[maker-devel] MAKER problems

[Carson Holt]

Hello,

Sorry about the problem with contacting us.  I've fixed the bug, it was related to some recent updates we performed on the server.  I needed re-enter the SMTP server into the mailing script, because of changes we made.

I examined the GFF3 file from your job, and I've identified the problem.  There was a single line that had commas in the "Name" attribute in the GFF3 file.  This was related to commas being found in the fasta header of your input file.  I've fixed the problem so the comma will be correctly escaped in the GFF3, and re-ran your job.  You can download the corrected GFF3 there from the MAKER web service.

Thanks,
Carson

On 2/16/10 2:40 PM, "Harry Hunter" <hhunter13 at hotmail.com> wrote:

To whom it may concern:

My name is Henry Hunter and I'm a current Graduate student at San Francisco State University. I apologize to be sending you this email directly, but every time I try to use the "Contact Us" option on the MAKER site it only gives me a "Software Error" message. I've been having problems opening the GFF3 files MAKER produces on Apollo. I have the most updated Apollo (December 2009) and have copied the command line from trying to open the GFF3 file on Apollo below. If I'm making an error, please let me know. Thank you for taking the time to read this and hope you have a wonderful day.



X11 STDERR

bash-3.2$ /Applications/Apollo.app/Contents/Resources/app/bin/apollo
APOLLO_ROOT set to /Applications/Apollo.app/Contents/Resources/app
Couldn't find JavaPath line in apollo.cfg file, trying to guess path to java...
/Applications/Apollo.app/Contents/Resources/app/bin/apollo: line 212: unalias: j
ava: not found
Using version of Java in /usr: /usr/bin/java
Web browser = netscape
Starting apollo (memory = 800M)...
/usr/bin/java -ms50M -Xmx800M -classpath /Applications/Apollo.app/Contents/Resou
rces/app/jars/apollo.jar:/Applications/Apollo.app/Contents/Resources/app/jars/bb
op.jar:/Applications/Apollo.app/Contents/Resources/app/jars/biojava.jar:/Applica
tions/Apollo.app/Contents/Resources/app/jars/ecp1_0beta.jar:/Applications/Apollo
.app/Contents/Resources/app/jars/ensj.jar:/Applications/Apollo.app/Contents/Reso
urces/app/jars/jakarta-oro-2.0.6.jar:/Applications/Apollo.app/Contents/Resources
/app/jars/jaxp.jar:/Applications/Apollo.app/Contents/Resources/app/jars/jnlp.jar
:/Applications/Apollo.app/Contents/Resources/app/jars/junit.jar:/Applications/Ap
ollo.app/Contents/Resources/app/jars/log4j-1.2.14.jar:/Applications/Apollo.app/C
ontents/Resources/app/jars/macify-1.1.jar:/Applications/Apollo.app/Contents/Reso
urces/app/jars/mysql-connector-java-3.1.8-bin.jar:/Applications/Apollo.app/Conte
nts/Resources/app/jars/obo.jar:/Applications/Apollo.app/Contents/Resources/app/j
ars/oboedit.jar:/Applications/Apollo.app/Contents/Resources/app/jars/org.mortbay
.jetty.jar:/Applications/Apollo.app/Contents/Resources/app/jars/patbinfree153.ja
r:/Applications/Apollo.app/Contents/Resources/app/jars/pg74.213.jdbc3.jar:/Appli
cations/Apollo.app/Contents/Resources/app/jars/psgr2.jar:/Applications/Apollo.ap
p/Contents/Resources/app/jars/servlet-tomcat.jar:/Applications/Apollo.app/Conten
ts/Resources/app/jars/te-common.jar:/Applications/Apollo.app/Contents/Resources/
app/jars/xerces.jar:/Applications/Apollo.app/Contents/Resources/app/data: -DAPOL
LO_ROOT=/Applications/Apollo.app/Contents/Resources/app -Dorg.xml.sax.driver=org
.apache.crimson.parser.XMLReaderImpl -Dlog4j.configuration=file:///Applications/
Apollo.app/Contents/Resources/app/conf/log4j.properties apollo.main.Apollo
INFO : APOLLO_ROOT: /Applications/Apollo.app/Contents/Resources/app
INFO : OS name: Mac OS X
INFO : OS arch: i386
INFO : Java version: 1.5.0_22
INFO : reading config file /Applications/Apollo.app/Contents/Resources/app/conf/
apollo.cfg
WARN : adding type Community GB to tier null, but another tier, New analysis res
ults, already has a type called Community GB(in tiers file /Users/cdsmith/.apoll
o/fly.tiers)
WARN : adding type EST Same Strain to tier null, but another tier, New analysis
results, already has a type called EST Same Strain(in tiers file /Users/cdsmith/
.apollo/fly.tiers)
WARN : adding type Community GB to tier null, but another tier, New analysis res
ults, already has a type called Community GB(in tiers file /Users/cdsmith/.apoll
o/fly.tiers)
WARN : adding type EST Same Strain to tier null, but another tier, New analysis
results, already has a type called EST Same Strain(in tiers file /Users/cdsmith/
.apollo/fly.tiers)
WARN : adding type Community GB to tier null, but another tier, New analysis res
ults, already has a type called Community GB(in tiers file /Users/cdsmith/.apoll
o/fly.tiers)
WARN : adding type EST Same Strain to tier null, but another tier, New analysis
results, already has a type called EST Same Strain(in tiers file /Users/cdsmith/
.apollo/fly.tiers)
INFO : using history file /Users/cdsmith/.apollo/apollo.history
INFO : using backup file /Users/cdsmith/.apollo/apollo.backup
INFO : running: /Applications/Apollo.app/Contents/Resources/app/bin/mac-set-jvm
WARN : Since you are not running an installed version of Apollo, I can't change
which JVM it uses.  Hopefully you have JDK1.5 or 1.6 set up as your default JVM.

INFO : this is Apollo Genome Annotation and Curation Tool, version 1.11.3, last
updated Dec 22 2009
INFO : set style to /Applications/Apollo.app/Contents/Resources/app/conf/gff3.style; style file source(s): /Applications/Apollo.app/Contents/Resources/app/conf/gff3.style, /Applications/Apollo.app/C
INFO : using tiers file /Users/cdsmith/.apollo/gff3.tiers
INFO : Loading OBO files: [/Applications/Apollo.app/Contents/Resources/app/obo-files/so.obo, /Applications/Apollo.app/Contents/Resources/app/obo-files/apollo.obo]
Exception in thread "Thread-2" java.lang.ArrayIndexOutOfBoundsException: 1
        at apollo.dataadapter.gff3.GFF3Entry.createFeature(GFF3Entry.java:354)
        at apollo.dataadapter.gff3.GFF3Adapter.parseGff(GFF3Adapter.java:537)
        at apollo.dataadapter.gff3.GFF3Adapter.getCurationSet(GFF3Adapter.java:140)
        at apollo.dataadapter.gff3.GFF3AdapterGUI.doOperation(GFF3AdapterGUI.java:198)
        at org.bdgp.swing.widget.DataAdapterChooser.doCommitWithExceptions(DataAdapterChooser.java:361)
        at apollo.main.DataLoader$ApolloAdapterChooser.doCommit(DataLoader.java:750)
        at org.bdgp.swing.widget.DataAdapterChooser$CommitRunnable.run(DataAdapterChooser.java:136)
        at java.lang.Thread.run(Thread.java:613)


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