snpEff and FASTQ Summary Statistics errors

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snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
Dear there,

When I used SnpEff in local galaxy instance, I got an error:
Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j


Also, when I used the FASTQ Summary Statistics, I got an error like this:
Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...

I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!


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Re: snpEff and FASTQ Summary Statistics errors

Björn Grüning-3
Hi Xiaofei,

> Dear there,
>
> When I used SnpEff in local galaxy instance, I got an error:
> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j

Which Java version do you use. Please make sure you are running Java 1.7.

> Also, when I used the FASTQ Summary Statistics, I got an error like this:
> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...

Can you give us the complete error message. The important part is missing.

Ciao,
Bjoern

> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
>>Can you give us the complete error message. The important part is missing.

Here is the whole thing for the error:

Traceback (most recent call last):
  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in
    if __name__ == "__main__": main()
  File "/Users/xiaofe

I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for  FASTQ Summary Statistics or CloundMap?

Thanks a lot!
________________________________________
From: Björn Grüning [[hidden email]]
Sent: Wednesday, April 02, 2014 10:35 AM
To: Wang, Xiaofei; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

> Dear there,
>
> When I used SnpEff in local galaxy instance, I got an error:
> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j

Which Java version do you use. Please make sure you are running Java 1.7.

> Also, when I used the FASTQ Summary Statistics, I got an error like this:
> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...

Can you give us the complete error message. The important part is missing.

Ciao,
Bjoern

> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>



___________________________________________________________
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Re: snpEff and FASTQ Summary Statistics errors

Daniel Blankenberg
Hi Xiaofei,

To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane?


Thanks for using Galaxy,

Dan


On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei <[hidden email]> wrote:

>>> Can you give us the complete error message. The important part is missing.
>
> Here is the whole thing for the error:
>
> Traceback (most recent call last):
>  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in
>    if __name__ == "__main__": main()
>  File "/Users/xiaofe
>
> I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for  FASTQ Summary Statistics or CloundMap?
>
> Thanks a lot!
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 10:35 AM
> To: Wang, Xiaofei; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear there,
>>
>> When I used SnpEff in local galaxy instance, I got an error:
>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>
> Which Java version do you use. Please make sure you are running Java 1.7.
>
>> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>
> Can you give us the complete error message. The important part is missing.
>
> Ciao,
> Bjoern
>
>> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
Oh, yes, here it is:

Traceback (most recent call last):
  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in <module>
    if __name__ == "__main__": main()
  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 32, in main
    base_counts = aggregator.get_base_counts_for_column( i )
  File "/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line 397, in get_base_counts_for_column
    return self.nuc_index_base[ column ]
IndexError: list index out of range
________________________________________
From: Daniel Blankenberg [[hidden email]]
Sent: Wednesday, April 02, 2014 11:14 AM
To: Wang, Xiaofei
Cc: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane?


Thanks for using Galaxy,

Dan


On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei <[hidden email]> wrote:

>>> Can you give us the complete error message. The important part is missing.
>
> Here is the whole thing for the error:
>
> Traceback (most recent call last):
>  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in
>    if __name__ == "__main__": main()
>  File "/Users/xiaofe
>
> I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for  FASTQ Summary Statistics or CloundMap?
>
> Thanks a lot!
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 10:35 AM
> To: Wang, Xiaofei; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear there,
>>
>> When I used SnpEff in local galaxy instance, I got an error:
>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>
> Which Java version do you use. Please make sure you are running Java 1.7.
>
>> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>
> Can you give us the complete error message. The important part is missing.
>
> Ciao,
> Bjoern
>
>> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
In reply to this post by Björn Grüning-3
>> When I used SnpEff in local galaxy instance, I got an error:
>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j




>Which Java version do you use. Please make sure you are running Java 1.7.




Yes, it is figured, when I changed the java version to 1.7. Thank you so much!




But, I got another error for snpEff.




java.lang.RuntimeException: Property: 'dm5.30.genome' not found
        at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)








What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.




Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )




<param name="genomeVersion" type="select" label="Genome">
                <option value="hg37">Human (hg37)<option>
                <option value="mm37.61">Mouse (mm37.61)<option>
        <param> 



________________________________________
From: Björn Grüning [[hidden email]]
Sent: Wednesday, April 02, 2014 10:35 AM
To: Wang, Xiaofei; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

> Dear there,
>
> When I used SnpEff in local galaxy instance, I got an error:
> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j

Which Java version do you use. Please make sure you are running Java 1.7.

> Also, when I used the FASTQ Summary Statistics, I got an error like this:
> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...

Can you give us the complete error message. The important part is missing.

Ciao,
Bjoern

> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>    http://galaxyproject.org/search/mailinglists/
>



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: snpEff and FASTQ Summary Statistics errors

Björn Grüning-3
Hi,

that means that the snpeff annotation is missing. You can install it
with the snpeff datamanager under your Admin panel. Have a look at the
wiki page about data-manager and the snpeff wrapper documentation.
You do not need to edit xml files. If so that is an bug in the wrapper
and we should fix it :)

Cheers,
Bjoern

Am 02.04.2014 19:34, schrieb Wang, Xiaofei:

>>> When I used SnpEff in local galaxy instance, I got an error:
>>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>
>
>
>
>> Which Java version do you use. Please make sure you are running Java 1.7.
>
>
>
>
> Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>
>
>
>
> But, I got another error for snpEff.
>
>
>
>
> java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>          at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>          at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>          at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>          at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>          at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>
>
>
>
>
>
>
>
> What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>
>
>
>
> Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>
>
>
>
> <param name="genomeVersion" type="select" label="Genome">
> <option value="hg37">Human (hg37)<option>
> <option value="mm37.61">Mouse (mm37.61)<option>
> <param>
>
>
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 10:35 AM
> To: Wang, Xiaofei; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear there,
>>
>> When I used SnpEff in local galaxy instance, I got an error:
>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>
> Which Java version do you use. Please make sure you are running Java 1.7.
>
>> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>
> Can you give us the complete error message. The important part is missing.
>
> Ciao,
> Bjoern
>
>> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>     http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>     http://galaxyproject.org/search/mailinglists/
>>
>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
In reply to this post by Wang, Xiaofei

Dear Bjoern,

As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome, I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.) Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty. 

Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?

I really appreciate for your help, and thank you so much for your patience!

Best,

Xiaofei

Data Manager

Choose your data managing option from below.

  • Access data managers - get data, build indexes, etc

  • View managed data by manager

  • View managed data by Tool Data Table



  • ________________________________________
  • From: Björn Grüning [[hidden email]]
  • Sent: Wednesday, April 02, 2014 12:55 PM
  • To: Wang, Xiaofei; Björn Grüning; [hidden email]
  • Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

  • Hi,

  • that means that the snpeff annotation is missing. You can install it
  • with the snpeff datamanager under your Admin panel. Have a look at the
  • wiki page about data-manager and the snpeff wrapper documentation.
  • You do not need to edit xml files. If so that is an bug in the wrapper
  • and we should fix it :)

