I believe the problem is that you are using --hirep_good at the end of your
parameters line and it is overwriting your previous -AS:nop:rbl settings.
You may want to move this to the beginning of the line. Also, I don't think
-AS:nop:rbl=0 is what you want (unless you are just cleaning up reads and
not assembling). Try setting both to 1, or leave off the --hirep_good and
just use defaults.
On Wed, Oct 21, 2015 at 11:14 AM, Rhiannon Mondav <rhiannon.mondav@xxxxxxxxx
wrote:
Greetings
I receive an error message when attempting assembly using mapping option
using MIRA 4.0.2. Error message and Manifest file follow.
*error message*
You are running a mapping job with:
*
* -AS:nop=2
*
* -AS:rbl=2
*
*
*
* A mapping assembly with the above parameter(s) >1 will probably not
produce *
* what you expect. For haploid organisms or for simple SNP search in
*
* multiploid organisms, maybe you should rethink your choice.
*
* However, certain use cases do benefit from the parameters you have
chosen. *
* E.g., doing clean mappings of multiploid organisms. If you think you
want *
* this, please use the following parameter to let MIRA continue:
*
* -NW:cmpm=warn
*
* or
*
* -NW:cmpm=no
*manifest file*
#######################################
##### MIRA MAPPING ILLUMINA CONFIG FILE #####
#######################################
# basic instructions
project = mgm4440411.3_map
job = genome,mapping,accurate
# setting general parameters for assembly
parameters = COMMON_SETTINGS \
-GE:not=8:mps=64 \
-AS:sep=on:nop=0:rbl=0:sd=off \
-SB:tor=off \
-CL:ascdc=off \
-CO:mr=on \
-DI:trt=/scratch/ \
-NW:cnfs=stop:cdrn=stop:ctp=stop:cac=stop \
-OUT:orc=off \
SOLEXA_SETTINGS = -AS:epoq=off:mrl=30:ardml=100:mrpc=2 \
-SB:bnb=on -CO:mrpg=4 -OUT:sssip=on \
--hirep_good \
--noclipping
# defining input data
readgroup = singlereadsolexa
data = ../mgm4440411.3_frhit_rcrtd.fna
default_qual=30
technology = solexa
# defining reference template
readgroup
as_reference
data = ../../AAA028-C07.fna
----------------------------------------
Thanks in advance
Rhiannon
Rhiannon Mondav | Evolutionary Biology Centre, Uppsala University, Sweden
