Error while clustering DNA sequences of genes

[Sidduppal]

I'm getting the following error when clustering DNA sequences of genes predicted using prodigal.

there must be an error: 4555074 deleted from 8264926 that now is empty, but not assigned to a cluster
there must be an error: 2084676 deleted from 4818957 that now is empty, but not assigned to a cluster
there must be an error: 1856143 deleted from 5943940 that now is empty, but not assigned to a cluster
there must be an error: 5296758 deleted from 711843 that now is empty, but not assigned to a cluster
there must be an error: 7150694 deleted from 6155612 that now is empty, but not assigned to a cluster
there must be an error: 8533816 deleted from 9452727 that now is empty, but not assigned to a cluster
there must be an error: 9521033 deleted from 8465434 that now is empty, but not assigned to a cluster
there must be an error: 2376789 deleted from 9427595 that now is empty, but not assigned to a cluster

I have attached the error and output file for your reference. Thanks!

mmseqs2.409914.out.txt mmseqs2.409914.err.txt