[mira_talk] Re: condensed log file
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 3 Mar 2012 00:36:11 +0100
On Mar 2, 2012, at 10:28 , Marcus Claesson wrote:
> I ran a Sourceforge binary of mira-3.4.0.1 with these parameters:
I see your point. Short answer: no, there is currently no way to reduce that
output. Most of it is indeed pretty boring for users who just want their stuff
assembled, but in case there is a problem or some kind of unexpected behaviour,
it helps me to at least get an idea of what is going on. This is somewhat vital
for larger assemblies where I cannot ask people to constantly rerun things for
2 weeks on their computers.
I'm sorry, but for projects like yours, you will have to live with logs of >=
1GiB. But then again, what's a GiB disk space anyway.
In case you wonder: there is a way to make the log even more verbose, I'd guess
around 200 to 300x larger, but it involves recompiling and I do have the
feeling that this is quite opposite of what you wanted :-)
> I had another case with an even bigger log file due to solexa file names
> being too long.
> I now know how to avoid that using -MI:somrnl=0 but there was an error
> message for every solexa read...
Hrm ... I think that this could be remedied, perhaps have MIRA report just the
first 1000 names which are too long. Or something like that. Could ease the
pressure a bit. I'm puttinhg that on my TODO (but no promises).
I couldn't help but quickly scan through the rest of the log, noticing a couple
of things:
1) you're doing an assembly with unpaired 454 and unpaired Illumina, is that
correct?
2) where did you get those ~200bp Illuminas from? By the look of the
statistics, they must be pretty good in quality ... clipped only some 4% of the
total bases and that's not worse than the 100bp reads I have seen so far.
B.
PS: and would you like to test drive the current development version with your
data set to comment on whether you think it's better or worse?
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