java error running RDP

[Maria Garcia]

Hello!

I am trying to run the assign_taxonomy.py using rdp but I am getting an error due to Java.  I installed Java, but I am still getting an error. Could someone please help me decipher the error?  I really appreciate the help thanks!


MacQIIME 223-1-41-155-wireles1x:qiime_ccase_data $ assign_taxonomy.py -i /Users/student/Desktop/qiime_ccase_data/otu.fasta -o /Users/student/Desktop/qiime_ccase_data/output/rdp_output -m rdp -r /Users/student/Desktop/qiime_ccase_data/sh_refs_qiime_ver7_dynamic_22.08.2016.fasta -t /Users/student/Desktop/qiime_ccase_data/sh_taxonomy_qiime_ver7_dynamic_22.08.2016.txt
Traceback (most recent call last):
  File "/macqiime/anaconda/bin/assign_taxonomy.py", line 417, in <module>
    main()
  File "/macqiime/anaconda/bin/assign_taxonomy.py", line 394, in main
    log_path=log_path)
  File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 860, in __call__
    max_memory=max_memory, tmp_dir=tmp_dir)
  File "/macqiime/anaconda/lib/python2.7/site-packages/bfillings/rdp_classifier.py", line 515, in train_rdp_classifier_and_assign_taxonomy
    tmp_dir=tmp_dir)
  File "/macqiime/anaconda/lib/python2.7/site-packages/bfillings/rdp_classifier.py", line 485, in train_rdp_classifier
    return app(training_seqs_file)
  File "/macqiime/anaconda/lib/python2.7/site-packages/bfillings/rdp_classifier.py", line 327, in __call__
    remove_tmp=remove_tmp)
  File "/macqiime/anaconda/lib/python2.7/site-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 "/Users/student/Desktop/qiime_ccase_data/"; java -Xmx4000M -cp "/macqiime/rdp_classifier_2.2/rdp_classifier-2.2.jar" edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker "/tmp/RdpTaxonomy_hXbJmA.txt" "/tmp/tmpcFztk8N6CMUutxRNgsF9.txt" 1 version1 cogent "/tmp/RdpTrainer_fF8sEm" > "/tmp/tmpDzXuULCXecUVsbZ6xXfu.txt" 2> "/tmp/tmpMsWtpXiZdi3rVChotprf.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
E-mail: James R. Cole at co...@msu.edu
    Qiong Wang at wang...@msu.edu
    James M. Tiedje at tie...@msu.edu


Exception in thread "main" java.lang.IllegalArgumentException:
Illegal taxonomy format at 716**715*7*genus
    at edu.msu.cme.rdp.classifier.train.TreeFactory.creatTaxidMap(TreeFactory.java:73)
    at edu.msu.cme.rdp.classifier.train.TreeFactory.<init>(TreeFactory.java:51)
    at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.<init>(ClassifierTraineeMaker.java:41)
    at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.main(ClassifierTraineeMaker.java:133)

[Yoshiki Vázquez Baeza]

Hello,

This looks fine, but how did you generate your taxonomy file, the error message seems to point that there's an invalid taxonomy format.

Thanks!

Yoshiki.

[Maria Garcia]

Hi Yoshiki,

I just downloaded it from Unite.  It worked fine when I ran the taxonomy file using the blast command. 

--Maria

[Yoshiki Vázquez Baeza]

Hello Maria,

I've forwarded this question to someone else, hopefully we'll hear back from them soon.

Thanks!

Yoshiki.

[Antonio González Peña]

Hi Maria,

Sorry for the delay. From the error I think there is something odd with your input reference files, could you send us the results of running:

head -n 5 /Users/student/Desktop/qiime_ccase_data/sh_refs_qiime_ver7_dynamic_22.08.2016.fasta /Users/student/Desktop/qiime_ccase_data/sh_taxonomy_qiime_ver7_dynamic_22.08.2016.txt

Thanks! 

[Juan Pedro Maestre Wic]

Hi Antonio,

Not sure what the resolution of that case was, but I have the same problem and here it is what you asked for.

