does anyone have used dbGAP data before? We downloaded a file from dbGAP which needs decryption tool from NCBI to open the data. But it was really a pain to decrypt the data, and I can't figure it out after playing with it for over 4 hours..... anyone can give me some guidance?
thanks!!
So when I run the command in the folder "SEQ_DATA", ## where the data directory and the tool directory are located:
./decryption.2.3.2-4/bin/configuration-assistant.perl
The output is below.
###############
cwd = '/Users/UserA/Desktop/SEQ_DATA'
checking for fastq-dump (local build)... no
checking for fastq-dump (decryption.2.3.2-4/bin/fastq-dump: not found)
checking for fastq-dump (decryption.2.3.2-4/bin/fastq-dump.exe: not found)
checking for fastq-dump (fastq-dump)... no
checking for sam-dump (local build)... no
checking for sam-dump (decryption.2.3.2-4/bin/sam-dump: not found)
checking for sam-dump (decryption.2.3.2-4/bin/sam-dump.exe: not found)
checking for sam-dump (sam-dump)... no
presuming to be run in decryption package
checking for vdb-config (local build)... no
checking for vdb-config (decryption.2.3.2-4/bin/vdb-config: found)... yes
Reading configuration
refseq/servers: not found
refseq/volumes: not found
refseq/paths: not found
repository: found
repository/site: not found
repository/remote: found
repository/remote/protected/CGI/resolver-cgi: 'http://www.ncbi.nlm.nih.gov/Traces/names/names.cgi'
repository/remote/main/NCBI/apps/refseq/volumes/refseq: 'refseq'
repository/remote/main/NCBI/apps/wgs/volumes/fuseWGS: 'wgs'
repository/remote/main/NCBI/apps/sra/volumes/fuse1000: 'sra-instant/reads/ByRun/sra'
repository/remote/main/NCBI/disabled: 'false'
repository/remote/main/NCBI/root: 'http://ftp-trace.ncbi.nlm.nih.gov/sra'
repository/user: found
repository/user/main/public/apps/refseq/volumes/refseq: 'refseq'
repository/user/main/public/root: '/Users/Jingjing/ncbi/public': does not exist
repository/user/main/public/cache-enabled: 'true'
repository/user/main/public/apps/sra/volumes/sraFlat: 'sra'
repository/user/main/public/apps/wgs/volumes/wgsFlat: 'wgs'
Configuration is correct
###################
The software even didn't ask for encryption password from us. Then when I run vdb-decrypt, I got the following msgs...
./decryption.2.3.2-4/bin/vdb-decrypt 12345(#project ID#)
2013-04-20T05:16:03 vdb-decrypt.2.3.2 err: file not found while opening encryption key within virtual file system module - unable to obtain a password
2013-04-20T05:16:03 vdb-decrypt.2.3.2: exiting: RC(rcVFS,rcEncryptionKey,rcOpening,rcFile,rcNotFound) (2665808984)
Do you know if we have still missed anything from dbGAP to decrypt the files?
Your kind help is highly appreciated.
thanks!!
So when I run the command in the folder "SEQ_DATA", ## where the data directory and the tool directory are located:
./decryption.2.3.2-4/bin/configuration-assistant.perl
The output is below.
###############
cwd = '/Users/UserA/Desktop/SEQ_DATA'
checking for fastq-dump (local build)... no
checking for fastq-dump (decryption.2.3.2-4/bin/fastq-dump: not found)
checking for fastq-dump (decryption.2.3.2-4/bin/fastq-dump.exe: not found)
checking for fastq-dump (fastq-dump)... no
checking for sam-dump (local build)... no
checking for sam-dump (decryption.2.3.2-4/bin/sam-dump: not found)
checking for sam-dump (decryption.2.3.2-4/bin/sam-dump.exe: not found)
checking for sam-dump (sam-dump)... no
presuming to be run in decryption package
checking for vdb-config (local build)... no
checking for vdb-config (decryption.2.3.2-4/bin/vdb-config: found)... yes
Reading configuration
refseq/servers: not found
refseq/volumes: not found
refseq/paths: not found
repository: found
repository/site: not found
repository/remote: found
repository/remote/protected/CGI/resolver-cgi: 'http://www.ncbi.nlm.nih.gov/Traces/names/names.cgi'
repository/remote/main/NCBI/apps/refseq/volumes/refseq: 'refseq'
repository/remote/main/NCBI/apps/wgs/volumes/fuseWGS: 'wgs'
repository/remote/main/NCBI/apps/sra/volumes/fuse1000: 'sra-instant/reads/ByRun/sra'
repository/remote/main/NCBI/disabled: 'false'
repository/remote/main/NCBI/root: 'http://ftp-trace.ncbi.nlm.nih.gov/sra'
repository/user: found
repository/user/main/public/apps/refseq/volumes/refseq: 'refseq'
repository/user/main/public/root: '/Users/Jingjing/ncbi/public': does not exist
repository/user/main/public/cache-enabled: 'true'
repository/user/main/public/apps/sra/volumes/sraFlat: 'sra'
repository/user/main/public/apps/wgs/volumes/wgsFlat: 'wgs'
Configuration is correct
###################
The software even didn't ask for encryption password from us. Then when I run vdb-decrypt, I got the following msgs...
./decryption.2.3.2-4/bin/vdb-decrypt 12345(#project ID#)
2013-04-20T05:16:03 vdb-decrypt.2.3.2 err: file not found while opening encryption key within virtual file system module - unable to obtain a password
2013-04-20T05:16:03 vdb-decrypt.2.3.2: exiting: RC(rcVFS,rcEncryptionKey,rcOpening,rcFile,rcNotFound) (2665808984)
Do you know if we have still missed anything from dbGAP to decrypt the files?
Your kind help is highly appreciated.
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