  • Cheers,
  • Bjoern

  • Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
  • >>> When I used SnpEff in local galaxy instance, I got an error:
  • >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
  • >
  • >
  • >
  • >
  • >> Which Java version do you use. Please make sure you are running Java 1.7.
  • >
  • >
  • >
  • >
  • > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
  • >
  • >
  • >
  • >
  • > But, I got another error for snpEff.
  • >
  • >
  • >
  • >
  • > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
  • >          at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
  • >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
  • >
  • >
  • >
  • >
  • >
  • >
  • >
  • >
  • > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
  • >
  • >
  • >
  • >
  • > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
  • >
  • >
  • >
  • >
  • > <param name="genomeVersion" type="select" label="Genome">
  • >               <option value="hg37">Human (hg37)<option>
  • >               <option value="mm37.61">Mouse (mm37.61)<option>
  • >       <param>
  • >
  • >
  • >
  • > ________________________________________
  • > From: Björn Grüning [[hidden email]]
  • > Sent: Wednesday, April 02, 2014 10:35 AM
  • > To: Wang, Xiaofei; [hidden email]
  • > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
  • >
  • > Hi Xiaofei,
  • >
  • >> Dear there,
  • >>
  • >> When I used SnpEff in local galaxy instance, I got an error:
  • >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
  • >
  • > Which Java version do you use. Please make sure you are running Java 1.7.
  • >
  • >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
  • >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
  • >
  • > Can you give us the complete error message. The important part is missing.
  • >
  • > Ciao,
  • > Bjoern
  • >
  • >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
  • >>
  • >>
  • >>
  • >>
  • >> ___________________________________________________________
  • >> Please keep all replies on the list by using "reply all"
  • >> in your mail client.  To manage your subscriptions to this
  • >> and other Galaxy lists, please use the interface at:
  • >>     http://lists.bx.psu.edu/
  • >>
  • >> To search Galaxy mailing lists use the unified search at:
  • >>     http://galaxyproject.org/search/mailinglists/
  • >>
  • >
  • >


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: snpEff and FASTQ Summary Statistics errors

Björn Grüning-3
Hi Xiaofei,

> Dear Bjoern,
> As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
> Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome,
> I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.)
> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty.

After SnpEff Databases > Execute you still need to pick genome of
interest and run "SnpEff Download". SnpEff Databases just downloads a
list of available genomes.

Hope that will help!
Bjoern

>
> Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?
>
> I really appreciate for your help, and thank you so much for your patience!
>
> Best,
>
> Xiaofei
> Data Manager
>
> Choose your data managing option from below.
>
>    *   Access data managers - get data, build indexes, etc
>
>       *   SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases
>
>       *   SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database
>
>       *   BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder
>
>       *   BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder
>
>       *   Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching
>
>    *   View managed data by manager
>
>       *   SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases
>
>       *   SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database
>
>       *   BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder
>
>       *   BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder
>
>       *   Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching
>
>    *   View managed data by Tool Data Table
>
>       *   snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases>
>
>       *   snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb>
>
>       *   snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb>
>
>       *   snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations>
>
>       *   bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes>
>
>       *   bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color>
>
>       *   all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta>
>    *
>    *
>    *
>    *   ________________________________________
>    *   From: Björn Grüning [[hidden email]]
>    *   Sent: Wednesday, April 02, 2014 12:55 PM
>    *   To: Wang, Xiaofei; Björn Grüning; [hidden email]
>    *   Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>    *
>    *   Hi,
>    *
>    *   that means that the snpeff annotation is missing. You can install it
>    *   with the snpeff datamanager under your Admin panel. Have a look at the
>    *   wiki page about data-manager and the snpeff wrapper documentation.
>    *   You do not need to edit xml files. If so that is an bug in the wrapper
>    *   and we should fix it :)
>    *
>    *   Cheers,
>    *   Bjoern
>    *
>    *   Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
>    *   >>> When I used SnpEff in local galaxy instance, I got an error:
>    *   >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >> Which Java version do you use. Please make sure you are running Java 1.7.
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > But, I got another error for snpEff.
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>    *   >          at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > <param name="genomeVersion" type="select" label="Genome">
>    *   >               <option value="hg37">Human (hg37)<option>
>    *   >               <option value="mm37.61">Mouse (mm37.61)<option>
>    *   >       <param>
>    *   >
>    *   >
>    *   >
>    *   > ________________________________________
>    *   > From: Björn Grüning [[hidden email]]
>    *   > Sent: Wednesday, April 02, 2014 10:35 AM
>    *   > To: Wang, Xiaofei; [hidden email]
>    *   > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>    *   >
>    *   > Hi Xiaofei,
>    *   >
>    *   >> Dear there,
>    *   >>
>    *   >> When I used SnpEff in local galaxy instance, I got an error:
>    *   >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>    *   >
>    *   > Which Java version do you use. Please make sure you are running Java 1.7.
>    *   >
>    *   >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>    *   >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>    *   >
>    *   > Can you give us the complete error message. The important part is missing.
>    *   >
>    *   > Ciao,
>    *   > Bjoern
>    *   >
>    *   >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>    *   >>
>    *   >>
>    *   >>
>    *   >>
>    *   >> ___________________________________________________________
>    *   >> Please keep all replies on the list by using "reply all"
>    *   >> in your mail client.  To manage your subscriptions to this
>    *   >> and other Galaxy lists, please use the interface at:
>    *   >>     http://lists.bx.psu.edu/
>    *   >>
>    *   >> To search Galaxy mailing lists use the unified search at:
>    *   >>     http://galaxyproject.org/search/mailinglists/
>    *   >>
>    *   >
>    *   >
>    *
>       *
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Open this post in threaded view
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
>After SnpEff Databases > Execute you still need to pick genome of
interest and run "SnpEff Download". SnpEff Databases just downloads a
list of available genomes.

You mean "SnpEff Download" under Data Manager? But, there is no response when I click on it.

Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response. But, when I go to Admin > Data > Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why?

When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time?

Thank you so much!

Best,

Xiaofei

________________________________________
From: Björn Grüning [[hidden email]]
Sent: Wednesday, April 02, 2014 4:17 PM
To: Wang, Xiaofei; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

> Dear Bjoern,
> As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
> Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome,
> I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.)
> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty.

After SnpEff Databases > Execute you still need to pick genome of
interest and run "SnpEff Download". SnpEff Databases just downloads a
list of available genomes.

Hope that will help!
Bjoern

>
> Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?
>
> I really appreciate for your help, and thank you so much for your patience!
>
> Best,
>
> Xiaofei
> Data Manager
>
> Choose your data managing option from below.
>
>    *   Access data managers - get data, build indexes, etc
>
>       *   SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases
>
>       *   SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database
>
>       *   BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder
>
>       *   BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder
>
>       *   Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching
>
>    *   View managed data by manager
>
>       *   SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases
>
>       *   SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database
>
>       *   BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder
>
>       *   BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder
>
>       *   Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching
>
>    *   View managed data by Tool Data Table
>
>       *   snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases>
>
>       *   snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb>
>
>       *   snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb>
>
>       *   snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations>
>
>       *   bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes>
>
>       *   bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color>
>
>       *   all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta>
>    *
>    *
>    *
>    *   ________________________________________
>    *   From: Björn Grüning [[hidden email]]
>    *   Sent: Wednesday, April 02, 2014 12:55 PM
>    *   To: Wang, Xiaofei; Björn Grüning; [hidden email]
>    *   Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>    *
>    *   Hi,
>    *
>    *   that means that the snpeff annotation is missing. You can install it
>    *   with the snpeff datamanager under your Admin panel. Have a look at the
>    *   wiki page about data-manager and the snpeff wrapper documentation.
>    *   You do not need to edit xml files. If so that is an bug in the wrapper
>    *   and we should fix it :)
>    *
>    *   Cheers,
>    *   Bjoern
>    *
>    *   Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
>    *   >>> When I used SnpEff in local galaxy instance, I got an error:
>    *   >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >> Which Java version do you use. Please make sure you are running Java 1.7.
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > But, I got another error for snpEff.
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>    *   >          at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>    *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>    *   >
>    *   >
>    *   >
>    *   >
>    *   > <param name="genomeVersion" type="select" label="Genome">
>    *   >               <option value="hg37">Human (hg37)<option>
>    *   >               <option value="mm37.61">Mouse (mm37.61)<option>
>    *   >       <param>
>    *   >
>    *   >
>    *   >
>    *   > ________________________________________
>    *   > From: Björn Grüning [[hidden email]]
>    *   > Sent: Wednesday, April 02, 2014 10:35 AM
>    *   > To: Wang, Xiaofei; [hidden email]
>    *   > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>    *   >
>    *   > Hi Xiaofei,
>    *   >
>    *   >> Dear there,
>    *   >>
>    *   >> When I used SnpEff in local galaxy instance, I got an error:
>    *   >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>    *   >
>    *   > Which Java version do you use. Please make sure you are running Java 1.7.
>    *   >
>    *   >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>    *   >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>    *   >
>    *   > Can you give us the complete error message. The important part is missing.
>    *   >
>    *   > Ciao,
>    *   > Bjoern
>    *   >
>    *   >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>    *   >>
>    *   >>
>    *   >>
>    *   >>
>    *   >> ___________________________________________________________
>    *   >> Please keep all replies on the list by using "reply all"
>    *   >> in your mail client.  To manage your subscriptions to this
>    *   >> and other Galaxy lists, please use the interface at:
>    *   >>     http://lists.bx.psu.edu/
>    *   >>
>    *   >> To search Galaxy mailing lists use the unified search at:
>    *   >>     http://galaxyproject.org/search/mailinglists/
>    *   >>
>    *   >
>    *   >
>    *
>       *
>



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: snpEff and FASTQ Summary Statistics errors

Björn Grüning-3


Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
>> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> You mean "SnpEff Download" under Data Manager? But, there is no response when I click on it.

