Error: Caused by: java.util.zip.ZipException: error in opening zip file

[gwolosh]

gene = D7X5Y8 completed! Realizando la peticion post... Exception in thread "main" java.lang.InternalError at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:755) at sun.misc.URLClassPath.getResource(URLClassPath.java:169) at java.net.URLClassLoader$1.run(URLClassLoader.java:194) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:190) at sun.misc.Launcher$ExtClassLoader.findClass(Launcher.java:229) at java.lang.ClassLoader.loadClass(ClassLoader.java:306) at java.lang.ClassLoader.loadClass(ClassLoader.java:295) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:247) at java.util.ResourceBundle$RBClassLoader.loadClass(ResourceBundle.java:435) at java.util.ResourceBundle$Control.newBundle(ResourceBundle.java:2289) at java.util.ResourceBundle.loadBundle(ResourceBundle.java:1364) at java.util.ResourceBundle.findBundle(ResourceBundle.java:1328) at java.util.ResourceBundle.findBundle(ResourceBundle.java:1282) at java.util.ResourceBundle.getBundleImpl(ResourceBundle.java:1224) at java.util.ResourceBundle.getBundle(ResourceBundle.java:705) at java.util.logging.Level.getLocalizedName(Level.java:223) at java.util.logging.SimpleFormatter.format(SimpleFormatter.java:64) at java.util.logging.StreamHandler.publish(StreamHandler.java:177) at java.util.logging.ConsoleHandler.publish(ConsoleHandler.java:88) at java.util.logging.Logger.log(Logger.java:478) at java.util.logging.Logger.doLog(Logger.java:500) at java.util.logging.Logger.logp(Logger.java:616) at org.apache.commons.logging.impl.Jdk14Logger.log(Jdk14Logger.java:99) at org.apache.commons.logging.impl.Jdk14Logger.info(Jdk14Logger.java:194) at org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:439) at org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397) at org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:323) at com.era7.lib.bioinfo.bioinfoutil.uniprot.UniprotProteinRetreiver.getUniprotDataFor(UniprotProteinRetreiver.java:41) at com.era7.bioinfo.annotation.FillDataFromUniprot.main(FillDataFromUniprot.java:88) at com.era7.bioinfo.annotation.FillDataFromUniprot.execute(FillDataFromUniprot.java:44) at com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:66) at com.era7.bioinfo.annotation.BG7.main(BG7.java:32) Caused by: java.util.zip.ZipException: error in opening zip file at java.util.zip.ZipFile.open(Native Method) at java.util.zip.ZipFile.(ZipFile.java:127) at java.util.jar.JarFile.(JarFile.java:135) at java.util.jar.JarFile.(JarFile.java:72) at sun.misc.URLClassPath$JarLoader.getJarFile(URLClassPath.java:646) at sun.misc.URLClassPath$JarLoader.access$600(URLClassPath.java:540) at sun.misc.URLClassPath$JarLoader$1.run(URLClassPath.java:607) at java.security.AccessController.doPrivileged(Native Method) at sun.misc.URLClassPath$JarLoader.ensureOpen(URLClassPath.java:599) at sun.misc.URLClassPath$JarLoader.getR

[pablopareja]

Hi @gwolosh

I'm not sure why you are getting this exception but it's likely that it may have something to do with the connection with the Uniprot WS and closing the connection from their side for some reason.

Could you provide me with the XML file you are using as input for the program FillDataFromUniprot ?

If that's not an option because of privacy issues, could you run the program again and see if you get the same exception at the very same execution point? (I mean right after you get as output 'gene = D7X5Y8 completed!' in this case)

[gwolosh]

This was run using the bg7_example_input_files.

Glenn (Gedaliah) Wolosh

On Dec 26, 2012, at 9:31 AM, Pablo Pareja Tobes wrote:

Hi @gwolosh

I'm not sure why you are getting this exception but it's likely that it may have something to do with the connection with the Uniprot WS and closing the connection from their side for some reason.

Could you provide me with the XML file you are using as input for the program FillDataFromUniprot ?

If that's not an option because of privacy issues, could you run the program again and see if you get the same exception at the very same execution point? (I mean right after you get as output 'gene = D7X5Y8 completed!' in this case)

— Reply to this email directly or view it on GitHub.

[pablopareja]

OK, but I'd need to have a look at your BLAST output XML file to gather more information about the possible cause _(AFAIK that one is not included in the bg7_example_inputfiles)

[gwolosh]

Is this the file you want -- bg7project_proteins_tBLASTn.xml

If so I don't see how to upload it.

Glenn (Gedaliah) Wolosh

On Dec 26, 2012, at 10:11 AM, Pablo Pareja Tobes wrote:

OK, but I'd need to have a look at your BLAST output XML file to gather more information about the possible cause (AFAIK that one is not included in the bg7_example_input_files)

— Reply to this email directly or view it on GitHub.

[pablopareja]

Yeah I meant that file. You can send it to me by e-mail (ppareja "at" era7 "dot" com) or give me a public URL from where I could download it.

