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bglindner / CEE6720_BIO6720

Course exercises for CEE/BIO6720.
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PHYLIP Issue on local device #12

Open mwarner43 opened 7 months ago

mwarner43 commented 7 months ago

I am having some trouble with PHYLIP on my computer, what is the path to access it on PACE? I think it may be easier at this point just to transfer my files to and from the cluster. Thanks!

bglindner commented 7 months ago

Hey, thanks for posing this question. I have the path to executables for phylip in the lab documentation but I think you must have found a solution based on closing the issue. I am going to re-open this just so it remains immediately visible in the issues tab.

Phylip is a really outdated tree building software and has enough quirks that I don't recommend using it unless you're certain you want to. I recommend trying FastTree:

  1. You can download a pre-compiled executable for Linux here:

http://www.microbesonline.org/fasttree/#Install

  1. If you wanted to download it directly to PACE, consider "curl":

curl -O http://www.microbesonline.org/fasttree/FastTree

  1. Then make sure your user can execute the file with:

chmod 755 FastTree

  1. To make sure it's working and see usage, call the tool with:

./FastTree -h

mwarner43 commented 7 months ago

I ensured my input file is in the right format, how can I fix this error in PHYLIP:

ERROR: a function asked for an inappropriate amount of memory: 0 bytes This can mean one of two things:

  1. The input file is incorrect (perhaps it was not saved as Text Only),
  2. There is a bug in the program. Please check your input file carefully. If it seems to be a bug, please mail joe (at) gs.washington.edu with the name of the program, your computer system type, a full description of the problem, and with the input data file. (which should be in the body of the message, not as an Attachment).

Also, I can't find a way to open the .tree file from FastTree in a way that is supported. I'm not sure if I can't visualize it, or if there's no output, as it keeps saying it expects 1538 for Shewanella but only got 1537.

mwarner43 commented 7 months ago

Also, thanks for the help above! I now have the software working but the outputs just aren't.

mwarner43 commented 7 months ago

I was able to fix the input for PHYLIP by running the alignment in Jalview and making sure it was saved as .phy

mwarner43 commented 7 months ago

My last issue that remains is visualizing the tree outputs from PHYLIP and FastTree. Both output files I cannot open and I'm not sure what application to use to see them. I tried using drawgram within PHYLIP but can't get that to work

bglindner commented 7 months ago

I recommend using an online tool like iToL: https://itol.embl.de/