It's a little bit complicated. If you click on the "SnpEff Download"
under Data Manager a progress ist started that will fetch a list of
available genomes that in a next step is shown under the tool "SnpEff
Databases" there you can choose which genome annotation you want to
install. To sum it up.

1. click "SnpEff Download"
2. choose one genome from "SnpEff Databases" and install it

> Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response.
> But, when I go to Admin > Data > Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why?

Then there is something missing from your reinstallation. The data
manager is a dependency of the snpeff package and should be installed as
well. Can you check if you need to reinstall the dependency manually
unter the snpeff tool in your admin panel?

Cheers,
Bjoern

> When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time?
>
> Thank you so much!
>
> Best,
>
> Xiaofei
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 4:17 PM
> To: Wang, Xiaofei; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear Bjoern,
>> As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
>> Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome,
>> I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.)
>> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty.
>
> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> Hope that will help!
> Bjoern
>
>>
>> Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?
>>
>> I really appreciate for your help, and thank you so much for your patience!
>>
>> Best,
>>
>> Xiaofei
>> Data Manager
>>
>> Choose your data managing option from below.
>>
>>     *   Access data managers - get data, build indexes, etc
>>
>>        *   SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases
>>
>>        *   SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database
>>
>>        *   BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder
>>
>>        *   BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder
>>
>>        *   Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching
>>
>>     *   View managed data by manager
>>
>>        *   SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases
>>
>>        *   SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database
>>
>>        *   BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder
>>
>>        *   BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder
>>
>>        *   Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching
>>
>>     *   View managed data by Tool Data Table
>>
>>        *   snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases>
>>
>>        *   snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb>
>>
>>        *   snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb>
>>
>>        *   snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations>
>>
>>        *   bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes>
>>
>>        *   bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color>
>>
>>        *   all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta>
>>     *
>>     *
>>     *
>>     *   ________________________________________
>>     *   From: Björn Grüning [[hidden email]]
>>     *   Sent: Wednesday, April 02, 2014 12:55 PM
>>     *   To: Wang, Xiaofei; Björn Grüning; [hidden email]
>>     *   Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>>     *
>>     *   Hi,
>>     *
>>     *   that means that the snpeff annotation is missing. You can install it
>>     *   with the snpeff datamanager under your Admin panel. Have a look at the
>>     *   wiki page about data-manager and the snpeff wrapper documentation.
>>     *   You do not need to edit xml files. If so that is an bug in the wrapper
>>     *   and we should fix it :)
>>     *
>>     *   Cheers,
>>     *   Bjoern
>>     *
>>     *   Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
>>     *   >>> When I used SnpEff in local galaxy instance, I got an error:
>>     *   >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >> Which Java version do you use. Please make sure you are running Java 1.7.
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > But, I got another error for snpEff.
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>>     *   >          at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > <param name="genomeVersion" type="select" label="Genome">
>>     *   >               <option value="hg37">Human (hg37)<option>
>>     *   >               <option value="mm37.61">Mouse (mm37.61)<option>
>>     *   >       <param>
>>     *   >
>>     *   >
>>     *   >
>>     *   > ________________________________________
>>     *   > From: Björn Grüning [[hidden email]]
>>     *   > Sent: Wednesday, April 02, 2014 10:35 AM
>>     *   > To: Wang, Xiaofei; [hidden email]
>>     *   > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>>     *   >
>>     *   > Hi Xiaofei,
>>     *   >
>>     *   >> Dear there,
>>     *   >>
>>     *   >> When I used SnpEff in local galaxy instance, I got an error:
>>     *   >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>>     *   >
>>     *   > Which Java version do you use. Please make sure you are running Java 1.7.
>>     *   >
>>     *   >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>>     *   >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>>     *   >
>>     *   > Can you give us the complete error message. The important part is missing.
>>     *   >
>>     *   > Ciao,
>>     *   > Bjoern
>>     *   >
>>     *   >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>>     *   >>
>>     *   >>
>>     *   >>
>>     *   >>
>>     *   >> ___________________________________________________________
>>     *   >> Please keep all replies on the list by using "reply all"
>>     *   >> in your mail client.  To manage your subscriptions to this
>>     *   >> and other Galaxy lists, please use the interface at:
>>     *   >>     http://lists.bx.psu.edu/
>>     *   >>
>>     *   >> To search Galaxy mailing lists use the unified search at:
>>     *   >>     http://galaxyproject.org/search/mailinglists/
>>     *   >>
>>     *   >
>>     *   >
>>     *
>>        *
>>
>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
>1. click "SnpEff Download"
>2. choose one genome from "SnpEff Databases" and install it

Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is:

java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'.
        You can try to download the database by running the following command:
                java -jar snpEff.jar download dm5.42

        at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)

I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem?

May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times):


Data Manager: snpeff_genomedb
value name path
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data

________________________________________
From: Björn Grüning [[hidden email]]
Sent: Thursday, April 03, 2014 5:25 AM
To: Wang, Xiaofei; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
>> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> You mean "SnpEff Download" under Data Manager? But, there is no response when I click on it.

It's a little bit complicated. If you click on the "SnpEff Download"
under Data Manager a progress ist started that will fetch a list of
available genomes that in a next step is shown under the tool "SnpEff
Databases" there you can choose which genome annotation you want to
install. To sum it up.

1. click "SnpEff Download"
2. choose one genome from "SnpEff Databases" and install it

> Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response.
> But, when I go to Admin > Data > Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why?

Then there is something missing from your reinstallation. The data
manager is a dependency of the snpeff package and should be installed as
well. Can you check if you need to reinstall the dependency manually
unter the snpeff tool in your admin panel?

