Hi all
I am trying to retrieve nucleotide ranges from a BLAST database using blastdbcmd with the -entry_batch option. According to the user manual, blastdbcmd can work with input ranges (in "start-end" format) as well as with strand ("plus/minus"). The query file looks like this:
comp185406_c0_seq1 1374-1472
comp185740_c0_seq1 405-506
When I run blastdbcmd I get the following error:
Error: comp185406_c0_seq1 1374-1472: OID not found
Error: comp185740_c0_seq1 405-506: OID not found
I don't get the error if I use only the sequence IDs and not with nucleotide ranges. I have tried adding "-entry" and "-range" to the input file but this does not help.
Any suggestions? I am doing this on a windows machine using blast 2.2.25+
Thanks
Daniel
I am trying to retrieve nucleotide ranges from a BLAST database using blastdbcmd with the -entry_batch option. According to the user manual, blastdbcmd can work with input ranges (in "start-end" format) as well as with strand ("plus/minus"). The query file looks like this:
comp185406_c0_seq1 1374-1472
comp185740_c0_seq1 405-506
When I run blastdbcmd I get the following error:
Error: comp185406_c0_seq1 1374-1472: OID not found
Error: comp185740_c0_seq1 405-506: OID not found
I don't get the error if I use only the sequence IDs and not with nucleotide ranges. I have tried adding "-entry" and "-range" to the input file but this does not help.
Any suggestions? I am doing this on a windows machine using blast 2.2.25+
Thanks
Daniel
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