I am contacting you all for I have met a problem with assign_taxonomy.py.
Traceback (most recent call last):
File "/usr/lib/qiime/bin/assign_taxonomy.py", line 429, in <module>
main()
File "/usr/lib/qiime/bin/assign_taxonomy.py", line 406, in main
log_path=log_path)
File "/usr/lib/python2.7/dist-packages/qiime/assign_taxonomy.py", line 864, in __call__
max_memory=max_memory, tmp_dir=tmp_dir)
File "/usr/lib/python2.7/dist-packages/bfillings/rdp_classifier.py", line 503, in train_rdp_classifier_and_assign_taxonomy
tmp_dir=tmp_dir)
File "/usr/lib/python2.7/dist-packages/bfillings/rdp_classifier.py", line 473, in train_rdp_classifier
return app(training_seqs_file)
File "/usr/lib/python2.7/dist-packages/bfillings/rdp_classifier.py", line 315, in __call__
remove_tmp=remove_tmp)
File "/usr/lib/python2.7/dist-packages/burrito/util.py", line 284, in __call__
'StdErr:\n%s\n' % open(errfile).read())
burrito.util.ApplicationError: Unacceptable application exit status: 255
Command:
cd "/home/galaxy/database/job_working_directory/000/287/working/"; java -Xmx15000M -cp "/usr/local/galaxy/galaxy/tools/IEG/external_tools/rdp_classifier_2.5/rdp_classifier-2.5.jar" edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker -t"/tmp/RdpTaxonomy_F7Lo5N.txt" -s /tmp/tmpaogprxD6nMsCedla5Gvd.txt -n1 -vversion1 -mcogent -o /tmp/RdpTrainer_fD8oex > "/tmp/tmpkB2JUbezVblCdlCwEoaL.txt" 2> "/tmp/tmpieq4YXoj9rCkHIm99FKy.txt"
StdOut:
StdErr:
Usage: java ClassifierTraineeMaker <tax_file> <rawseq.fa> <trainsetNo> <version> <version_modification> <output_directory>
This program will create 4 output training files to be used by the classifier:
bergeyTrainingTree.xml, genus_wordConditionalProbList.txt, logWordPrior.txt and wordConditionalProbIndexArr.txt
Command line arguments:
--tax_file contains the hierarchical taxonomy information in the following format:
taxid*taxon name*parent taxid*depth*rank
Fields taxid, the parent taxid and depth should be in integer format
depth indicates the depth from the root taxon.
Note: the depth for the root is 0
EX: 44*ROOT*1*0*domain
--rawseq.fa contains the raw training sequences in fasta format
The header of this fasta file starts with ">",
followed by the sequence name, white space(s)
and a list taxon names seperated by ';' with highest rank taxon first.
Ex: >seq1 ROOT;Ph1;Fam1;G1
Note: a sequence can only be assigned to the lowest rank taxon.
--trainsetNo is a integer. It's used to marked the training information.
--version indicates the version of the hierarchical taxonomy
Ex: Bacteria Nomenclature
--version_modification holds the modifcation information of the taxonomy if any
Ex: Acidobacterium Added
--output_directory specifies the output directory.