Ladas40

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

ADD REPLYlink written 2.8 years ago by MarcinKosinski10

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

 


 

ADD REPLYlink written 2.8 years ago by MarcinKosinski10
1

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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Vagelis Ladas40

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

ADD REPLYlink written 2.8 years ago by MarcinKosinski10
0
gravatar for sourabhdattawad
18 months ago by
sourabhdattawad0 wrote:

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/

ADD COMMENTlink written 18 months ago by sourabhdattawad0
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