Search Results Web results ValueError: too many values to unpack for GRD database

[monica steffi matchado]

Dear All,

I am trying to use GRD database for qiime de novo clustering approach. But I am getting the following error;

Traceback (most recent call last):
  File "/nfs/home/users/monica188/.conda/envs/qiime1/bin/pick_de_novo_otus.py", line 4, in <module>
    __import__('pkg_resources').run_script('qiime==1.9.1', 'pick_de_novo_otus.py')
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1462, in run_script
    exec(code, namespace, namespace)
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/pick_de_novo_otus.py", line 180, in <module>
    main()
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/pick_de_novo_otus.py", line 177, in main
    status_update_callback=status_update_callback)
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/upstream.py", line 306, in run_pick_de_novo_otus
    close_logger_on_success=close_logger_on_success)
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/qiime/workflow/util.py", line 122, in call_commands_serially
    raise WorkflowError(msg)
qiime.workflow.util.WorkflowError:

*** ERROR RAISED DURING STEP: Assign taxonomy
Command run was:
 assign_taxonomy.py -o denovo_clustering_97_GRD/uclust_assigned_taxonomy -i denovo_clustering_97_GRD/rep_set//seqs_rep_set.fasta --reference_seqs_fp /nfs/home/users/monica188/Hyper_region_analysis/train_GRD/sequence.fasta --id_to_taxonomy_fp /nfs/home/users/monica188/Hyper_region_analysis/train_GRD/GRD*.txt
Command returned exit status: 1
Stdout:

Stderr
Traceback (most recent call last):
  File "/nfs/home/users/monica188/.conda/envs/qiime1/bin/assign_taxonomy.py", line 4, in <module>
    __import__('pkg_resources').run_script('qiime==1.9.1', 'assign_taxonomy.py')
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1462, in run_script
    exec(code, namespace, namespace)
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/assign_taxonomy.py", line 417, in <module>
    main()
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/qiime-1.9.1-py2.7.egg-info/scripts/assign_taxonomy.py", line 386, in main
    taxon_assigner = taxon_assigner_constructor(params)
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 1234, in __init__
    self.id_to_taxonomy = self._parse_id_to_taxonomy_file(id_to_taxonomy_f)
  File "/nfs/home/users/monica188/.conda/envs/qiime1/lib/python2.7/site-packages/qiime/assign_taxonomy.py", line 117, in _parse_id_to_taxonomy_file
    identifier, taxonomy = map(strip, line.split('\t'))
ValueError: too many values to unpack

I have also attached my sequence file taxonomic file for your reference

https://drive.google.com/file/d/1r52HSBQot9cKRnGttz9bNb-gVn1ODDvp/view?usp=sharing

[TonyWalters]

Standard disclamer-qiime 1 isn't updated, and QIIME 2 should be used (https://qiime2.org/) unless there is a specific reason to use QIIME 1.

I haven't used this database, so I don't know if it works in qiime 1, but from your command:

--id_to_taxonomy_fp /nfs/home/users/monica188/Hyper_region_analysis/train_GRD/GRD*.txt

it's using a wildcard * character. What was the original command, and what's in the parameters file? It shouldn't use * characters-it should be a single file used for the taxonomy mapping.

[monica steffi matchado]

Hi Tony,

Thank you for the reply. We wanted to try denovo otu clustering approach.

Even If the change the file name, It gave the same error. I used the following command:

pick_de_novo_otus.py -i multiple_split/seqs.fna -f -o denovo_clustering_97_GRD -p parameter_GRD_97

paramfile:

assign_taxonomy:id_to_taxonomy_fp /nfs/home/users/GRD_all_edited.txt
assign_taxonomy:reference_seqs_fp /nfs/home/users/sequence.fasta

[TonyWalters]

Well, you might have to do some troubleshooting on the GRD_all_edited.txt file, since that's probably where the problem is

I'd first make a copy of  /nfs/home/users/GRD_all_edited.txt

You can run the specific command that is failing (I changed the path here for the --id_to_taxonomy file, you might have to change other file paths if they have changed since the first command was ran):

assign_taxonomy.py -o denovo_clustering_97_GRD/uclust_assigned_taxonomy -i denovo_clustering_97_GRD/rep_set//seqs_rep_set.fasta --reference_seqs_fp /nfs/home/users/monica188/Hyper_region_analysis/train_GRD/sequence.fasta --id_to_taxonomy_fp  /nfs/home/users/GRD_all_edited.txt

You will want to make sure the  /nfs/home/users/GRD_all_edited.txt file is tab-delimited, with a single tab, and the first column as the sequence ID and the second column as the taxonomy mapping. It may worth looking at it in a plain text editor to make sure there aren't extra lines of text in there too. It should look like the file described here: http://qiime.org/documentation/file_formats.html#id-to-taxonomy-map