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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>
>
>
> ___________________________________________________________
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