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 <xfw...@ku.edu> 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; galaxy-dev@lists.bx.psu.edu
> 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 [d...@bx.psu.edu]
> Sent: Wednesday, April 02, 2014 11:14 AM
> To: Wang, Xiaofei
> Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu
> 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 <xfw...@ku.edu> 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 [bjoern.gruen...@gmail.com]
>> Sent: Wednesday, April 02, 2014 10:35 AM
>> To: Wang, Xiaofei; galaxy-dev@lists.bx.psu.edu
>> 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!
>>> 
>>> 
>>> 
>>> 
>>> ___________________________________________________________
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>>> 
>> 
>> 
>> 
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
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>> 
> 
> 
> 
> 


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