magicblast errors using SRA

Question

[susan.klein]

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)

Answer 1

[susan.klein]

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.

:(