Using UNITE database

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Roody_UF

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Sep 13, 2016, 11:37:56 AM9/13/16
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Hello Dearest Qiime forum reader!

I am attempting to assign taxonomy to a set of ITS fungal data using the UNITE ref sequences. Using this command:

assign_taxonomy.py -i UNITE_picked_otus/UNITE_rep_set1.fna -r sh_refs_qiime_ver7_99_22.08.2016.fasta -t sh_taxonomy_qiime_ver7_99_22.08.2016.txt

I am getting an error that indicates that the same error.  That indicates that the looking for OTUs using the greengenes from the file it cannot find. What am I missing from my command that it is not accepting my --id_to_taxonomy_fp file from the -t command? 

Here is the error message: 

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 222, in main
    option_parser, opts, args = parse_command_line_parameters(**script_info)
  File "/usr/lib/python2.7/dist-packages/qcli/option_parsing.py", line 313, in parse_command_line_parameters
    opts,args = parser.parse_args(command_line_args)
  File "/usr/lib/python2.7/optparse.py", line 1384, in parse_args
    values = self.get_default_values()
  File "/usr/lib/python2.7/optparse.py", line 1329, in get_default_values
    defaults[option.dest] = option.check_value(opt_str, default)
  File "/usr/lib/python2.7/optparse.py", line 770, in check_value
    return checker(self, opt, value)
  File "/usr/lib/python2.7/dist-packages/qcli/option_parsing.py", line 41, in check_existing_filepath
    "option %s: file does not exist: %r" % (opt, value))
optparse.OptionValueError: option --id_to_taxonomy_fp: file does not exist: '# /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt'
-----

What am I missing from my command that makes it run the UNITE -r and -t files rather than the default gg database file? 

Thanks so much!
-Roody

Colin Brislawn

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Sep 13, 2016, 12:44:32 PM9/13/16
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Hello Roody,

I think I know what's going wrong here. Take look at the documentation for assign_taxonomy.py 

The input -i should be your rep_set.fna file created by OTU picking. The -r referance should be the fasta file, UNITE_picked_otus/UNITE_rep_set1.fna -r sh_refs_qiime_ver7_99_22.08.2016.fasta.

Once you switch around the -i and -r, let me know how this runs.

Keep in touch,
Colin

Roody_UF

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Sep 13, 2016, 1:10:32 PM9/13/16
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So I am still getting the same error with both codes: 
 assign_taxonomy.py -r UNITE_picked_otus/rep_set1.fna -i sh_refs_qiime_ver7_99_22.08.2016.fasta -t sh_taxonomy_qiime_ver7_99_22.08.2016.txt

and 

assign_taxonomy.py -i UNITE_picked_otus/rep_set1.fna -r sh_refs_qiime_ver7_99_22.08.2016.fasta -t sh_taxonomy_qiime_ver7_99_22.08.2016.txt

Could it be a problem with my rep_set.fna file? 
 pick_rep_set.py -i seqs_otus.txt -f ~/Itu/seqs.fna -o rep_set1.fna

Thanks!

Embriette

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Sep 13, 2016, 1:16:05 PM9/13/16
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Hi Roody,

Try typing in the full paths and see if that resolves your issue.

Thanks!
Embriette

Roody_UF

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Sep 13, 2016, 1:26:55 PM9/13/16
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good thought, Embriette!
assign_taxonomy.py -i /home/dyrdahlyoung/Itu/UNITE_rep_set.fasta -r sh_refs_qiime_ver7_99_22.08.2016.fasta -t sh_taxonomy_qiime_ver7_99_22.08.2016.txt

gives me the same error. I am working in the directory where the -r and -t files are located. 

I have qiime installed on a virtual box on my PC, not the big Linux server where I am currently working. I am going to give that a try. 



Roody_UF

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Sep 13, 2016, 1:46:08 PM9/13/16
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the command ran on my virtual box. I will look for another qiime_config file to see if there are "#"s. But the qiime configure that I saw I deleted the # line that I saw. 

Thanks both!

Embriette

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Sep 13, 2016, 1:48:00 PM9/13/16
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That is certainly curious. Let me know how it goes-if you're still getting errors, we'll see what we can do to get to the bottom of it!

Roody_UF

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Sep 13, 2016, 1:51:56 PM9/13/16
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I am pretty well stumped on the server error as well. But I will keep you posted. I really want to finish this analysis and it looks like it will be happening on my Virtual box rather than the server. 

Thanks!

Colin Brislawn

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Sep 13, 2016, 1:57:34 PM9/13/16
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Hello Roody,

This command you ran looks really good to me:
assign_taxonomy.py -i /home/dyrdahlyoung/Itu/UNITE_rep_set.fasta -r sh_refs_qiime_ver7_99_22.08.2016.fasta -t sh_taxonomy_qiime_ver7_99_22.08.2016.txt
 
What error does it throw again? 

