Question: Noclassdeffounderror In Picard Paired Read Mate Fixer
0
Nicolas Quizon • 10 wrote:
Dear Galaxy Gurus,
I am a student and still new to Galaxy. I am encountering an error
when
trying to run the Picard Paired Read Mate Fixer with default settings
on
Galaxy. The code only runs for a few seconds before failing and
displaying
the error message.
## exit code=1; stdout=
[Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation
INPUT=[/usr/lib/galaxy-server/database/files/000/dataset_85.dat]
OUTPUT=/usr/lib/galaxy-server/database/tmp/tmpxhbz3T
SORT_ORDER=coordinate
VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false
COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
CREATE_MD5_FILE=false
[Mon Aug 19 16:46:15 EDT 2013] Executing as root@biolinux-pbcn6 on
Linux
3.2.0-43-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_27-b27; Picard
version: 1.91()
[Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation
done.
Elapsed time: 0.00 minutes.
Runtime.totalMemory()=378470400
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.NoClassDefFoundError:
org/itadaki/bzip2/BZip2InputStream
at
net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:84
)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgr
am.java:177)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandL
ineProgram.java:119)
at
net.sf.picard.sam.FixMateInformation.main(FixMateInformation.java:76)
Caused by: java.lang.ClassNotFoundException:
org.itadaki.bzip2.BZip2InputStream
at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
... 4 more
For input I am using data that I have successfully mapped with BWA
for
Illumina. I currently have Python version 2.7.3 and Java version
1.6.0_27,
and an working on a machine running Ubuntu 12.04.2 LTS.
Any help is greatly appreciated!
Thanks!
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•
modified 5.2 years ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
5.2 years ago by
Nicolas Quizon • 10
