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!
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/
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!
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/
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!
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/
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!
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/
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 [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!
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/
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 [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!
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/
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 [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!
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/
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 xfwang@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 [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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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 [dan@bx.psu.edu] Sent: Thursday, April 03, 2014 3:17 PM To: Wang, Xiaofei Cc: galaxy-dev@lists.bx.psu.edu 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 xfwang@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 [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!
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/
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galaxy-dev@lists.galaxyproject.org
-
Björn Grüning -
Daniel Blankenberg -
Wang, Xiaofei