First,I tried assign_taxonomy.py -i otus/rep_set.fna -m blast -r ../SILVA_128_QIIME_release/rep_set/rep_set_16S_only/97/97_otus_16S.fasta -t ../SILVA_128_QIIME_release/taxonomy/16S_only/97/consensus_taxonomy_7_levels.txt .The result was also mismatched. I am using qiime1.9.1 not qiime1.8.I do not know if this is the reason.
When I tried assign_taxonomy.py -i otus/rep_set.fna -m rdp -o rdp_assigned_taxonomy -r ../SILVA_128_QIIME_release/rep_set/rep_set_16S_only/97/97_otus_16S.fasta -t ../SILVA_128_QIIME_release/taxonomy/16S_only/97/consensus_taxonomy_7_levels.txt.It came
Traceback (most recent call last):
File "/usr/local/bin/assign_taxonomy.py", line 417, in <module>
main()
File "/usr/local/bin/assign_taxonomy.py", line 394, in main
log_path=log_path)
File "/usr/local/lib/python2.7/dist-packages/qiime/assign_taxonomy.py", line 860, in __call__
max_memory=max_memory, tmp_dir=tmp_dir)
File "/usr/local/lib/python2.7/dist-packages/bfillings/rdp_classifier.py", line 515, in train_rdp_classifier_and_assign_taxonomy
tmp_dir=tmp_dir)
File "/usr/local/lib/python2.7/dist-packages/bfillings/rdp_classifier.py", line 485, in train_rdp_classifier
return app(training_seqs_file)
File "/usr/local/lib/python2.7/dist-packages/bfillings/rdp_classifier.py", line 327, in __call__
remove_tmp=remove_tmp)
File "/usr/local/lib/python2.7/dist-packages/burrito/util.py", line 285, in __call__
'StdErr:\n%s\n' % open(errfile).read())
burrito.util.ApplicationError: Unacceptable application exit status: 1
Command:
cd "/home/qiime/Desktop/silvatest_no_ulcust/"; java -Xmx4000M -cp "/qiime_software/rdpclassifier-2.2-release/rdp_classifier-2.2.jar" edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker "/tmp/RdpTaxonomy_oyPPOo.txt" "/tmp/tmpcDuwMkGwIlYSNPWtkut9.txt" 1 version1 cogent "/tmp/RdpTrainer_4jJhbO" > "/tmp/tmpvWCRae9y7RJXriI1dhkH.txt" 2> "/tmp/tmpgEO5fcWXtxBjLB23ZOH7.txt"
StdOut:
StdErr:
Copyright 2006 Michigan State University Board of Trustees.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Authors's mailng address:
Center for Microbial Ecology
2225A Biomedical Physical Science
Michigan State University
East Lansing, Michigan USA 48824-4320
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at edu.msu.cme.rdp.classifier.train.RawHierarchyTree.initWordOccurrence(RawHierarchyTree.java:108)
at edu.msu.cme.rdp.classifier.train.TreeFactory.addSequencewithLineage(TreeFactory.java:211)
at edu.msu.cme.rdp.classifier.train.TreeFactory.addSequence(TreeFactory.java:139)
at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.<init>(ClassifierTraineeMaker.java:47)
at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.main(ClassifierTraineeMaker.java:133)
By the way, when I used pick_open_reference_otus.py to assign taxonomy on my miseq data against Silva128 data base,the mismatched problem came.But when I used pick_closed_reference_otus.py to assign taxonomy on the same miseq data against Silva128 data base,it can assign the OTUs correctly.
Thank you for the help.