Cheers,
Bjoern

> When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time?
>
> Thank you so much!
>
> Best,
>
> Xiaofei
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 4:17 PM
> To: Wang, Xiaofei; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear Bjoern,
>> As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
>> Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome,
>> I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.)
>> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty.
>
> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> Hope that will help!
> Bjoern
>
>>
>> Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?
>>
>> I really appreciate for your help, and thank you so much for your patience!
>>
>> Best,
>>
>> Xiaofei
>> Data Manager
>>
>> Choose your data managing option from below.
>>
>>     *   Access data managers - get data, build indexes, etc
>>
>>        *   SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases
>>
>>        *   SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database
>>
>>        *   BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder
>>
>>        *   BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder
>>
>>        *   Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching
>>
>>     *   View managed data by manager
>>
>>        *   SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases
>>
>>        *   SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database
>>
>>        *   BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder
>>
>>        *   BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder
>>
>>        *   Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching
>>
>>     *   View managed data by Tool Data Table
>>
>>        *   snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases>
>>
>>        *   snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb>
>>
>>        *   snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb>
>>
>>        *   snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations>
>>
>>        *   bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes>
>>
>>        *   bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color>
>>
>>        *   all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta>
>>     *
>>     *
>>     *
>>     *   ________________________________________
>>     *   From: Björn Grüning [[hidden email]]
>>     *   Sent: Wednesday, April 02, 2014 12:55 PM
>>     *   To: Wang, Xiaofei; Björn Grüning; [hidden email]
>>     *   Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>>     *
>>     *   Hi,
>>     *
>>     *   that means that the snpeff annotation is missing. You can install it
>>     *   with the snpeff datamanager under your Admin panel. Have a look at the
>>     *   wiki page about data-manager and the snpeff wrapper documentation.
>>     *   You do not need to edit xml files. If so that is an bug in the wrapper
>>     *   and we should fix it :)
>>     *
>>     *   Cheers,
>>     *   Bjoern
>>     *
>>     *   Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
>>     *   >>> When I used SnpEff in local galaxy instance, I got an error:
>>     *   >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >> Which Java version do you use. Please make sure you are running Java 1.7.
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > But, I got another error for snpEff.
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>>     *   >          at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > <param name="genomeVersion" type="select" label="Genome">
>>     *   >               <option value="hg37">Human (hg37)<option>
>>     *   >               <option value="mm37.61">Mouse (mm37.61)<option>
>>     *   >       <param>
>>     *   >
>>     *   >
>>     *   >
>>     *   > ________________________________________
>>     *   > From: Björn Grüning [[hidden email]]
>>     *   > Sent: Wednesday, April 02, 2014 10:35 AM
>>     *   > To: Wang, Xiaofei; [hidden email]
>>     *   > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>>     *   >
>>     *   > Hi Xiaofei,
>>     *   >
>>     *   >> Dear there,
>>     *   >>
>>     *   >> When I used SnpEff in local galaxy instance, I got an error:
>>     *   >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>>     *   >
>>     *   > Which Java version do you use. Please make sure you are running Java 1.7.
>>     *   >
>>     *   >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>>     *   >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>>     *   >
>>     *   > Can you give us the complete error message. The important part is missing.
>>     *   >
>>     *   > Ciao,
>>     *   > Bjoern
>>     *   >
>>     *   >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>>     *   >>
>>     *   >>
>>     *   >>
>>     *   >>
>>     *   >> ___________________________________________________________
>>     *   >> Please keep all replies on the list by using "reply all"
>>     *   >> in your mail client.  To manage your subscriptions to this
>>     *   >> and other Galaxy lists, please use the interface at:
>>     *   >>     http://lists.bx.psu.edu/
>>     *   >>
>>     *   >> To search Galaxy mailing lists use the unified search at:
>>     *   >>     http://galaxyproject.org/search/mailinglists/
>>     *   >>
>>     *   >
>>     *   >
>>     *
>>        *
>>
>
>



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
In reply to this post by Wang, Xiaofei
Dear there,

I am still stuck there for FASTQ Summary Statistics. Could you give me some clues to fix it?

Thanks a lot!

Best,

Xiaofei
________________________________________
From: Wang, Xiaofei
Sent: Wednesday, April 02, 2014 11:21 AM
To: Daniel Blankenberg
Cc: Björn Grüning; [hidden email]
Subject: RE: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Oh, yes, here it is:

Traceback (most recent call last):
  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in <module>
    if __name__ == "__main__": main()
  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 32, in main
    base_counts = aggregator.get_base_counts_for_column( i )
  File "/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line 397, in get_base_counts_for_column
    return self.nuc_index_base[ column ]
IndexError: list index out of range
________________________________________
From: Daniel Blankenberg [[hidden email]]
Sent: Wednesday, April 02, 2014 11:14 AM
To: Wang, Xiaofei
Cc: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane?


Thanks for using Galaxy,

Dan


On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei <[hidden email]> wrote:

>>> Can you give us the complete error message. The important part is missing.
>
> Here is the whole thing for the error:
>
> Traceback (most recent call last):
>  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in
>    if __name__ == "__main__": main()
>  File "/Users/xiaofe
>
> I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for  FASTQ Summary Statistics or CloundMap?
>
> Thanks a lot!
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 10:35 AM
> To: Wang, Xiaofei; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear there,
>>
>> When I used SnpEff in local galaxy instance, I got an error:
>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>
> Which Java version do you use. Please make sure you are running Java 1.7.
>
>> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>
> Can you give us the complete error message. The important part is missing.
>
> Ciao,
> Bjoern
>
>> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/
>




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: snpEff and FASTQ Summary Statistics errors

Daniel Blankenberg
Hi Xiaofei,

Can you provide some sample data that is causing the issue for you?

Thanks,

Dan


On Apr 3, 2014, at 11:46 AM, Wang, Xiaofei <[hidden email]> wrote:

> Dear there,
>
> I am still stuck there for FASTQ Summary Statistics. Could you give me some clues to fix it?
>
> Thanks a lot!
>
> Best,
>
> Xiaofei
> ________________________________________
> From: Wang, Xiaofei
> Sent: Wednesday, April 02, 2014 11:21 AM
> To: Daniel Blankenberg
> Cc: Björn Grüning; [hidden email]
> Subject: RE: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Oh, yes, here it is:
>
> Traceback (most recent call last):
>  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in <module>
>    if __name__ == "__main__": main()
>  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 32, in main
>    base_counts = aggregator.get_base_counts_for_column( i )
>  File "/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line 397, in get_base_counts_for_column
>    return self.nuc_index_base[ column ]
> IndexError: list index out of range
> ________________________________________
> From: Daniel Blankenberg [[hidden email]]
> Sent: Wednesday, April 02, 2014 11:14 AM
> To: Wang, Xiaofei
> Cc: Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
> To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane?
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei <[hidden email]> wrote:
>
>>>> Can you give us the complete error message. The important part is missing.
>>
>> Here is the whole thing for the error:
>>
>> Traceback (most recent call last):
>> File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in
>>   if __name__ == "__main__": main()
>> File "/Users/xiaofe
>>
>> I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for  FASTQ Summary Statistics or CloundMap?
>>
>> Thanks a lot!
>> ________________________________________
>> From: Björn Grüning [[hidden email]]
>> Sent: Wednesday, April 02, 2014 10:35 AM
>> To: Wang, Xiaofei; [hidden email]
>> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>>
>> Hi Xiaofei,
>>
>>> Dear there,
>>>
>>> When I used SnpEff in local galaxy instance, I got an error:
>>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>>
>> Which Java version do you use. Please make sure you are running Java 1.7.
>>
>>> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>>> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>>
>> Can you give us the complete error message. The important part is missing.
>>
>> Ciao,
>> Bjoern
>>
>>> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>>>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>  http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>  http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>>
>
>
>
>


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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
Yes, here it is in the attachment. It is part of my illumina sequences and I only used it to be the test data for local galaxy to run CloudMap. In fact, I am sure the FASTQ Summary Statistics works on it pretty well on the public Galaxy website for this test data.

Thank you so much!

Best,

Xiaofei
________________________________________
From: Daniel Blankenberg [[hidden email]]
Sent: Thursday, April 03, 2014 3:17 PM
To: Wang, Xiaofei
Cc: [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Hi Xiaofei,

Can you provide some sample data that is causing the issue for you?

