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Automatically exported from code.google.com/p/phyutility
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.
Original issue reported on code.google.com by [email protected]
on 27 Sep 2010 at 4:58
Attachments:
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.
Original issue reported on code.google.com by [email protected]
on 10 Jul 2008 at 2:36
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.
Original issue reported on code.google.com by [email protected]
on 27 Feb 2008 at 11:48
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.
Original issue reported on code.google.com by [email protected]
on 25 Apr 2008 at 11:46
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
Original issue reported on code.google.com by [email protected]
on 10 Jul 2012 at 7:58
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
Original issue reported on code.google.com by [email protected]
on 25 Jan 2011 at 4:21
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.
Original issue reported on code.google.com by [email protected]
on 5 Mar 2009 at 10:08
Attachments:
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.
Original issue reported on code.google.com by [email protected]
on 13 Feb 2008 at 7:34
With version 2.1, is there a way to turn *off* the logs by default?
Thanks,
Steve
Original issue reported on code.google.com by [email protected]
on 18 Oct 2007 at 2:19
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.
Original issue reported on code.google.com by [email protected]
on 4 Apr 2008 at 9:21
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!
Original issue reported on code.google.com by [email protected]
on 10 Dec 2009 at 7:48
Attachments:
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?
Original issue reported on code.google.com by [email protected]
on 12 Feb 2013 at 9:11
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