Fatal error when writing weights file

[drdna]

The twisst run appears to be completing but then fails when it tries to write the outfile:

Traceback (most recent call last): File "twisst.py", line 690, in for x in range(nTopos): weightsFile.write("#topo" + str(x+1) + " " + topos[x].write(format = 9) + "\n") File "/home/farman/anaconda_ete/lib/python3.6/gzip.py", line 260, in write data = memoryview(data) TypeError: memoryview: a bytes-like object is required, not 'str'

[simonhmartin]

Are you running with python 3? Twisst is currently written only for python 2.

[drdna]

Hi Simon,

Thanks for you response. I thought it was running in python2 but when I checked it was still under python3. Having problems with python2 now - segmentation fault - will try and troubleshoot.

Mark

On Sep 12, 2018, at 6:38 PM, Simon martin notifications@github.com<mailto:notifications@github.com> wrote:

Are you running with python 3? Twisst is currently written only for python 2.

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Mark L. Farman Professor, Department of Plant Pathology Associate Director, UK-Healthcare Genomics 225 Plant Science Building 1405 Veteran's Dr. University of Kentucky Lexington, KY 40546 USA tel: (859) 218-0728 fax: (859) 323-1961

[drdna]

Hi Simon,

As a follow-up to my previous email, I was wondering of you had any thoughts on why twisst was failing to produce any output for several tree topologies at taxa values of 6, 7 and 8?

Cheers,

Mark

Mark L. Farman Professor, Department of Plant Pathology Associate Director, UK-Healthcare Genomics 225 Plant Science Building 1405 Veteran's Dr. University of Kentucky Lexington, KY 40546 USA tel: (859) 218-0728 fax: (859) 323-1961

[simonhmartin]

Hi Mark, Can you expand on what you mean by "failing to produce any output for several tree topologies"? Is there no output file? or is it missing columns? I have never tried to use Twisst for 8 taxa, because the output file should have 135135 columns! In theory it is possible to specify just the topologies you are interested in as additional input file, but that feature is untested. -Simon

[drdna]

Hi Simon,

OK, in doing some “troubleshooting, it appears that it was an issue with the Linux environment running on the supercomputer I am using. I don’t normally use this machine but decided to try it for the twisst runs. For some reason, when I use cat, less, more, tail, etc. to view the output files, it only displays a fraction of the weights columns that are in the output file. However, when I download to my local machine, or awk the fields in the last line of data, everything is present in the file. Not sure what’s happening but it's very strange because it’s only the weights line has this problem.

Sorry for troubling you with this.

Mark

On Sep 26, 2018, at 5:04 AM, Simon martin notifications@github.com<mailto:notifications@github.com> wrote:

Hi Mark, Can you expand on what you mean by "failing to produce any output for several tree topologies"? Is there no output file? or is it missing columns? I have never tried to use Twisst for 8 taxa, because the output file should have 135135 columns! In theory it is possible to specify just the topologies you are interested in as additional input file, but that feature is untested. -Simon

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Mark L. Farman Professor, Department of Plant Pathology Associate Director, UK-Healthcare Genomics 225 Plant Science Building 1405 Veteran's Dr. University of Kentucky Lexington, KY 40546 USA tel: (859) 218-0728 fax: (859) 323-1961