Pablo

[gwolosh]

Let me know when you get the file

http://sirius2.umdnj.edu/~woloshgm/downloads/bg7project_proteins_tBLASTn.xml.gz

Glenn (Gedaliah) Wolosh gwolosh@gmail.com

On Dec 26, 2012, at 10:32 AM, Pablo Pareja Tobes wrote:

Yeah I meant that file. You can send it to me by e-mail (ppareja "at" era7 "dot" com) or give me a public URL from where I could download it.

Pablo

— Reply to this email directly or view it on GitHub.

[pablopareja]

Hey, I already downloaded your file, I was having a look at it but I didn't see anything strange so far. Could you send me as well all the files that were created by the program till you got this exception?

Thanks.

[gwolosh]

http://sirius2.umdnj.edu/~woloshgm/downloads/testout.tgz and http://sirius2.umdnj.edu/~woloshgm/downloads/test_bg7.o33115.gz

Glenn (Gedaliah) Wolosh

On Dec 27, 2012, at 6:13 AM, Pablo Pareja Tobes wrote:

Hey, I already downloaded your file, I was having a look at it but I didn't see anything strange so far. Could you send me as well all the files that were created by the program till you got this exception?

Thanks.

— Reply to this email directly or view it on GitHub.

[pablopareja]

Hi Glenn,

Thanks for the files. I've been having a look at all this and apparently there's no reason to get this exception. The only possibility I can think about is that the Uniprot WS could be closing the connection or something like that making the program crash, (I just checked out that the program had already gathered the information from more than 1000 proteins, and this looks to me like a value big enough as for them to somehow prevent you getting more information at least for a while)

I tried to add a quick fix for this kind of situations adding a try-catch block that encloses the part where this is carried out; however for some reason I don't understand this exception is not properly managed and the program keeps crashing.

So, I can think of two different workarounds for this:

1. Use Bio4j instead and you'll get rid of all this limitations/trouble with Uniprot WS (actually one of the reasons for us to start Bio4j project was this...)
2. You can try to launch that part of the pipeline again and see if they don't close the connection this time. For this you can comment out your executions.xml file up to the program com.era7.bioinfo.annotation.FillDataFromUniprot so that you don't have to spend time running the same things again.

Hope this helps,

Pablo

[gwolosh]

OK, thanks

Glenn (Gedaliah) Wolosh

On Dec 27, 2012, at 10:11 AM, Pablo Pareja Tobes wrote:

Hi Glenn,

Thanks for the files. I've been having a look at all this and apparently there's no reason to get this exception. The only possibility I can think about is that the Uniprot WS could be closing the connection or something like that making the program crash, (I just checked out that the program had already gathered the information from more than 1000 proteins, and this looks to me like a value big enough as for them to somehow prevent you getting more information at least for a while)

I tried to add a quick fix for this kind of situations adding a try-catch block that encloses the part where this is carried out; however for some reason I don't understand this exception is not properly managed and the program keeps crashing.

So, I can think of two different workarounds for this:

Use Bio4j instead and you'll get rid of all this limitations/trouble with Uniprot WS (actually one of the reasons for us to start Bio4j project was this...) You can try to launch that part of the pipeline again and see if they don't close the connection this time. For this you can comment out your executions.xml file up to the program com.era7.bioinfo.annotation.FillDataFromUniprot so that you don't have to spend time running the same things again. Hope this helps,

Pablo

— Reply to this email directly or view it on GitHub.

[gwolosh]

Hi,

I ran it again and it crashed in the same place.

Glenn (Gedaliah) Wolosh

On Dec 27, 2012, at 10:11 AM, Pablo Pareja Tobes wrote:

Hi Glenn,

Thanks for the files. I've been having a look at all this and apparently there's no reason to get this exception. The only possibility I can think about is that the Uniprot WS could be closing the connection or something like that making the program crash, (I just checked out that the program had already gathered the information from more than 1000 proteins, and this looks to me like a value big enough as for them to somehow prevent you getting more information at least for a while)

I tried to add a quick fix for this kind of situations adding a try-catch block that encloses the part where this is carried out; however for some reason I don't understand this exception is not properly managed and the program keeps crashing.

So, I can think of two different workarounds for this:

Use Bio4j instead and you'll get rid of all this limitations/trouble with Uniprot WS (actually one of the reasons for us to start Bio4j project was this...) You can try to launch that part of the pipeline again and see if they don't close the connection this time. For this you can comment out your executions.xml file up to the program com.era7.bioinfo.annotation.FillDataFromUniprot so that you don't have to spend time running the same things again. Hope this helps,

Pablo

— Reply to this email directly or view it on GitHub.

[pablopareja]

Hi Glenn,

I ran the program 'FillDataFromUniprot' with the exact same data and jar file that you passed me and I didn't get any exception, the program completed successfully. So I don't know what else can I do right now to help you figure out what's going on when you execute it in your machine... :confused:

Pablo

[eparejatobes]

closing this, reopen if there's any further info available