[martintay]

Input file "intree"

Hi Bas,

I just installed the stand alone version on my mac and have been trying to run it.
It seems that drawtree is looking for the input tree file "intree" which was not made.
Is there some configuration settings I missing for drawtree to allow it to accept cladogram.ph files?

Many thanks,
Martin

[dutilh]

Hi Bas,

I just installed the stand alone version on my mac and have been trying to run it.
It seems that drawtree is looking for the input tree file "intree" which was not made.
Is there some configuration settings I missing for drawtree to allow it to accept cladogram.ph files?

Many thanks,
Martin

Hi Martin,
The drawtree program is used to visualize the cladogram, taking a Phylip bracketnotation as input, and outputting a PNG image. It is called from within crAss (v1.2) with the following system call (with branch lengths):

echo -e "output.$size_correction.cladogram.ph\n$crAss_dir/fontfile\nV\nN\nL\nA\nD\nM\n0\n0\\nF\nHelvetica\nC\n0.5\nY\n" | $drawtree_exe

Something is probably going wrong with this system call. There are three variables, as indicated with the dollar sign (basic if you know some Perl...):
- $size_correction is either "minimum", "reads", "shot", or "wootters"
- $crAss_dir/fontfile is the location of the file "fontfile" that drawtree uses (it should be in the directory where the crAss.pl script is)
- $drawtree_exe is the location of the drawtree executable in your shell

By default, drawtree looks for a Phylip cladogram file called "infile", but as you can see above, the input file should be called "output.$size_correction.cladogram.ph". This means the location of the input file in the system call was not passed correctly, possibly as a result of different use of "echo" on a Mac.

As a solution, you could try running the drawtree command on your command line. Alternatively, and this may be the easiest solution, is not to use drawtree but another program to visualize the cladogram files (the four "output.$size_correction.cladogram.ph" files in the output directory). You could use any tree plotting program for this, such as FigTree, NJPlot, or the website http://itol.embl.de/ are just a few examples. Those programs take the bracketnotation in the *.ph files as input and show you a cladogram (tree) as output. This is all that drawtree does as well.

Good luck, let me know if/where you get stuck!
Bas

[martintay]

Hi Bas,

Thanks for the advice, it is indeed the echo command that was giving the problem.
I continued on manually and got what I needed.

Cheers,
Martin

[brettin]

Hi,

I would like to try crAss.pl out on a metagenome study.

Two treatments
Three time points
Three technical replicates per time point

I have a cross assembly of all the samples, though I do not have an ace file. The assembler that I used produces only a fasta file of assembled contigs.

I'm wondering how to use crass.pl properly on this study. Any guidance would be greatly appreciated. Thanks.

[dutilh]

Hi Brettin, the new version of crAss can also take a SAM file as input. This allows you to first make cross-contigs, and then do the read mapping back to those contigs for example with Bowtie2, which creates a SAM file which you could use as input. You can find the latest crAss version on SourceForge (https://sourceforge.net/projects/crass/). Best! Bas

Hi,

I would like to try crAss.pl out on a metagenome study.

Two treatments
Three time points
Three technical replicates per time point

I have a cross assembly of all the samples, though I do not have an ace file. The assembler that I used produces only a fasta file of assembled contigs.

I'm wondering how to use crass.pl properly on this study. Any guidance would be greatly appreciated. Thanks.