ncbi error C++ exception
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Entering edit mode
6.9 years ago
bitpir ▴ 240

Hi there, I encounter this problem when I tried to run rpsblast:

/ncbi-blast-2.6.0+/bin/rpsblast -query /data/1400_to_4999_combined_protein_id_ac -db Pfam -out /data/rpsout

Warning: [rpsblast] Error initializing remote BLAST database data loader: Protein BLAST database 'Pfam nr' does not exist in the NCBI servers
Error: NCBI C++ Exception:
    T0 "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_350334_130.14.22.10_9008__PrepareRelease_Linux64-Centos_1481139955/c++/compilers/unix/../../src/objmgr/data_source.cpp", line 359: Error: ncbi::objects::CDataSource::x_Map() - CDataSource::x_Map(): object already mapped: N4ncbi7objects10CSeq_annotE obj: 0x4d2a610 N4ncbi7objects15CSeq_annot_InfoE info: 0x4e90ad0 was: 0x4c9e790

Does anyone know what this means? Thanks!

blast ncbi • 7.8k views
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1400_to_4999_combined_protein_id_ac is a fasta fle or a file with GIs / accessions? If it is an accession numbers file, the problem is probably the same described here: Q: do blast search using gi numbers

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2
Entering edit mode
6.9 years ago

Could it have anything to do with

Protein BLAST database 'Pfam nr' does not exist in the NCBI servers

Try using a database that exists and see if the error persists.

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2
Entering edit mode
6.9 years ago
bitpir ▴ 240

Thank you for your responses! I think I figured out the error. This happens when there's duplicate queries in the file (1400_to_4999_combined_protein_id_ac, which contains gi numbers). If I sort and output the unique gi numbers, the C++ error went away. The error "Protein BLAST database 'Pfam nr' does not exist in the NCBI servers" still exists, but rpsblast still runs and outputs the search results! I think that error is printed by default. Based on my correspondence with the NCBI's blast-helpdesk, blast-2.6.0+ still accepts gi numbers as queries, at least for rpsblast! Hope this is helpful for anyone who runs into the same problem as me!

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