Question: magicblast errors using SRA
0
gravatar for susan.klein
2.5 years ago by
susan.klein50
Oceania
susan.klein50 wrote:

Hi,

anyone using magicblast to search SRAs ? I find that some SRAs work while others give errors like below. Also anyone know who to ask??

Thanks,

S.

searching SRR4484512 VDB: 2016-11-03T02:53:40 . err: query unauthorized while resolving tree within virtual file system module - failed to resolve accession 'SRR4484512' - Access denied - please request permission to access phs000424/GRU-IRB in dbGaP ( 403 ) Error: NCBI C++ Exception: T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_290577_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1471676586/c++/compilers/unix/../../src/sra/readers/sra/vdbread.cpp", line 485: Error: ncbi::objects::CVDB::CVDB() - Cannot open VDB: SRR4484512 (0x9be50398: directory not found while opening manager within virtual file system module)

searching SRR4485019 VDB: 2016-11-03T02:53:41 . err: query unauthorized while resolving tree within virtual file system module - failed to resolve accession 'SRR4485019' - Access denied - please request permission to access phs000424/GRU-IRB in dbGaP ( 403 ) Error: NCBI C++ Exception: T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_290577_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1471676586/c++/compilers/unix/../../src/sra/readers/sra/vdbread.cpp", line 485: Error: ncbi::objects::CVDB::CVDB() - Cannot open VDB: SRR4485019 (0x9be50398: directory not found while opening manager within virtual file system module)

searching SRR4486396 VDB: 2016-11-03T02:53:42 . err: query unauthorized while resolving tree within virtual file system module - failed to resolve accession 'SRR4486396' - Access denied - please request permission to access phs000424/GRU-IRB in dbGaP ( 403 ) Error: NCBI C++ Exception: T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_290577_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1471676586/c++/compilers/unix/../../src/sra/readers/sra/vdbread.cpp", line 485: Error: ncbi::objects::CVDB::CVDB() - Cannot open VDB: SRR4486396 (0x9be50398: directory not found while opening manager within virtual file system module)

searching SRR4474405 VDB: 2016-11-03T02:53:44 . err: query unauthorized while resolving tree within virtual file system module - failed to resolve accession 'SRR4474405' - Access denied - please request permission to access phs000424/GRU-IRB in dbGaP ( 403 ) Error: NCBI C++ Exception: T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_290577_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1471676586/c++/compilers/unix/../../src/sra/readers/sra/vdbread.cpp", line 485: Error: ncbi::objects::CVDB::CVDB() - Cannot open VDB: SRR4474405 (0x9be50398: directory not found while opening manager within virtual file system module)

searching SRR4447443 VDB: 2016-11-03T02:53:45 . err: query unauthorized while resolving tree within virtual file system module - failed to resolve accession 'SRR4447443' - Access denied - please request permission to access phs000668/HMB-IRB in dbGaP ( 403 ) Error: NCBI C++ Exception: T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_290577_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1471676586/c++/compilers/unix/../../src/sra/readers/sra/vdbread.cpp", line 485: Error: ncbi::objects::CVDB::CVDB() - Cannot open VDB: SRR4447443 (0x9be50398: directory not found while opening manager within virtual file system module)

blast • 1.1k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by susan.klein50
0
gravatar for susan.klein
2.5 years ago by
susan.klein50
Oceania
susan.klein50 wrote:

ah I worked it out - they are protected SRAs.. so if you are scripting against their full list of experiments, you have to filter them out.. or ignore the errors. Annoyingly the read data is deemed to contain individual person data so there's no way to get around it.

:(

ADD COMMENTlink written 2.5 years ago by susan.klein50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1505 users visited in the last hour