Thanks,

Dan


On Apr 3, 2014, at 11:46 AM, Wang, Xiaofei <[hidden email]> wrote:

> Dear there,
>
> I am still stuck there for FASTQ Summary Statistics. Could you give me some clues to fix it?
>
> Thanks a lot!
>
> Best,
>
> Xiaofei
> ________________________________________
> From: Wang, Xiaofei
> Sent: Wednesday, April 02, 2014 11:21 AM
> To: Daniel Blankenberg
> Cc: Björn Grüning; [hidden email]
> Subject: RE: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Oh, yes, here it is:
>
> Traceback (most recent call last):
>  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in <module>
>    if __name__ == "__main__": main()
>  File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 32, in main
>    base_counts = aggregator.get_base_counts_for_column( i )
>  File "/Users/xiaofeiwang/softwares/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line 397, in get_base_counts_for_column
>    return self.nuc_index_base[ column ]
> IndexError: list index out of range
> ________________________________________
> From: Daniel Blankenberg [[hidden email]]
> Sent: Wednesday, April 02, 2014 11:14 AM
> To: Wang, Xiaofei
> Cc: Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
> To get the complete error message, can you click on the bug icon (left-most icon at the bottom of the expanded history item) of the error’d dataset and copy and paste from the page that loads in the middle pane?
>
>
> Thanks for using Galaxy,
>
> Dan
>
>
> On Apr 2, 2014, at 12:04 PM, Wang, Xiaofei <[hidden email]> wrote:
>
>>>> Can you give us the complete error message. The important part is missing.
>>
>> Here is the whole thing for the error:
>>
>> Traceback (most recent call last):
>> File "/Users/xiaofeiwang/softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in
>>   if __name__ == "__main__": main()
>> File "/Users/xiaofe
>>
>> I know it seems weird, but it is the complete message. May I ask a question about this? Is it required rpy for  FASTQ Summary Statistics or CloundMap?
>>
>> Thanks a lot!
>> ________________________________________
>> From: Björn Grüning [[hidden email]]
>> Sent: Wednesday, April 02, 2014 10:35 AM
>> To: Wang, Xiaofei; [hidden email]
>> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>>
>> Hi Xiaofei,
>>
>>> Dear there,
>>>
>>> When I used SnpEff in local galaxy instance, I got an error:
>>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>>
>> Which Java version do you use. Please make sure you are running Java 1.7.
>>
>>> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>>> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>>
>> Can you give us the complete error message. The important part is missing.
>>
>> Ciao,
>> Bjoern
>>
>>> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>>>
>>>
>>>
>>>
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>  http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>  http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>> http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>> http://galaxyproject.org/search/mailinglists/
>>
>
>
>
>


___________________________________________________________
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t1_galaxy.fq (8M) Download Attachment
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
In reply to this post by Wang, Xiaofei
Oh, hooray, I figured it out.
what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again:
java -jar snpEff.jar download dm5.42

Thank you so much!

Best,

Xiaofei
_____________________________________
From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Thursday, April 03, 2014 10:31 AM
To: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

>1. click "SnpEff Download"
>2. choose one genome from "SnpEff Databases" and install it

Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is:

java.lang.RuntimeException:     ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'.
        You can try to download the database by running the following command:
                java -jar snpEff.jar download dm5.42

        at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58)
        at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
        at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)

I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem?

May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times):


Data Manager: snpeff_genomedb
value   name    path
dm5.42  dm5.42 : Drosophila_melanogaster : dm5.42       /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42  dm5.42 : Drosophila_melanogaster : dm5.42       /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42  dm5.42 : Drosophila_melanogaster : dm5.42       /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42  dm5.42 : Drosophila_melanogaster : dm5.42       /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42  dm5.42 : Drosophila_melanogaster : dm5.42       /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data

________________________________________
From: Björn Grüning [[hidden email]]
Sent: Thursday, April 03, 2014 5:25 AM
To: Wang, Xiaofei; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
>> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> You mean "SnpEff Download" under Data Manager? But, there is no response when I click on it.

It's a little bit complicated. If you click on the "SnpEff Download"
under Data Manager a progress ist started that will fetch a list of
available genomes that in a next step is shown under the tool "SnpEff
Databases" there you can choose which genome annotation you want to
install. To sum it up.

1. click "SnpEff Download"
2. choose one genome from "SnpEff Databases" and install it

> Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response.
> But, when I go to Admin > Data > Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why?

Then there is something missing from your reinstallation. The data
manager is a dependency of the snpeff package and should be installed as
well. Can you check if you need to reinstall the dependency manually
unter the snpeff tool in your admin panel?

Cheers,
Bjoern

> When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time?
>
> Thank you so much!
>
> Best,
>
> Xiaofei
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 4:17 PM
> To: Wang, Xiaofei; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear Bjoern,
>> As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
>> Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome,
>> I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.)
>> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty.
>
> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> Hope that will help!
> Bjoern
>
>>
>> Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?
>>
>> I really appreciate for your help, and thank you so much for your patience!
>>
>> Best,
>>
>> Xiaofei
>> Data Manager
>>
>> Choose your data managing option from below.
>>
>>     *   Access data managers - get data, build indexes, etc
>>
>>        *   SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases
>>
>>        *   SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database
>>
>>        *   BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder
>>
>>        *   BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder
>>
>>        *   Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching
>>
>>     *   View managed data by manager
>>
>>        *   SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases
>>
>>        *   SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database
>>
>>        *   BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder
>>
>>        *   BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder
>>
>>        *   Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching
>>
>>     *   View managed data by Tool Data Table
>>
>>        *   snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases>
>>
>>        *   snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb>
>>
>>        *   snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb>
>>
>>        *   snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations>
>>
>>        *   bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes>
>>
>>        *   bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color>
>>
>>        *   all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta>
>>     *
>>     *
>>     *
>>     *   ________________________________________
>>     *   From: Björn Grüning [[hidden email]]
>>     *   Sent: Wednesday, April 02, 2014 12:55 PM
>>     *   To: Wang, Xiaofei; Björn Grüning; [hidden email]
>>     *   Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>>     *
>>     *   Hi,
>>     *
>>     *   that means that the snpeff annotation is missing. You can install it
>>     *   with the snpeff datamanager under your Admin panel. Have a look at the
>>     *   wiki page about data-manager and the snpeff wrapper documentation.
>>     *   You do not need to edit xml files. If so that is an bug in the wrapper
>>     *   and we should fix it :)
>>     *
>>     *   Cheers,
>>     *   Bjoern
>>     *
>>     *   Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
>>     *   >>> When I used SnpEff in local galaxy instance, I got an error:
>>     *   >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >> Which Java version do you use. Please make sure you are running Java 1.7.
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > But, I got another error for snpEff.
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>>     *   >          at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>>     *   >          at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>>     *   >
>>     *   >
>>     *   >
>>     *   >
>>     *   > <param name="genomeVersion" type="select" label="Genome">
>>     *   >               <option value="hg37">Human (hg37)<option>
>>     *   >               <option value="mm37.61">Mouse (mm37.61)<option>
>>     *   >       <param>
>>     *   >
>>     *   >
>>     *   >
>>     *   > ________________________________________
>>     *   > From: Björn Grüning [[hidden email]]
>>     *   > Sent: Wednesday, April 02, 2014 10:35 AM
>>     *   > To: Wang, Xiaofei; [hidden email]
>>     *   > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>>     *   >
>>     *   > Hi Xiaofei,
>>     *   >
>>     *   >> Dear there,
>>     *   >>
>>     *   >> When I used SnpEff in local galaxy instance, I got an error:
>>     *   >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>>     *   >
>>     *   > Which Java version do you use. Please make sure you are running Java 1.7.
>>     *   >
>>     *   >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>>     *   >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>>     *   >
>>     *   > Can you give us the complete error message. The important part is missing.
>>     *   >
>>     *   > Ciao,
>>     *   > Bjoern
>>     *   >
>>     *   >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>>     *   >>
>>     *   >>
>>     *   >>
>>     *   >>
>>     *   >> ___________________________________________________________
>>     *   >> Please keep all replies on the list by using "reply all"
>>     *   >> in your mail client.  To manage your subscriptions to this
>>     *   >> and other Galaxy lists, please use the interface at:
>>     *   >>     http://lists.bx.psu.edu/
>>     *   >>
>>     *   >> To search Galaxy mailing lists use the unified search at:
>>     *   >>     http://galaxyproject.org/search/mailinglists/
>>     *   >>
>>     *   >
>>     *   >
>>     *
>>        *
>>
>
>



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
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___________________________________________________________
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
I am sorry to bother again about this problem.

