Merging contigs: Minimus2 error

Question

[fiona.newberry]

I am using minimus2 to merge overlapping contigs to improve my assembly.

I am getting the following error from minimus2 in .runAmos.log

CONSTRUCTIONTIME /opt/software/conda_env/opt/mummer-3.23/mummer PHE_1_CDHIT.ntref 29.47
/opt/software/conda_env/opt/mummer-3.23/mummer: cannot open file "1.qry.seq" or file "1.qry.seq" is empty
ERROR: mummer and/or mgaps returned non-zero
!!! 2019-12-19 15:36:28  Command: /opt/software/conda_env/bin/nucmer -maxmatch -c 40 1.ref.seq PHE_1_CDHIT.qry.seq -p PHE_1_CDHIT exited with status: 1
!!! END - Elapsed time: 0d 0h 0m 37s

These are the output files it is making:

1.mgaps 
1.ref.seq
1.ntref
1.runAmos.log
1.qry.seq

And one directory:

1.bnk

Any help would be appreciated.