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geraldinepascal / FROGS

FROGS is a galaxy/CLI workflow designed to produce an OTUs count matrix from high depth sequencing amplicon data.
GNU General Public License v3.0
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Error testing on Frogs #33

Closed jzegarrav closed 5 years ago

jzegarrav commented 6 years ago

When i run:

root@raquel-X555LDB:/home/raquel/FROGS-master/test# bash test.sh /home/raquel/FROGS-master/ 2 4 /tmp/results

Frogs can't found RDPTools jar classes:

Step preprocess tum awu 5 17:42:20 PET 2018 Step clustering tum awu 5 17:43:36 PET 2018 Step remove_chimera tum awu 5 17:44:20 PET 2018 Step filters tum awu 5 17:45:57 PET 2018 Step affiliation_OTU tum awu 5 17:45:58 PET 2018 Exception in thread "main" java.lang.NoClassDefFoundError: edu/msu/cme/rdp/taxatree/interfaces/TreeVisitor at edu.msu.cme.rdp.classifier.cli.ClassifierMain.main(ClassifierMain.java:67) Caused by: java.lang.ClassNotFoundException: edu.msu.cme.rdp.taxatree.interfaces.TreeVisitor at java.net.URLClassLoader.findClass(URLClassLoader.java:381) at java.lang.ClassLoader.loadClass(ClassLoader.java:424) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331) at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ... 1 more Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 754, in run self.target(*self.args, **self.__kwargs) File "/home/raquel/FROGS-master//app/affiliation_OTU.py", line 192, in process_rdp rdp_cmd.submit(log_file) File "/home/raquel/FROGS-master/lib/frogsUtils.py", line 140, in submit subprocess.check_output( self.get_cmd(), shell=True ) File "/usr/lib/python2.7/subprocess.py", line 574, in check_output raise CalledProcessError(retcode, cmd, output=output) CalledProcessError: Command 'taskset -c 0 java -Xmx4g -jar /home/raquel/FROGS-master/libexec/classifier.jar classify -c 0.0 -t /home/raquel/FROGS-master//test/data/db.fasta.properties -o /tmp/results/1533509158.25_11883_1533509158.25_11883_04-filters.fasta_0.rdp /tmp/results/1533509158.25_11883_04-filters.fasta_0' returned non-zero exit status 1

Traceback (most recent call last): File "/home/raquel/FROGS-master//app/affiliation_OTU.py", line 370, in Blast(args.reference, args.input_fasta, blast_out_list[0], args.nb_cpus).submit(log_blast_list[0]) File "/home/raquel/FROGS-master/lib/frogsUtils.py", line 135, in submit FH_log.write( '# ' + self.description + ' (' + os.path.basename(self.program) + ' version : ' + self.get_version() + ')\n' ) File "/home/raquel/FROGS-master//app/affiliation_OTU.py", line 75, in get_version return Cmd.get_version(self, 'stdout').split()[1].strip() IndexError: list index out of range Error in affiliation_OTU

I copied all rdptools jars to libexec.

Help please

mariabernard commented 6 years ago

Hi,

thanks trying to use FROGS.

Could you please copy and paste the results of: ls -l /home/raquel/FROGS-master/libexec

Regards