27 September 2013

Aphaenogaster, mason, Trinity, velvet, oases, and khmer

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Week Notes 23-27 September


Working on accepted revisions to final Medicago manuscript.

Gotelli/Brody lab meeting


Corrie Moreau

  • ant macroevolution
  • gut microbiota


Had to restart mason job for velvet assembly - crashed due to inadequate memory. Rather than restart entire oases_pipeline.py script, hand-coded each step and started at velvetg.


Karhunen, M., Merilä, J., Leinonen, T., Cano, J.M. & Ovaskainen, O. (2013). driftsel: an R package for detecting signals of natural selection in quantitative traits. Molecular Ecology Resources, 13, 746–754. Retrieved September 23, 2013,

  • discussed as similar approach to the Bergman and Coop method for evaluating selection on quantitative traits on Haldane’s Sieve

McIntire, E.J.B. & Fajardo, A. (2013). Facilitation as a ubiquitous driver of biodiversity. New Phytologist, n/a–n/a.

  • interesting review greatly supporting ideas I had in my Ecology paper, sadly not cited…

Russell, J.A., Moreau, C.S., Goldman-Huertas, B., Fujiwara, M., Lohman, D.J. & Pierce, N.E. (2009). Bacterial gut symbionts are tightly linked with the evolution of herbivory in ants. Proceedings of the National Academy of Sciences, 106, 21236–21241.

  • research from Corrie Moreau’s seminar



Even on mason with 120gb vmem, velvetg seems to be crapping out…

Running smaller test analyses at single kmer.

Re-working velvet assembly with diginorm, followed by flash on antlab.

digital normalization

Already cloned khmer repository, but wanted to update to the bleeding edge branch. To do this run

git checkout --track origin/bleeding-edge

and then

git status

to check that now on bleeding-edge branch and future pull will bring in updates.


For this section

We can combine the orphaned reads into a single file:

for i in *.se.qc.fq.gz.keep.abundfilt
   pe_orphans=$(basename $i .se.qc.fq.gz.keep.abundfilt).pe.qc.fq.gz.keep.abundfilt.se
   newfile=$(basename $i .se.qc.fq.gz.keep.abundfilt).se.qc.keep.abundfilt.fq.gz
   cat $i $pe_orphans | gzip -c > $newfile

error in cat that $pe_orphans did not exist. solved by adding touch $pe_orphans after creating

Though…ended up not needing it as I only had paired-end reads. So it goes.



velvet, even with 120GB, seems to have inadequate memory on mason. not sure why as velvet memory calculator says that 70GB RAM should be adequate

wrote script to perform assembly using Trinity

RNAseq tutorial on (Bioconductor)[http://www.bioconductor.org/packages/2.12/data/experiment/html/RnaSeqTutorial.html]


Installed Trinity following these instructions

curl -L http://sourceforge.net/projects/trinityrnaseq/files/latest/download?source=files > trinity.tar.gz
tar xzf trinity.tar.gz
cd trinityrnaseq*

Behavioral adaptation to thermal stress

Started new undergrad on new project examining behavioral adaptation to thermal stress. As we couldn’t find fresh Aphaenogaster, using Pogo.


Thomas, M.A., Roemer, G.W., Donlan, C.J., Dickson, B.G., Matocq, M. & Malaney, J. (2013). Ecology: Gene tweaking for conservation. Nature, 501, 485–486.

  • incredible salesmanship. absolutely no reason to think that single-gene “tweaking” will prevent any species extinction.


Some useful resources for mapping in R

Geneland: Guillot, G., Renaud, S., Ledevin, R., Michaux, J. & Claude, J. (2012). A Unifying Model for the Analysis of Phenotypic, Genetic and Geographic Data. Systematic Biology, sys038.

marmap: Pante, E. & Simon-Bouhet, B. (2013). marmap: A Package for Importing, Plotting and Analyzing Bathymetric and Topographic Data in R. PLoS ONE, 8, e73051.

rangemapper: http://rangemapper.orn.mpg.de/



Meet with Nicole to go over validating DNA extraction

Uploaded protocol for DNA extraction to climate-cascade repository


Added protocols to climate-cascade repository. Write in markdown format, but nice to have pdf. With help found how to change some of the defaul compilation options in pandoc to pdf, specifically to have smaller margins. Also change pdf compiler to xelatex to allow unicode symbols.

pandoc file. -o file.pdf --latex-engine=xelatex -H margins.sty

Wrote stupidly simple bash script that will compile all markdown files to pdf with these options…in repository.


Final revisions to MEE manuscript…


Ostrom et al (1997) Establishing pathways of energy flow for insect predators using stable isotope ratios: field and laboratory evidence. Oecologia 109: 108-113.

  • for discussion with KM



Received shipment of colonies from NCSU. Total massacre - colonies were shipped with watertubes but not packed tightly and the water tubes drowned and crushed the colonies. Only 11 of 37 survived.


Neither trinity or velvet-oases jobs on mason successful…good think that the diginorm strategy works.

climate-cascade meeting

Discussed stable isotopes

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