I would like to use Drosophila melanogaster : BDGP5.74. I did the two steps you suggested to me to install the annotation. I also did from command line. But, there is no the option of BDGP5.74 from the "Genome" drop-down menu in SnpEff. The version of SnpEff is version 1.0 and I used SnpEfff in CloudMap workflow. Do you know why and how to figure it out? (In fact, it works fine for BDGP5.66.)

Thanks

Best,

Xiaofei
________________________________________
From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Thursday, April 03, 2014 3:52 PM
To: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Oh, hooray, I figured it out.
what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again:
java -jar snpEff.jar download dm5.42

Thank you so much!

Best,

Xiaofei
_____________________________________
From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Thursday, April 03, 2014 10:31 AM
To: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

>1. click "SnpEff Download"
>2. choose one genome from "SnpEff Databases" and install it

Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is:

java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'.
You can try to download the database by running the following command:
java -jar snpEff.jar download dm5.42

at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58)
at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)

I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem?

May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times):


Data Manager: snpeff_genomedb
value name path
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data

________________________________________
From: Björn Grüning [[hidden email]]
Sent: Thursday, April 03, 2014 5:25 AM
To: Wang, Xiaofei; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
>> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> You mean "SnpEff Download" under Data Manager? But, there is no response when I click on it.

It's a little bit complicated. If you click on the "SnpEff Download"
under Data Manager a progress ist started that will fetch a list of
available genomes that in a next step is shown under the tool "SnpEff
Databases" there you can choose which genome annotation you want to
install. To sum it up.

1. click "SnpEff Download"
2. choose one genome from "SnpEff Databases" and install it

> Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response.
> But, when I go to Admin > Data > Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why?

Then there is something missing from your reinstallation. The data
manager is a dependency of the snpeff package and should be installed as
well. Can you check if you need to reinstall the dependency manually
unter the snpeff tool in your admin panel?

Cheers,
Bjoern

> When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time?
>
> Thank you so much!
>
> Best,
>
> Xiaofei
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 4:17 PM
> To: Wang, Xiaofei; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear Bjoern,
>> As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
>> Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome,
>> I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.)
>> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty.
>
> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> Hope that will help!
> Bjoern
>
>>
>> Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?
>>
>> I really appreciate for your help, and thank you so much for your patience!
>>
>> Best,
>>
>> Xiaofei
>> Data Manager
>>
>> Choose your data managing option from below.
>>
>> * Access data managers - get data, build indexes, etc
>>
>> * SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases
>>
>> * SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database
>>
>> * BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder
>>
>> * BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder
>>
>> * Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching
>>
>> * View managed data by manager
>>
>> * SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases
>>
>> * SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database
>>
>> * BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder
>>
>> * BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder
>>
>> * Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching
>>
>> * View managed data by Tool Data Table
>>
>> * snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases>
>>
>> * snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb>
>>
>> * snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb>
>>
>> * snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations>
>>
>> * bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes>
>>
>> * bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color>
>>
>> * all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta>
>> *
>> *
>> *
>> * ________________________________________
>> * From: Björn Grüning [[hidden email]]
>> * Sent: Wednesday, April 02, 2014 12:55 PM
>> * To: Wang, Xiaofei; Björn Grüning; [hidden email]
>> * Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>> *
>> * Hi,
>> *
>> * that means that the snpeff annotation is missing. You can install it
>> * with the snpeff datamanager under your Admin panel. Have a look at the
>> * wiki page about data-manager and the snpeff wrapper documentation.
>> * You do not need to edit xml files. If so that is an bug in the wrapper
>> * and we should fix it :)
>> *
>> * Cheers,
>> * Bjoern
>> *
>> * Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
>> * >>> When I used SnpEff in local galaxy instance, I got an error:
>> * >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>> * >
>> * >
>> * >
>> * >
>> * >> Which Java version do you use. Please make sure you are running Java 1.7.
>> * >
>> * >
>> * >
>> * >
>> * > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>> * >
>> * >
>> * >
>> * >
>> * > But, I got another error for snpEff.
>> * >
>> * >
>> * >
>> * >
>> * > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>> * > at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>> * >
>> * >
>> * >
>> * >
>> * > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>> * >
>> * >
>> * >
>> * >
>> * > <param name="genomeVersion" type="select" label="Genome">
>> * > <option value="hg37">Human (hg37)<option>
>> * > <option value="mm37.61">Mouse (mm37.61)<option>
>> * > <param>
>> * >
>> * >
>> * >
>> * > ________________________________________
>> * > From: Björn Grüning [[hidden email]]
>> * > Sent: Wednesday, April 02, 2014 10:35 AM
>> * > To: Wang, Xiaofei; [hidden email]
>> * > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>> * >
>> * > Hi Xiaofei,
>> * >
>> * >> Dear there,
>> * >>
>> * >> When I used SnpEff in local galaxy instance, I got an error:
>> * >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>> * >
>> * > Which Java version do you use. Please make sure you are running Java 1.7.
>> * >
>> * >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> * >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>> * >
>> * > Can you give us the complete error message. The important part is missing.
>> * >
>> * > Ciao,
>> * > Bjoern
>> * >
>> * >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>> * >>
>> * >>
>> * >>
>> * >>
>> * >> ___________________________________________________________
>> * >> Please keep all replies on the list by using "reply all"
>> * >> in your mail client. To manage your subscriptions to this
>> * >> and other Galaxy lists, please use the interface at:
>> * >> http://lists.bx.psu.edu/
>> * >>
>> * >> To search Galaxy mailing lists use the unified search at:
>> * >> http://galaxyproject.org/search/mailinglists/
>> * >>
>> * >
>> * >
>> *
>> *
>>
>
>



___________________________________________________________
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
Dear there,

Could someone tell me why there is no Drosophila melanogaster :  BDGP 5.74 in the drop-down menu of SnpEff for local Galaxy? 

In fact, I could find it (BDGP 5.74) in SnpEff Databases and also download it from SnpEff Download (Data manager: Admin > Manage local data (beta)). But, I still can not find it in the menu of SnpEff after downloading and installing it by the "two-steps" as below.

Thanks a lot!

Best,

Xiaofei

From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Friday, April 11, 2014 5:52 PM
To: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

I am sorry to bother again about this problem.

I would like to use Drosophila melanogaster : BDGP5.74. I did the two steps you suggested to me to install the annotation. I also did from command line. But, there is no the option of BDGP5.74 from the "Genome" drop-down menu in SnpEff. The version of SnpEff is version 1.0 and I used SnpEfff in CloudMap workflow. Do you know why and how to figure it out? (In fact, it works fine for BDGP5.66.)

Thanks

Best,

Xiaofei
________________________________________
From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Thursday, April 03, 2014 3:52 PM
To: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Oh, hooray, I figured it out.
what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again:
java -jar snpEff.jar download dm5.42

Thank you so much!

Best,

Xiaofei
_____________________________________
From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Thursday, April 03, 2014 10:31 AM
To: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

>1. click "SnpEff Download"
>2. choose one genome from "SnpEff Databases" and install it

Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is:

java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'.
You can try to download the database by running the following command:
java -jar snpEff.jar download dm5.42

at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58)
at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)

I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem?

May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times):


Data Manager: snpeff_genomedb
value name path
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data

________________________________________
From: Björn Grüning [[hidden email]]
Sent: Thursday, April 03, 2014 5:25 AM
To: Wang, Xiaofei; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
>> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> You mean "SnpEff Download" under Data Manager? But, there is no response when I click on it.

It's a little bit complicated. If you click on the "SnpEff Download"
under Data Manager a progress ist started that will fetch a list of
available genomes that in a next step is shown under the tool "SnpEff
Databases" there you can choose which genome annotation you want to
install. To sum it up.

1. click "SnpEff Download"
2. choose one genome from "SnpEff Databases" and install it

> Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response.
> But, when I go to Admin > Data > Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why?

