Issue with SRA to FASTQ Conversion

[Arupsss]

I have downloaded a SRA file from here. Now, I want to convert it into Fastq format.

So, what I did is following,

1) Download SRA Toolkit from here. (MS Windows 64 bit architecture - as I am using windows 7 64 bit)

2) Put SRA file on "sratoolkit.2.1.10-win64\bin"

3) Run command "fastq-dump SRR493095.sra"

However, I can't understand why it is giving error ?

Error is given here.

Can anybody help me why is this happening ?

[GenoMax]

Did you look at the ncbi_error_report.xml file?
If you can't find anything obvious can you post the contents of that file?

[Arupsss]

Did you look at the ncbi_error_report.xml file?
If you can't find anything obvious can you post the contents of that file?

I have uploaded it in http://pastebin.ca/2162892 .

[Richard Finney]

Look here:

http://www.umanitoba.ca/afs/plant_science/psgendb/local/pkg/gbench-2.4.5/src/sra/sdk/libs/kdb/kdb.c

The error " <Result rc="RC(rcDB,rcMgr,rcOpening,rcPath,rcIncorrect)"/>" (from your pastebin at http://pastebin.ca/2162892 ) output appears to be generated by this code :

case kptFile:
case kptFile | kptAlias:
rc = KDirectoryOpenSraArchiveRead_silent ( dir, &ldir, false, path );
if ( rc != 0 )
rc = KDirectoryOpenTarArchiveRead_silent ( dir, &ldir, false, path );
if ( rc == 0 )
{
/* recheck this newly opened directory for KDB/KFS type */
type = KDBPathType ( ldir, "." );

/* it its not the KDB type we wanted fail */
if (( type != pathtype ) && (type != (pathtype | kptAlias )))
{
KDirectoryRelease (ldir);
ldir = NULL;
rc = RC ( rcDB, rcMgr, rcOpening, rcPath, rcIncorrect );
}
}
else if ( rc != 0 )
{
rc = RC ( rcDB, rcMgr, rcOpening, rcPath, rcIncorrect );
}
break;
}


Hmmm ...
I'd suggest specifying the full path to the SRA data file.

[GenoMax]

I think you need to run the command like below. I just verified that it works.

fastq-dump ./SRR493095.sra (if the file is in the same directory), otherwise provide full path to where your file is located.

[Arupsss]

I think you need to run the command like below. I just verified that it works.

fastq-dump ./SRR493095.sra (if the file is in the same directory), otherwise provide full path to where your file is located.

I tried with full path also giving the same error. However, is there any way to download fastq format file for 150 bps reads ?

[Arupsss]

Look here:

http://www.umanitoba.ca/afs/plant_science/psgendb/local/pkg/gbench-2.4.5/src/sra/sdk/libs/kdb/kdb.c

The error " <Result rc="RC(rcDB,rcMgr,rcOpening,rcPath,rcIncorrect)"/>" (from your pastebin at http://pastebin.ca/2162892 ) output appears to be generated by this code :

case kptFile:
case kptFile | kptAlias:
rc = KDirectoryOpenSraArchiveRead_silent ( dir, &ldir, false, path );
if ( rc != 0 )
rc = KDirectoryOpenTarArchiveRead_silent ( dir, &ldir, false, path );
if ( rc == 0 )
{
/* recheck this newly opened directory for KDB/KFS type */
type = KDBPathType ( ldir, "." );

/* it its not the KDB type we wanted fail */
if (( type != pathtype ) && (type != (pathtype | kptAlias )))
{
KDirectoryRelease (ldir);
ldir = NULL;
rc = RC ( rcDB, rcMgr, rcOpening, rcPath, rcIncorrect );
}
}
else if ( rc != 0 )
{
rc = RC ( rcDB, rcMgr, rcOpening, rcPath, rcIncorrect );
}
break;
}


Hmmm ...
I'd suggest specifying the full path to the SRA data file.

I tried with full path also giving the same error. However, is there any way to convert .sra to fastq format ?

[GenoMax]

I am not sure what to tell you. I am able to run the command and get the fastq file without any problem from that exact .sra file.

Try re-downloading the .sra file (in case it somehow got corruputed during the donwload).

[Richard Finney]

fastq-dump should work
If it's SOLID data, I recommend abi-dump (I've had better luck with it).

Looking at your pastebin, I think you need the full path to your executable "fastq-dump".

<Binary path="/c/sratoolkit.2.1.10-win64/bin/fastq-dump" type="not found"/>


Try putting an ".exe" file name extension if that is in the real name of the file.

[Arupsss]

Thanks a lot. I am trying to start from first. Another point is that after your previous days help, I get stuck on this and this. Can you help me about those ? BTW thanks a lot for your kind help.

[Arupsss]

Thanks a lot. However, one question is,

is it enough to just download Sra Toolkit and run the above command ? Is any other step required for windows 7 61 bit ?

[Arupsss]

I am not sure what to tell you. I am able to run the command and get the fastq file without any problem from that exact .sra file.

Try re-downloading the .sra file (in case it somehow got corruputed during the donwload).

Thanks a lot GenoMax. You are right. I started from the first. Download everything again. And works nicely. Thanks.

[GenoMax]

I have answered the questions you posted here in the respective threads.

I get stuck on this and this. Can you help me about those ?