Help with FastTree - getting a blank tree file

Question

[catiewilliams31]

Hello,

I've aligned my 16S rRNA (originally from Illumina sequencing) data using PyNAST, and have been trying to make a tree using FastTree out of the resultant .fasta file. I correctly installed FastTree as described online, and am using a Mac.

When typing in the following code however, I get an error message (also below) and a 0 bytes, blank text file output. Does anyone know what I'm doing wrong?

edi54-93:pynast_aligned catiewilliams$ ./FastTree -gtr -nt Chem6_aligned.fasta > tree_file
-bash: ./FastTree: No such file or directory

Thanks!

[catiewilliams31]

I should mention using ./FastTree was the advice of someone from FastTree - I also tried "FastTree -gtr ..." and again got a blank text file (but with no error message this time)

[5heikki]

You have to issue the ./FastTree command in the dir where you have the FastTree executable file. Alternatively, you can add it to your $PATH by editing ~/.bash_profile

tl:dr, you did not install FastTree correctly.

[catiewilliams31]

Ahh yes, just realised my dir was wrong. Retried it using the correct directory but have still only got a blank text file. Tried re-downloading and reinstalling FastTree but this has still not fixed the issue.

[5heikki]

When you issued the command from the FastTree dir, did you give a correct path to the input file, i.e. ./FastTree -gtr -nt /where/is/this/file/Chem6_aligned.fasta > tree_file instead of ./FastTree -gtr -nt Chem6_aligned.fasta > tree_file

Answer 1

[Daniel]

You don't have FastTree installed where you think it is from the look of it. Ignore the rest of the line, just type ./fasttree. If you get anything other than what is bellow, you're not in the right directory to run the program. If that is the case, then try opening up the directory where you have fasttree 'installed' and get the FULL path. You can do this by typing pwd and use that instead of the '.' at the beginning, or if you're in graphical, right click and look for the details.

Expected output of typing fasttree or ./fasttree (if you're in the right directory):

sbi6dap@assembler:~$ fasttree 
Usage for FastTree version 2.1.3 SSE3:
  FastTree protein_alignment > tree
  FastTree -nt nucleotide_alignment > tree
  FastTree -nt -gtr < nucleotide_alignment > tree
FastTree accepts alignments in fasta or phylip interleaved formats

Common options (must be before the alignment file):
  -quiet to suppress reporting information
  -nopr to suppress progress indicator
  -log logfile -- save intermediate trees, settings, and model details
  -fastest -- speed up the neighbor joining phase & reduce memory usage
        (recommended for >50,000 sequences)
  -n <number> to analyze multiple alignments (phylip format only)
        (use for global bootstrap, with seqboot and CompareToBootstrap.pl)
  -nosupport to not compute support values
  -intree newick_file to set the starting tree(s)
  -intree1 newick_file to use this starting tree for all the alignments
        (for faster global bootstrap on huge alignments)
  -pseudo to use pseudocounts (recommended for highly gapped sequences)
  -gtr -- generalized time-reversible model (nucleotide alignments only)
  -noml to turn off maximum-likelihood
  -nome to turn off minimum-evolution NNIs and SPRs
        (recommended if running additional ML NNIs with -intree)
  -nome -mllen with -intree to optimize branch lengths for a fixed topology
  -cat # to specify the number of rate categories of sites (default 20)
      or -nocat to use constant rates
  -gamma -- after optimizing the tree under the CAT approximation,
      rescale the lengths to optimize the Gamma20 likelihood
  -constraints constraintAlignment to constrain the topology search
       constraintAlignment should have 1s or 0s to indicates splits
  -expert -- see more options
For more information, see http://www.microbesonline.org/fasttree/