komais / phyutility Goto Github PK

What steps will reproduce the problem?
1. Run -clean command with any frequence
2.
3.

What is the expected output? What do you see instead?
Either an empty output file or no output.

What version of the product are you using? On what operating system?
latest. Mac OS 10.5

Please provide any additional information below.
This happens with either a fasta or nexus input file.  The file has only 6 
taxa, but over 200,000 bp.

What steps will reproduce the problem?
With version 2.1, running leaf stability on a tree file with :0.0000-style 
branch lengths embedded 
fails.

Removal of the branch lengths leads to the expected output.

What steps will reproduce the problem?
1. Root tree or set of trees
2. phyutility -pr -in rooted.phy -out ingroup.phy -names T101
3.

What is the expected output? What do you see instead?
My trees consist of 100 ingroup taxa and a single outgroup taxon. I expect
to get a rooted tree consisting of only the ingroup taxa. Instead, I get
the exact same set of trees (with all taxa).

What version of the product are you using? On what operating system?
v 2.2

Please provide any additional information below.

What steps will reproduce the problem?
1. I ran leaf stability index for a set of 700 trees of about 300 taxa
2. Also tried running it for a smaller number of trees (10) but with same 
300 taxa

What is the expected output? What do you see instead?
Instead of leaf stability indices, I get (for full trees):
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.util.ArrayList.<init>(Unknown Source)
        at java.util.ArrayList.<init>(Unknown Source)
        at jade.tree.Node.<init>(Node.java:39)
        at jade.tree.TreeReader.readTree(TreeReader.java:50)
        at phyutility.mainrunner.Main.leafStab(Main.java:554)
        at phyutility.mainrunner.Main.runArgs(Main.java:359)
        at phyutility.mainrunner.Main.<init>(Main.java:66)
        at phyutility.mainrunner.Main.main(Main.java:1509)

and (for reduced number of trees):
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at jade.math.NChooseM.iterate(NChooseM.java:68)
        at phyutility.leafstability.Runner.initializeRun(Runner.java:47)
        at phyutility.leafstability.Runner.<init>(Runner.java:23)
        at phyutility.mainrunner.Main.leafStab(Main.java:560)
        at phyutility.mainrunner.Main.runArgs(Main.java:359)
        at phyutility.mainrunner.Main.<init>(Main.java:66)
        at phyutility.mainrunner.Main.main(Main.java:1509)

What version of the product are you using? On what operating system?
Phyutility 2.2 on Windows XP

Please provide any additional information below.
I tried increasing the memory allocation using the java command but even 
after increasing it to 1GB I still get the same error message. Am not sure 
if the memory allocation increase didn't work or the program still can't 
handle the trees.

I have alignment files in FASTA format that I want to concatenate.  I am using 
version 2.2.4. When I invoke the concat module of Phyutility, the concatenated 
file is in NEXUS format.  I can't tell from the code how to instruct Phyutility 
to output in FASTA format instead.

Here is my exact command...

java -jar phyutility.jar -concat -in *_nttrim.fasta -out concat -log logout

Thanks!
Laura

Hello all,
I'm trying to use phyutility to concatenate amino acid sequences and it seems 
to me that amino acid are not supported by phyutility, am I right?

Thanks,
Best,
Mathieu

What steps will reproduce the problem?
1. convert nexus tree to newick
2. input tree has branch lengths in decimals 0.0000etc
3. output tree has modified small decimals into E-4 and E-8

What is the expected output? What do you see instead?
many programs cannot read branch lengths written shorthand like that

What version of the product are you using? On what operating system?
v 2.2, mac osx

Please provide any additional information below.

What steps will reproduce the problem?
1. java -Xmx1500m -jar phyutility.jar -tt 100 -in file1.nex -out
trimfile1.out -derb
2.
3.

What is the expected output? What do you see instead?
The error message repeats the following:
A non SQL error occured.
java.lang.NullPointerException
        at phyutility.drb.WwdEmbedded.addTree(WwdEmbedded.java:112)
        at
phyutility.jebl2jade.NexusToJade.getJadeFromJeblNexusDerby(NexusToJade.java:57)
        at phyutility.mainrunner.Main.getNewickFromNexusDerby(Main.java:1103)
        at phyutility.mainrunner.Main.thin(Main.java:935)
        at phyutility.mainrunner.Main.runArgs(Main.java:371)
        at phyutility.mainrunner.Main.<init>(Main.java:66)
        at phyutility.mainrunner.Main.main(Main.java:1509)
 . . . exception thrown:


What version of the product are you using? On what operating system?
MacOSX_Intel with Java 1.5 and am using phyutility v2.2

Please provide any additional information below.

With version 2.1, is there a way to turn *off* the logs by default?

Thanks,
Steve

What steps will reproduce the problem?
1. add two sequences of same name in  a file, and concat it with another file.
2.
3.

What is the expected output? What do you see instead?
all sequences are expected to be the same length. the sequence with two
copies in one file is longer, and aligning weird.

What version of the product are you using? On what operating system?
v2.2 on Ubuntu 7.10

Please provide any additional information below.
This is not a problem with the code. An error message stating that there
are two sequences of same name in one file would be nice.

What steps will reproduce the problem?
1. run phyutility on a newick file containing a taxon name with a dash
2. execute tree file in paup (alignment file contains single quotes around that 
taxon)
3. ERROR!  

What is the expected output? What do you see instead?
Phyutility should check for the list of characters not recognized by macclade 
or paup and put 
single quotes around those taxa.  Other scripts check for this, including 
seqConverger.pl, which 
unfortunately doesn't convert tree files.

What version of the product are you using? On what operating system?
v.2.2.1
Mac OS 10.6

Please provide any additional information below.
it would be great to have this extra conversion step included in the next 
version.  Thanks for an 
otherwise great program!

What steps will reproduce the problem?
1.the command is  "java -jar phyutility.jar -ls -in ./59genes/59single_gene"
2. three are three trees with no branch length and supporting values, the 
format is newick


What is the expected output? What do you see instead?
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String 
index out of range: 0
    at java.lang.String.charAt(String.java:686)
    at jade.tree.TreeReader.readTree(Unknown Source)
    at phyutility.mainrunner.Main.leafStab(Unknown Source)
    at phyutility.mainrunner.Main.runArgs(Unknown Source)
    at phyutility.mainrunner.Main.<init>(Unknown Source)
    at phyutility.mainrunner.Main.main(Unknown Source)

What version of the product are you using? On what operating system?
version 2.2.6, lunix

Please provide any additional information below.
I am not sure which kind of tree should be used, rooted or unrooted? If there 
are same taxa in each tree is required?