When blastn finds query matches on the minus strand of the searched sequence, this leads to a malformed -range option when calling blastdbcmd. The -range option of blastdbcmd requires that the start value be less than the end value. In the case where the match is on the (-)strand, blastn outputs the start value as greater than the end value. No error message is generated when this format is passed to blastdbcmd in a batch file, but the -range option is ignored and the match sequence is not trimmed. The result is the entire sequence of the match is written to the .hitdb.fsa file.
When blastn finds query matches on the minus strand of the searched sequence, this leads to a malformed -range option when calling blastdbcmd. The -range option of blastdbcmd requires that the start value be less than the end value. In the case where the match is on the (-)strand, blastn outputs the start value as greater than the end value. No error message is generated when this format is passed to blastdbcmd in a batch file, but the -range option is ignored and the match sequence is not trimmed. The result is the entire sequence of the match is written to the .hitdb.fsa file.