{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/qiime/issues/2136","repository_url":"https://api.github.com/repos/biocore/qiime","labels_url":"https://api.github.com/repos/biocore/qiime/issues/2136/labels{/name}","comments_url":"https://api.github.com/repos/biocore/qiime/issues/2136/comments","events_url":"https://api.github.com/repos/biocore/qiime/issues/2136/events","html_url":"https://github.com/biocore/qiime/issues/2136","id":142130534,"number":2136,"title":"error of rdp classifier by using assign_taxonomy.py in qiime","user":{"login":"KaiFeng007","id":17958536,"avatar_url":"https://avatars.githubusercontent.com/u/17958536?v=3","gravatar_id":"","url":"https://api.github.com/users/KaiFeng007","html_url":"https://github.com/KaiFeng007","followers_url":"https://api.github.com/users/KaiFeng007/followers","following_url":"https://api.github.com/users/KaiFeng007/following{/other_user}","gists_url":"https://api.github.com/users/KaiFeng007/gists{/gist_id}","starred_url":"https://api.github.com/users/KaiFeng007/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KaiFeng007/subscriptions","organizations_url":"https://api.github.com/users/KaiFeng007/orgs","repos_url":"https://api.github.com/users/KaiFeng007/repos","events_url":"https://api.github.com/users/KaiFeng007/events{/privacy}","received_events_url":"https://api.github.com/users/KaiFeng007/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-03-20T05:12:24Z","updated_at":"2016-09-07T23:31:29Z","closed_at":"2016-04-12T14:39:50Z","body":"Dear friends,\r\n\r\nI want to use assign_taxonomy.py to make rdp classifier species based on GreenGene database.\r\nThen I run the code:\r\n`/usr/lib/qiime/bin/assign_taxonomy.py -i /home/galaxy/user_data/datasets/000/dataset_459.dat -m rdp -t /usr/local/galaxy/galaxy/tools/IEG/RDP/rdp_classifier_2.11/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt -r /usr/local/galaxy/galaxy/tools/IEG/RDP/rdp_classifier_2.11/gg_13_8_otus/rep_set/97_otus.fasta -o rdp_assigned  -c 0.5`\r\n\r\nBut there was an error for this, like this:\r\n\r\n> 1. Traceback (most recent call last):\r\n> 2. File \"/usr/lib/qiime/bin/assign_taxonomy.py\", line 429, in <module>\r\n> 3. main()\r\n> 4. File \"/usr/lib/qiime/bin/assign_taxonomy.py\", line 406, in main\r\n> 5. log_path=log_path)\r\n> 6. File \"/usr/lib/python2.7/dist-packages/qiime/assign_taxonomy.py\", line 864, in __call__\r\n> 7. max_memory=max_memory, tmp_dir=tmp_dir)\r\n> 8. File \"/usr/lib/python2.7/dist-packages/bfillings/rdp_classifier.py\", line 503, in train_rdp_classifier_and_assign_taxonomy\r\n> 9. tmp_dir=tmp_dir)\r\n> 10. File \"/usr/lib/python2.7/dist-packages/bfillings/rdp_classifier.py\", line 473, in train_rdp_classifier\r\n> 11. return app(training_seqs_file)\r\n> 12. File \"/usr/lib/python2.7/dist-packages/bfillings/rdp_classifier.py\", line 315, in __call__\r\n> 13. remove_tmp=remove_tmp)\r\n> 14. File \"/usr/lib/python2.7/dist-packages/burrito/util.py\", line 284, in __call__\r\n> 15. 