Compiling ncbi-blast itself appears to have gone fine. Where I have issues with is multi-partite blast databases. The error messages are worrying, but maybe it's not a big deal after all?
For instance:
Untarring iteratively, from 1->15 (tar zxvpf nt.$N.tar.gz, based on the example from NCBI's website, where tar zxvpf on a 16S microbial)
Followed by blastdbcheck
Edit: Though if I ignore the error message
Does this mean working as intended? (...and there is indeed a newer version of ncbi blast, 2.2.28+, now that I think about it). But strangely, nr (through the same workflow) gives me the following error message, even though both are extracted to the same path.
For instance:
Code:
update_blastdb.pl nt Connected to NCBI Downloading nt (16 volumes) ... Downloading nt.00.tar.gz... [OK] [...]
Code:
nt.nal nt.00.nhd nt.00.nhi ....
Code:
blastdbcheck -db nt Writing messages to <stdout> at verbosity (Summary) ISAM testing is ENABLED. Legacy testing is DISABLED. By default, testing 200 randomly sampled OIDs. Testing 16 volume(s). /data5/Programs/blast_db/nt.00 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.01 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.02 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.03 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.04 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.05 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.06 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.07 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.08 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.09 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.10 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.11 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.12 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.13 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.14 / MetaData: [ERROR] caught exception. /data5/Programs/blast_db/nt.15 / MetaData: [ERROR] caught exception. Result=FAILURE. 16 errors reported in 16 volume(s). Testing 1 alias(es). Result=SUCCESS. No errors reported for 1 alias(es). Total errors: 16
Code:
blastn -db nt BLASTN 2.2.27+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. Database: Nucleotide collection (nt) 20,064,200 sequences; 50,694,274,412 total letters BLAST engine error: Empty CBlastQueryVector
Code:
blastn -db nr BLAST Database error: No alias or index file found for nucleotide database [nr] in search path [/data5/Programs/blast_db:/Programs/blastdb::]
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