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 [dan@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 xfwang@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.gruening@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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