[mira_talk] Re: MIRA error
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 27 May 2015 23:40:29 +0200
On 27 May 2015, at 21:27 , David Sannino <drs357@xxxxxxxxxxx> wrote:
This is my manifest file if that helps:
It does.
parameters = COMMON_SETTINGS -GE:not=0 -AS:nop=4,sd=on,bts=3600 -CL:asjdc=on
-HS:nrr=100,mnr=yes -SB:sbuip=2 -NW:cmrnl=warn,acv=105 \
-SB:buip has no effect in de-novo assemblies, only in mappings.
SOLEXA_SETTINGS -AS:mrpc=10 -CO:msr=on,msrme=0 -CL:bsqc=on
-AL:bip=100,egp=yes -CO:mgqrt=25 \
-CO:msr:msrme have no effect in de-novo assemblies, only in mappings.
-AL:bip=100 effectively transforms the banded Smith-Waterman for alignments
into a full matrix computation SW. I suspect this only increases run-time but
does not lead to better quality. Maybe something less drastic? 30 or so should
be ample enough. Or stay with the default.
For Illumina, I think that -CL:bsqc=on is a pretty bad idea. For reference: I
never ever at all switch it on in my assemblies.
SANGER_SETTINGS -AS:mrpc=2 -DP:ure=on -CL:pvlc=on,qc=on,bsqc=on -CL:bsqc=on
-AL:bip=100,egp=yes -CO:mgqrt=25 \
PCBIOHQ_SETTINGS -AS:mrpc=5 -CL:pec=on -CL:bsqc=on -AL:bip=100,egp=yes
-CO:mgqrt=25
Ouch. Here, -AL:bip=100 will hurt … a lot (as these reads are quite a deal
longer than short Illuminas). Remember that runtime of a full Smith-Waterman is
quadratic to the length of the sequences involved.
Furthermore, if I’m not totally mistaken, I think I changed the algorithms of
MIRA to detect when it runs into a band limit during SW and automatically redo
the computation in those cases. Need to check and eventually update the docs on
this.
I suggest leaving -AL:bip as it is set by default.
B.
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