Then there is something missing from your reinstallation. The data
manager is a dependency of the snpeff package and should be installed as
well. Can you check if you need to reinstall the dependency manually
unter the snpeff tool in your admin panel?

Cheers,
Bjoern

> When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time?
>
> Thank you so much!
>
> Best,
>
> Xiaofei
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 4:17 PM
> To: Wang, Xiaofei; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear Bjoern,
>> As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
>> Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome,
>> I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.)
>> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty.
>
> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> Hope that will help!
> Bjoern
>
>>
>> Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?
>>
>> I really appreciate for your help, and thank you so much for your patience!
>>
>> Best,
>>
>> Xiaofei
>> Data Manager
>>
>> Choose your data managing option from below.
>>
>> * Access data managers - get data, build indexes, etc
>>
>> * SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases
>>
>> * SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database
>>
>> * BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder
>>
>> * BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder
>>
>> * Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching
>>
>> * View managed data by manager
>>
>> * SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases
>>
>> * SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database
>>
>> * BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder
>>
>> * BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder
>>
>> * Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching
>>
>> * View managed data by Tool Data Table
>>
>> * snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases>
>>
>> * snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb>
>>
>> * snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb>
>>
>> * snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations>
>>
>> * bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes>
>>
>> * bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color>
>>
>> * all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta>
>> *
>> *
>> *
>> * ________________________________________
>> * From: Björn Grüning [[hidden email]]
>> * Sent: Wednesday, April 02, 2014 12:55 PM
>> * To: Wang, Xiaofei; Björn Grüning; [hidden email]
>> * Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>> *
>> * Hi,
>> *
>> * that means that the snpeff annotation is missing. You can install it
>> * with the snpeff datamanager under your Admin panel. Have a look at the
>> * wiki page about data-manager and the snpeff wrapper documentation.
>> * You do not need to edit xml files. If so that is an bug in the wrapper
>> * and we should fix it :)
>> *
>> * Cheers,
>> * Bjoern
>> *
>> * Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
>> * >>> When I used SnpEff in local galaxy instance, I got an error:
>> * >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>> * >
>> * >
>> * >
>> * >
>> * >> Which Java version do you use. Please make sure you are running Java 1.7.
>> * >
>> * >
>> * >
>> * >
>> * > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>> * >
>> * >
>> * >
>> * >
>> * > But, I got another error for snpEff.
>> * >
>> * >
>> * >
>> * >
>> * > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>> * > at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>> * >
>> * >
>> * >
>> * >
>> * > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>> * >
>> * >
>> * >
>> * >
>> * > <param name="genomeVersion" type="select" label="Genome">
>> * > <option value="hg37">Human (hg37)<option>
>> * > <option value="mm37.61">Mouse (mm37.61)<option>
>> * > <param>
>> * >
>> * >
>> * >
>> * > ________________________________________
>> * > From: Björn Grüning [[hidden email]]
>> * > Sent: Wednesday, April 02, 2014 10:35 AM
>> * > To: Wang, Xiaofei; [hidden email]
>> * > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>> * >
>> * > Hi Xiaofei,
>> * >
>> * >> Dear there,
>> * >>
>> * >> When I used SnpEff in local galaxy instance, I got an error:
>> * >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>> * >
>> * > Which Java version do you use. Please make sure you are running Java 1.7.
>> * >
>> * >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> * >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>> * >
>> * > Can you give us the complete error message. The important part is missing.
>> * >
>> * > Ciao,
>> * > Bjoern
>> * >
>> * >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>> * >>
>> * >>
>> * >>
>> * >>
>> * >> ___________________________________________________________
>> * >> Please keep all replies on the list by using "reply all"
>> * >> in your mail client. To manage your subscriptions to this
>> * >> and other Galaxy lists, please use the interface at:
>> * >> http://lists.bx.psu.edu/
>> * >>
>> * >> To search Galaxy mailing lists use the unified search at:
>> * >> http://galaxyproject.org/search/mailinglists/
>> * >>
>> * >
>> * >
>> *
>> *
>>
>
>



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: snpEff and FASTQ Summary Statistics errors

Wang, Xiaofei
Dear folks,

Why could not I find BDGP 5.74 in the drop-down menu of SnpEff? If I want to use this version, what should I do or what other steps do I need to install it?

Thank you so much!


From: Wang, Xiaofei
Sent: Monday, April 14, 2014 9:50 AM
To: Björn Grüning; [hidden email]
Subject: RE: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Dear there,

Could someone tell me why there is no Drosophila melanogaster :  BDGP 5.74 in the drop-down menu of SnpEff for local Galaxy? 

In fact, I could find it (BDGP 5.74) in SnpEff Databases and also download it from SnpEff Download (Data manager: Admin > Manage local data (beta)). But, I still can not find it in the menu of SnpEff after downloading and installing it by the "two-steps" as below.

Thanks a lot!

Best,

Xiaofei

From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Friday, April 11, 2014 5:52 PM
To: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

I am sorry to bother again about this problem.

I would like to use Drosophila melanogaster : BDGP5.74. I did the two steps you suggested to me to install the annotation. I also did from command line. But, there is no the option of BDGP5.74 from the "Genome" drop-down menu in SnpEff. The version of SnpEff is version 1.0 and I used SnpEfff in CloudMap workflow. Do you know why and how to figure it out? (In fact, it works fine for BDGP5.66.)

Thanks

Best,

Xiaofei
________________________________________
From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Thursday, April 03, 2014 3:52 PM
To: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Oh, hooray, I figured it out.
what I did is to go to this folder /Users/pablocingolani/snpEff and download the database by command again:
java -jar snpEff.jar download dm5.42

Thank you so much!

Best,

Xiaofei
_____________________________________
From: [hidden email] [[hidden email]] on behalf of Wang, Xiaofei [[hidden email]]
Sent: Thursday, April 03, 2014 10:31 AM
To: Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

>1. click "SnpEff Download"
>2. choose one genome from "SnpEff Databases" and install it

Yes, I need to wait a few minutes to get response. But, after these two steps, I got an error again when I run the snpEff, here it is:

java.lang.RuntimeException: ERROR: Cannot read file '/Users/pablocingolani/snpEff/./data/dm5.42/snpEffectPredictor.bin'.
You can try to download the database by running the following command:
java -jar snpEff.jar download dm5.42

at ca.mcgill.mcb.pcingola.snpEffect.SnpEffectPredictor.load(SnpEffectPredictor.java:58)
at ca.mcgill.mcb.pcingola.snpEffect.Config.loadSnpEffectPredictor(Config.java:377)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1006)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)

I tried to download the database by command line: java -jar snpEff.jar download dm5.42, but still got this error. How should I figure out this problem?

May I ask one more question about this? After 1 and 2 steps, what is it going to be shown in Data Manager? I mean in snpeff annotation, the third part of Data Manager (View managed data by Tool Data Table). When I click on snpeff annotations on View managed data by Tool Data Table, there is nothing there. Is it correct? Actually, when I clicked on snpeff genomedb, it showed like this (I installed the genome several times):


Data Manager: snpeff_genomedb
value name path
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data
dm5.42 dm5.42 : Drosophila_melanogaster : dm5.42 /Users/xiaofeiwang/softwares/galaxy-dist/tool-data/snpEff/data

________________________________________
From: Björn Grüning [[hidden email]]
Sent: Thursday, April 03, 2014 5:25 AM
To: Wang, Xiaofei; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors

Am 03.04.2014 04:34, schrieb Wang, Xiaofei:
>> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> You mean "SnpEff Download" under Data Manager? But, there is no response when I click on it.

It's a little bit complicated. If you click on the "SnpEff Download"
under Data Manager a progress ist started that will fetch a list of
available genomes that in a next step is shown under the tool "SnpEff
Databases" there you can choose which genome annotation you want to
install. To sum it up.

1. click "SnpEff Download"
2. choose one genome from "SnpEff Databases" and install it

> Unfortunately, I tried to uninstall the snpEff tool shed and re-install it again to see if I can get response.
> But, when I go to Admin > Data > Manage local data (beta) this time, there is no snpEff data manager and only the BWA and Fetching genome (I installed them by myself) are left there. Do you know why?

