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?
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?
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