'StdErr:\\n%s\\n' % open(errfile).read())\r\n> 16. burrito.util.ApplicationError: Unacceptable application exit status: 255\r\n> 17. Command:\r\n> 18. cd \"/home/fengkai/\"; java -Xmx4000M -cp \"/usr/local/galaxy/galaxy/tools/IEG/RDP/rdp_classifier_2.2/rdp_classifier-2.2.jar\" edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker -t\"/tmp/RdpTaxonomy_ah4Qrz.txt\" -s /tmp/tmpTsCzltjvSc4I28M9mSqL.txt -n1 -vversion1 -mcogent -o /tmp/RdpTrainer_SHVTbk > \"/tmp/tmpidRxgzrP5KyqAxlJeayZ.txt\" 2> \"/tmp/tmpbeYtFNHuqcu6j144hMSs.txt\"\r\n> 19. StdOut:\r\n> 20. \r\n> 21. StdErr:\r\n> 22. Usage: java ClassifierTraineeMaker <tax_file> <rawseq.fa> <trainsetNo> <version> <version_modification> <output_directory>\r\n> 23. This program will create 4 output training files to be used by the classifier: \r\n> 24. bergeyTrainingTree.xml, genus_wordConditionalProbList.txt, logWordPrior.txt and wordConditionalProbIndexArr.txt\r\n> 25. Command line arguments:\r\n> 26. --tax_file contains the hierarchical taxonomy information in the following format:\r\n> 27. taxid*taxon name*parent taxid*depth*rank\r\n> 28. Fields taxid, the parent taxid and depth should be in integer format\r\n> 29. depth indicates the depth from the root taxon.\r\n> 30. Note: the depth for the root is 0\r\n> 31. EX: 44*ROOT*1*0*domain\r\n> 32. --rawseq.fa contains the raw training sequences in fasta format\r\n> 33. The header of this fasta file starts with \">\", \r\n> 34. followed by the sequence name, white space(s) \r\n> 35. and a list taxon names seperated by ';' with highest rank taxon first.\r\n> 36. Ex: >seq1     ROOT;Ph1;Fam1;G1\r\n> 37. Note: a sequence can only be assigned to the lowest rank taxon.\r\n> 38. --trainsetNo is a integer. It's used to marked the training information.\r\n> 39. --version indicates the version of the hierarchical taxonomy\r\n> 40. Ex: Bacteria Nomenclature\r\n> 41. --version_modification holds the modifcation information of the taxonomy if any\r\n> 42. Ex: Acidobacterium Added\r\n> 43. --output_directory specifies the output directory\r\n\r\nThe qiime version is 1.9.0 and the rdp classifier version is 2.11, but when I met this problem, I have tried to different version of rdp classifier, including rdp_classifier-2.2, rdp_classifier-2.5, rdp_classifier-2.10.1 and 2.11. But all of these got similar problem like above.\r\n\r\nSo what should I do next? Someone could help me? Thanks!"},"comment":{"url":"https://api.github.com/repos/biocore/qiime/issues/comments/245451084","html_url":"https://github.com/biocore/qiime/issues/2136#issuecomment-245451084","issue_url":"https://api.github.com/repos/biocore/qiime/issues/2136","id":245451084,"user":{"login":"gregcaporaso","id":192372,"avatar_url":"https://avatars.githubusercontent.com/u/192372?v=3","gravatar_id":"","url":"https://api.github.com/users/gregcaporaso","html_url":"https://github.com/gregcaporaso","followers_url":"https://api.github.com/users/gregcaporaso/followers","following_url":"https://api.github.com/users/gregcaporaso/following{/other_user}","gists_url":"https://api.github.com/users/gregcaporaso/gists{/gist_id}","starred_url":"https://api.github.com/users/gregcaporaso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gregcaporaso/subscriptions","organizations_url":"https://api.github.com/users/gregcaporaso/orgs","repos_url":"https://api.github.com/users/gregcaporaso/repos","events_url":"https://api.github.com/users/gregcaporaso/events{/privacy}","received_events_url":"https://api.github.com/users/gregcaporaso/received_events","type":"User","site_admin":false},"created_at":"2016-09-07T23:31:29Z","updated_at":"2016-09-07T23:31:29Z","body":"@AlbertWuYZ, can you please post your question to the [QIIME Forum](http://forum.qiime.org)? We try to address these types of technical support questions there, as it's then easier for others to find answers when they have the same questions. Thank you!"}}
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