Then there is something missing from your reinstallation. The data
manager is a dependency of the snpeff package and should be installed as
well. Can you check if you need to reinstall the dependency manually
unter the snpeff tool in your admin panel?

Cheers,
Bjoern

> When I search the tool sheds like BWA data manager, I did not find there is snpEff data manager. Do you know where could I find it? Why the snpEff data manager has been there last time?
>
> Thank you so much!
>
> Best,
>
> Xiaofei
>
> ________________________________________
> From: Björn Grüning [[hidden email]]
> Sent: Wednesday, April 02, 2014 4:17 PM
> To: Wang, Xiaofei; Björn Grüning; [hidden email]
> Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>
> Hi Xiaofei,
>
>> Dear Bjoern,
>> As your suggestion, I tried to install the snpEff annotation. But, I think I am still be stuck there. What I did is:
>> Admin > Data > Manage local data (beta), then the message is shown as below. (For the BWA and Fetching genome,
>> I installed them from tool_sheds by myself. For the SnpEff staff, it has been there when I checked the data manager.)
>> Next, I clicked on SnpEff Databases > Execute. But, when I checked the snpeff annotations in View managed data by Tool Data Table part, it is still empty.
>
> After SnpEff Databases > Execute you still need to pick genome of
> interest and run "SnpEff Download". SnpEff Databases just downloads a
> list of available genomes.
>
> Hope that will help!
> Bjoern
>
>>
>> Could you give me more details about how to install the annotation with the snpeff data manager under the Admin panel?
>>
>> I really appreciate for your help, and thank you so much for your patience!
>>
>> Best,
>>
>> Xiaofei
>> Data Manager
>>
>> Choose your data managing option from below.
>>
>> * Access data managers - get data, build indexes, etc
>>
>> * SnpEff Databases<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_databases%2F3.4> - Read the list of available snpEff databases
>>
>> * SnpEff Download<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager_snpeff_download%2F3.4> - Download a new database
>>
>> * BWA index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_index_builder_data_manager%2F0.0.1> - builder
>>
>> * BWA Color index<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fbwa_color_space_index_builder_data_manager%2F0.0.1> - builder
>>
>> * Reference Genome<http://127.0.0.1:8080/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager_fetch_genome_all_fasta%2F0.0.1> - fetching
>>
>> * View managed data by manager
>>
>> * SnpEff Databases<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_databases%2F0.0.1> - Read the list of available snpEff databases
>>
>> * SnpEff Download<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fsnpeff%2Fdata_manager%2Fdata_manager_snpeff_download%2F0.0.1> - Download a new database
>>
>> * BWA index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_index_builder%2F0.0.1> - builder
>>
>> * BWA Color index<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_bwa_index_builder%2Fdata_manager%2Fbwa_color_space_index_builder%2F0.0.1> - builder
>>
>> * Reference Genome<http://127.0.0.1:8080/data_manager/manage_data_manager?id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fdata_manager_fetch_genome_all_fasta%2Fdata_manager%2Ffetch_genome_all_fasta%2F0.0.1> - fetching
>>
>> * View managed data by Tool Data Table
>>
>> * snpeff_databases<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_databases>
>>
>> * snpeff_genomedb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_genomedb>
>>
>> * snpeff_regulationdb<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_regulationdb>
>>
>> * snpeff_annotations<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=snpeff_annotations>
>>
>> * bwa_indexes<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes>
>>
>> * bwa_indexes_color<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=bwa_indexes_color>
>>
>> * all_fasta<http://127.0.0.1:8080/data_manager/manage_data_table?table_name=all_fasta>
>> *
>> *
>> *
>> * ________________________________________
>> * From: Björn Grüning [[hidden email]]
>> * Sent: Wednesday, April 02, 2014 12:55 PM
>> * To: Wang, Xiaofei; Björn Grüning; [hidden email]
>> * Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>> *
>> * Hi,
>> *
>> * that means that the snpeff annotation is missing. You can install it
>> * with the snpeff datamanager under your Admin panel. Have a look at the
>> * wiki page about data-manager and the snpeff wrapper documentation.
>> * You do not need to edit xml files. If so that is an bug in the wrapper
>> * and we should fix it :)
>> *
>> * Cheers,
>> * Bjoern
>> *
>> * Am 02.04.2014 19:34, schrieb Wang, Xiaofei:
>> * >>> When I used SnpEff in local galaxy instance, I got an error:
>> * >>> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>> * >
>> * >
>> * >
>> * >
>> * >> Which Java version do you use. Please make sure you are running Java 1.7.
>> * >
>> * >
>> * >
>> * >
>> * > Yes, it is figured, when I changed the java version to 1.7. Thank you so much!
>> * >
>> * >
>> * >
>> * >
>> * > But, I got another error for snpEff.
>> * >
>> * >
>> * >
>> * >
>> * > java.lang.RuntimeException: Property: 'dm5.30.genome' not found
>> * > at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:92)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:481)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:444)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:345)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:96)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.readConfig(SnpEff.java:245)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320)
>> * > at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83)
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * >
>> * > What does this mean? I found the similar error on this thead http://dev.list.galaxyproject.org/snpEff-on-Galaxy-td4659332.html, but there is no reply.
>> * >
>> * >
>> * >
>> * >
>> * > Does this mean I need to add genome to Galaxy? Following this webpage: http://snpeff.sourceforge.net/SnpEff_manual.html? If yes, could you give me an example how to edit the snpEffect.xml file in dm (Drosophila) case as below? (In fact, on the drap-down menu of Genome in snpEff, there is different options for genome. Why the error shows '*.genome' not found? )
>> * >
>> * >
>> * >
>> * >
>> * > <param name="genomeVersion" type="select" label="Genome">
>> * > <option value="hg37">Human (hg37)<option>
>> * > <option value="mm37.61">Mouse (mm37.61)<option>
>> * > <param>
>> * >
>> * >
>> * >
>> * > ________________________________________
>> * > From: Björn Grüning [[hidden email]]
>> * > Sent: Wednesday, April 02, 2014 10:35 AM
>> * > To: Wang, Xiaofei; [hidden email]
>> * > Subject: Re: [galaxy-dev] snpEff and FASTQ Summary Statistics errors
>> * >
>> * > Hi Xiaofei,
>> * >
>> * >> Dear there,
>> * >>
>> * >> When I used SnpEff in local galaxy instance, I got an error:
>> * >> Exception in thread "main" java.lang.UnsupportedClassVersionError: ca/mcgill/mcb/pcingola/snpSift/SnpSift : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClassCond(ClassLoader.j
>> * >
>> * > Which Java version do you use. Please make sure you are running Java 1.7.
>> * >
>> * >> Also, when I used the FASTQ Summary Statistics, I got an error like this:
>> * >> Traceback (most recent call last): File "/Users/...../softwares/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/9b7b4e0ca9db/fastq_stats/fastq_stats.py", line 48, in if __name__ == "__main__": main() File "/Users/...
>> * >
>> * > Can you give us the complete error message. The important part is missing.
>> * >
>> * > Ciao,
>> * > Bjoern
>> * >
>> * >> I tried to google and solve them by myself. But I really do not know how to do that. Could anybody give me some clue? Thanks a lot for your help!
>> * >>
>> * >>
>> * >>
>> * >>
>> * >> ___________________________________________________________
>> * >> Please keep all replies on the list by using "reply all"
>> * >> in your mail client. To manage your subscriptions to this
>> * >> and other Galaxy lists, please use the interface at:
>> * >> http://lists.bx.psu.edu/
>> * >>
>> * >> To search Galaxy mailing lists use the unified search at:
>> * >> http://galaxyproject.org/search/mailinglists/
>> * >>
>> * >
>> * >
>> *
>> *
>>
>
>



___________________________________________________________
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___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/