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(CommandLineProgram.java:177)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.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.