Make.contigs is not creating Group file

I am using Mothur v 1.48 and make.contigs does not create a .groups file when using decompressed fastq files as input. Because of this I am getting several different errors.
Could you please help me with this?

Hi -

1.48 generates a count_file in make.contigs and no longer generates a groups or names file unless explicitly needed for some reason. The updated workflow can be seen in the MiSeq SOP


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