Also, could you run this command for us?
print_qiime_config.py -t


Thanks!
Colin


Roody_UF

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Sep 13, 2016, 2:06:21 PM9/13/16
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the error is this: 
dyrdahlyoung@if-plp-haustorium2:~/Itu/UNTIE_databases$  qiime > assign_taxonomy.py -r rep_set1.fn -i sh_refs_qiime_ver7_99_22.08.2016.fasta -t sh_taxonomy_qiime_ver7_99_22.08.2016.txt
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 222, in main
    option_parser, opts, args = parse_command_line_parameters(**script_info)
  File "/usr/lib/python2.7/dist-packages/qcli/option_parsing.py", line 313, in parse_command_line_parameters
    opts,args = parser.parse_args(command_line_args)
  File "/usr/lib/python2.7/optparse.py", line 1384, in parse_args
    values = self.get_default_values()
  File "/usr/lib/python2.7/optparse.py", line 1329, in get_default_values
    defaults[option.dest] = option.check_value(opt_str, default)
  File "/usr/lib/python2.7/optparse.py", line 770, in check_value
    return checker(self, opt, value)
  File "/usr/lib/python2.7/dist-packages/qcli/option_parsing.py", line 41, in check_existing_filepath
    "option %s: file does not exist: %r" % (opt, value))
optparse.OptionValueError: option --id_to_taxonomy_fp: file does not exist: '# /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt'

The print_qiime_config.py -tf is:
System information
==================
         Platform:      linux2
   Python version:      2.7.6 (default, Jun 22 2015, 17:58:13)  [GCC 4.8.2]
Python executable:      /usr/bin/python

QIIME default reference information
===================================
For details on what files are used as QIIME's default references, see here:

Dependency versions
===================
                QIIME library version:  1.9.1
                 QIIME script version:  1.9.1
      qiime-default-reference version:  0.1.3
                        NumPy version:  1.8.2
                        SciPy version:  0.13.3
                       pandas version:  0.17.1
                   matplotlib version:  1.3.1
                  biom-format version:  2.1.4
                         h5py version:  2.5.0 (HDF5 version: 1.8.11)
                         qcli version:  0.1.0
                         pyqi version:  0.3.2
                   scikit-bio version:  0.2.3
                       PyNAST version:  1.2.2
                      Emperor version:  0.9.51
                      burrito version:  0.9.1
             burrito-fillings version:  0.1.1
                    sortmerna version:  SortMeRNA version 2.0, 29/11/2014
                    sumaclust version:  SUMACLUST Version 1.0.00
                        swarm version:  Swarm 1.2.19 [May 25 2016 14:36:46]
                                gdata:  Installed.
RDP Classifier version (if installed):  rdp_classifier-2.2.jar
          Java version (if installed):  1.8.0_66

QIIME config values
===================
For definitions of these settings and to learn how to configure QIIME, see here:

                     blastmat_dir:      /opt/qiime_deps/blast-2.2.22-release/data
                  cluster_jobs_fp:      None
      pick_otus_reference_seqs_fp:      /usr/lib/python2.7/dist-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta
                    jobs_to_start:      1
pynast_template_alignment_blastdb:      None
                qiime_scripts_dir:      /usr/lib/qiime/bin/
                      working_dir:      .
     pynast_template_alignment_fp:      /usr/share/qiime/data/core_set_aligned.fasta.imputed
                    python_exe_fp:      python
                         temp_dir:      /tmp/
assign_taxonomy_reference_seqs_fp:      # /usr/share/qiime/data/gg_13_8_otus/rep_set/97_otus.fasta
                      blastall_fp:      /opt/qiime_deps/blast-2.2.22-release/bin/blastall
                 seconds_to_sleep:      60
assign_taxonomy_id_to_taxonomy_fp:      # /usr/share/qiime/data/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt

QIIME full install test results
===============================
...........................
----------------------------------------------------------------------
Ran 27 tests in 0.676s

OK



Thanks!

Colin Brislawn

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Sep 13, 2016, 2:11:19 PM9/13/16
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Oh perfect. Thank you for posting your full command and error message.

dyrdahlyoung@if-plp-haustorium2:~/Itu/UNTIE_databases$  qiime > assign_taxonomy.py -r rep_set1.fn -i sh_refs_qiime_ver7_99_22.08.2016.fasta -t sh_taxonomy_qiime_ver7_99_22.08.2016.txt

Looks like your -r and -i are mixed up! Your input -i should be your rep_set.fna file from OTU picking, while your -r referance file is from unite. Try running this:
assign_taxonomy.py -i rep_set1.fn -r sh_refs_qiime_ver7_99_22.08.2016.fasta -t sh_taxonomy_qiime_ver7_99_22.08.2016.txt


Let me know how that works,
Colin


Roody_UF

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Sep 13, 2016, 2:19:48 PM9/13/16
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I ran that command and got the same error message on the server. It worked fine in the virtual box, let me know if you come up with something brilliant with the config_all error message. 

best & thanks!
Roo

Colin Brislawn

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Sep 13, 2016, 2:56:49 PM9/13/16
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Hello Roody,

Thanks for trying all these things for us. I'm surprised that changing the input files does nothing to change the error message. It's like the script is not using the inputs at all, and just using the defaults...

Perhaps a Qiime dev can comment more.

Colin
 

Roody_UF

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Sep 13, 2016, 2:59:56 PM9/13/16
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I am stumped too. I hope one of them will jump in this is pretty annoying if it is a bug. 
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