Running Minimus2 in reference vs query mode

[thakurshalabh]

Hello all,

I have recently started to use minimus2 for merging contigs from different assemblies. I followed the steps shown on its tutorial page and merged sequences from two assemblies say (S1.fasta with 28095 sequences) and (S2.fasta with 31623 sequences) together into one file S1-S2.seq. I was also able to run the toAmos command on S1-S2.seq and generate an S1-S2.afg file. However, when I run minimus2 on S1-S2.afg file using command "minimus2 S1-S2 -D REFCOUNT=28095"
the program exit at step 13 showing an error "nucmer -maxmatch -c 40 S1-S2.ref.seq S1-S2.qry.seq -p S1-S2 exited with status: 1".

On investigating the runAmos.log file I found that step 13 was to run dumpread program and create S1-S2.qry.seq file (as shown by log file below). But dumpread failed to write any sequence in S1-S2.qry.seq file which may have lead to above error.

!!! 2017-10-22 18:00:54 Doing step 13
!!! 2017-10-22 18:00:54 Running: dumpreads -m 28095 S1-S2.bnk > S1-S2.qry.seq
Objects seen: 94
Objects written: 0

I'm not sure what wrong is happening here. Because when REFCOUNT=0, the program runs perfectly fine. Can anyone suggest me how to fix this or what might be the cause of this error?

[gringer]

Should the refcount be the sum of the count of the two assemblies (i.e. 60528, not 28905)?

[thakurshalabh]

Thank you for your suggestion. But as per the instructions in the tutorial, the value of the REFCOUNT parameter should be equal to the number of sequences in the reference assembly which in this case is assembly S1.

http://amos.sourceforge.net/wiki/index.php/Minimus2

Also, I tried with different values for REFCOUNT (1, 10, 20, 25, ...) and it worked fine. So does that mean 28905 is too high for REFCOUNT? Then, how should I decide what value to choose?