[Bioperl-l] Query about Hyphy wrapper module "SLAC.pm"

Albert Vilella avilella at gmail.com
Fri Dec 7 05:32:43 EST 2007

Hi Johan,

It would be great if you could upload an example reproducible case:


Maybe simply doing a tar.gz of the directory with the sample files and
the script, and a simple
explanation on how to run it. If you have any special "env" vars
regarding tmp files, could you
specify those as well?



On Dec 5, 2007 11:35 AM, Johan Nilsson <johan.nilsson at sh.se> wrote:
> Hello,
> I have a bunch of multiple sequence alignments of protein coding genes,
> which I would like to analyse with the SLAC method of the HyPhy package. I
> tried using the SLAC.pm module in bioperl-run, but I could not get it to
> work properly.
> Basically, for each MSA file, I create the Bio::Tree::Tree and
> Bio::SimpleAlign objects ($tree and $aln, respectively) required as
> arguments to SLAC, and call the method with: "($rc,$result) =
> $slac->run($aln,$tree)" in a loop procedure in my script.
> When I choose not to save the tmp files (the default option in SLAC.pm),
> the program complains that it cannot find the file
> "$whatevertmpdir/wrapper.bf", and returns $rc=0 for all but the first MSA
> (which works fine). Apparently, it looks for the wrapper.bf file in the
> first tmp dir created, which is deleted in the end of the first SLAC call.
> If instead I choose to save the tempfiles ($slac->save_tempfiles('TRUE')),
> all calls to SLAC give returncode 1, and no error message is received.
> However, when I look at the resulting $result hashref, it turns out that
> all results are for the FIRST alignment read. I've made sure there is
> nothing strange with my loop procedure, and I checked that the tree and
> alignment objects look OK for each MSA. Apparently, it does create new
> "results.tsv" files in the tmp directory after each run, but it is
> identical each time it's created. Also, it only creates ONE tmp directory,
> no matter how many times SLAC is executed (I would imagine it was supposed
> to save each result in separate tmp dirs?)
> Thus, it seems to me like the errors occur because something goes wrong in
> the creation of temporary files. Have I done something wrong here, or have
> any other of you experienced the same problem?
> Best regards
> /Johan
> --
> Johan Nilsson, Ph.D.
> School of Life Sciences
> Södertörns University College
> S-141 89 Huddinge, Sweden
> E-mail: johan.nilsson at sh.se
> Phone: +46 8 608 47 05, +46 70 456 10 51
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