A couple of small things have been bugging me about mothur. None have been serious enough to warrant having their own thread, but I think they’ve just about achieved critical mass for posting. Some are new to Mothur 12. Some have been around for a while.
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Get.oturep leaves *.names.temp files under Windows version 12. No biggie. We just delete them.
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This sequence of commands will always crash mothur (linux or windows)):
read.otu(list=some.list,group=some.groups)
venn(calc=sobs-chao)
#error message thrown
venn(calc=sharedsobs-sharedchao)
Somehow, the error message (trying to calculate single mode estimators while in shared mode) leaves the system volatile so when the correct command is keyed in, it crashes. Again no biggie. Restart mothur and continue where you left off.
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Classify.seqs should append the method used to the output file names. That way, you won’t accidentally clobber your output if you use different methods for, say, phylotype analysis and classifying otu. But then, mothur should never ever ever clobber files without asking the user’s permission anyway…
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Similarly for Venn diagram output. The group names should be appended to the output file names so as to mitigate mothur’s clobbermania.
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The read.tree command needs a name= option. This will decrease the size of my mothur log file by 1/2 as there wont be any
“XXX is in your groupfile and not in your tree. It will be disregarded.” messages in it. -
Classify.otu doesn’t really seem to “get” the name option. Or at least, not completely. Or else it wouldn’t fill the other 1/2 of my log file with: “XXX is not in your taxonomy file. I will not include it in the consensus.”
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get.sharedseqs should take a shared= option. Not that it takes that long to recalculate the shared data from the list and group files, but if the shared file exists anyway, why not use it? Less typing AND it makes for a more consistent user experience.
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Mothur will switch into single-mode after a shared analysis. Try this:
read.otu(list=some.list,group=some.groups)
collect.single()
will pump out individual collector curves for EACH of your groups. But then type:
rarefaction.single()
and mothur will generate the rarefaction curve for ONLY the last group. But wait! Now do this:
read.otu(list=some.list,group=some.groups)
rarefaction.single()
and mothur will generate the rarefaction curves for EACH of your groups. But then type:
collect.single()
and mothur will generate the collector curves for ONLY the last of your groups. Funky, no?
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On the Windows version of Mothur 12, the confidence interval code for shared analysis is incomplete. It works fine for the Linux version. This wouldn’t be a huge deal except that Mothur creates 12 columns of header information and only 4 columns of actual numbers… which borks my R scripts for generating plots. Temporary fixes: a) fix my R code b) delete the heading info c) use an older version of mothur d) use the Linux version or e) wait for the next version of mothur.
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Some of these things would be almost as fast for me to fix as they are to whine about. Casual contributions to coding mothur would be greatly facilitated by setting up either a SVN or CVS system.
Congrats on getting mothur this far. I’m only hard on ya coz I love ya
Robin