problems with SRA Toolkit setup for csra

[Wallysb01]

I'm trying to set up the newest SRA toolkit to be able to deal with these new csra files, but I can't seem to get the configuration-assistant.perl script to work correctly. It appears I don't have the scheme files loaded or installed?

I simply uncompressed the Mac 64 bit binaries and run the configuration-assistant script and get the following:

==========================================
The SRA toolkit documentation page is
http://www.ncbi.nlm.nih.gov/Traces/sra/std
==========================================

checking for vdb-config (local build)... no
checking for vdb-config (./vdb-config: found)... yes
checking configuration files... '/Users/Walter/.ncbi/ncbi-config.kfg
/Users/Walter/Bioinformatics/Tools/sratoolkit.2.1.10-mac64/bin/ncbi/config.kfg
/Users/Walter/Bioinformatics/Tools/sratoolkit.2.1.10-mac64/bin/ncbi/vdb-copy.kfg'
checking refseq configuration... paths=/Users/Walter/ncbi/refseq
checking /Users/Walter/ncbi/refseq... ok
checking /Users/Walter/ncbi/refseq for invalid empty reference files... none found
checking krypto configuration... pwfile=/Users/Walter/.ncbi/.vdbpass
Do you want to update VDB password? [y/N] Y
checking for vdb-passwd (local build)... no
checking for vdb-passwd (./vdb-passwd: found)... yes
Changing password
New password:
Retype new password:
password updated ok
checking schema configuration... not found
--------------------------------------
WARNING: SCHEMA FILES CANNOT BE FOUND.
IT COULD CAUSE LOADERS TO FAIL.
--------------------------------------

Does anyone have a suggestion, this seems new and under documented.

[srasdk]

This is a warning - it will not affect you since you will use dumpers (fastq-dump, etc...), not loaders

[xhyuo]

This is a warning - it will not affect you since you will use dumpers (fastq-dump, etc...), not loaders

Hi, i have a question when i used SRA.

First, it worked well in Windows system as i used fastq-dump on the .csra file to generate the .fastq file. But such things were not happened in the Linux system.
And i want to use sam-dump. However, every time it said that "sam-dump has stopped working" in the windows system.

How you ever met that problem before?

[srasdk]

No. "stop working" may mean the program is crushing. What SRR accession are you looking at?

Did you try contact SRA help desk?
go to SRA home page:

http://www.ncbi.nlm.nih.gov/Traces/sra/

and click "Write to help desk" in the lower right corner

[xhyuo]

No. "stop working" may mean the program is crushing. What SRR accession are you looking at?

Did you try contact SRA help desk?
go to SRA home page:

http://www.ncbi.nlm.nih.gov/Traces/sra/

and click "Write to help desk" in the lower right corner

Thank you for your reply!

Now it works. I've already sam-dump the .csra file and then transferred it into .bam file.

One question occurred to me that since the raw data i got .csra file is documented as paired-end. It should be two files per sample. Am i right?
Are there any problems in the .bam file i got?

Thanks!