(qiime1) jm44736-mac@wireless-10-147-84-55:~$ head -n 5 /Users/jm44736-mac/jpqiime/Shared_Folder_wd/refdata/its_31_01_16_otus/sh_refs_qiime_ver7_97_s_31.01.2016.fasta 

>SH020468.07FU_AB818017_reps

CCGAGTGTAAAAACTCCAACCCGTGTGAACCTACCTACAAAAACGTTGCTTCGGCGGGTCCGCCCGCCGGAGGTGCCAAACTCTTGAATTTTCAGCAGTCTCTGAGCAAAAAAACAAAAATAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCGGTATTCCGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCAGGCCCCCCGGGGCCTGGTGTTGGGGCGCCCGGGTCCCTGACCGGGCCCGGGGCCCCCAAGTACATCGGCGGTCTCGCCGGTACGCCGAGCGCAGTAAGACGCGGTAAAACGCGCCCCTCGCCCGGACCGTGCCGGCGCGCACCTGCCGCTAAACCCCCCAAATTCTAAA

>SH465869.07FU_UDB004660_reps_singleton

GGAAGGACATTATCGAAACAAATGGGGGGAAGACTGTCGCTGGCCCTCGGGCATGTGCACGTCGACCTCTTCATACACACACACCTGTGCACCTTTGGTAGGTCTTCGAAAGAGGATCTATGATTATCATCACACCCTGTCGTATGGCCAGAATGTCTATATCACATAATACAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGATTTTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCATTGAATTCTCAACCATGTCTTGATTGATTTCAAGGCATTGGCTTGGACTGTGGGGGTTGCTGGCTGCGAAAGCGGTCGGCTCTCCTGAAATGCATTAGCAAGTCTCTTTGGACGTGCACGGCCTTTCGACGTGATAATGATCGTCGTGGCTGGAGCGTACACATGCTTGCTTCGAAAACCCTCTTGAGCTTCGGCTCAAATTGACTTGGAACTCGACCTCAAATCAGG

>SH012276.07FU_U68322_reps_singleton

(qiime1) jm44736-mac@wireless-10-147-84-55:~$  head -n 5 /Users/jm44736-mac/jpqiime/Shared_Folder_wd/refdata/its_31_01_16_otus/sh_taxonomy_qiime_ver7_97_s_31.01.2016.txt

SH020468.07FU_AB818017_reps k__Fungi;p__Ascomycota;c__Sordariomycetes;o__Magnaporthales;f__Magnaporthaceae;g__Pyricularia;s__Pyricularia sp

SH465869.07FU_UDB004660_reps_singleton k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Boletales;f__unidentified;g__unidentified;s__Boletales sp

SH012276.07FU_U68322_reps_singleton k__Fungi;p__Ascomycota;c__Eurotiomycetes;o__Ascosphaerales;f__Ascosphaeraceae;g__Ascosphaera;s__Ascosphaera asterophora

SH009881.07FU_EF634074_reps k__Fungi;p__Basidiomycota;c__Agaricomycetes;o__Thelephorales;f__Thelephoraceae;g__Tomentella;s__Tomentella sp

SH003789.07FU_KC966369_reps_singleton k__Fungi;p__Ascomycota;c__unidentified;o__unidentified;f__unidentified;g__unidentified;s__Ascomycota sp

If you guys could help me out, it would be awesome.

Thanks!

JP.

[Jenya Kopylov]

Hi Juan,

Could you paste the error that you receive? Knowing the line at which RDP throws an error will be useful (e.g. as written "Illegal taxonomy format at 716**715*7*genus" from Maria's post).

Thanks!

Jenya

[Juan Pedro Maestre Wic]

Jenya,

The error is :Illegal taxonomy format at 1256**1255*7*genus

at edu.msu.cme.rdp.classifier.train.TreeFactory.creatTaxidMap(TreeFactory.java:73)

at edu.msu.cme.rdp.classifier.train.TreeFactory.<init>(TreeFactory.java:51)

at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.<init>(ClassifierTraineeMaker.java:41)

at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.main(ClassifierTraineeMaker.java:133)

That being said, I already figured out that it is a problem of the 2016 release of the UNITE database. The releases from 2017, 2015, and 2011 work perfectly.

Thanks!

JP.

[Jenya Kopylov]

Ok, thanks for letting us know. Good luck with the rest of your project.

Jenya