error in validate_mapping_file

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mallamu...@gmail.com

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Nov 24, 2020, 11:00:37 AM11/24/20
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Hello Dear QIIME users
please help me out here as I am getting an unwanted error while running the command  validate_mapping_file.py
please help out here
Traceback (most recent call last):
  File "/usr/local/bin/validate_mapping_file.py", line 162, in <module>
    main()
  File "/usr/local/bin/validate_mapping_file.py", line 158, in main
    disable_primer_check, added_demultiplex_field, suppress_html)
  File "/usr/local/lib/python2.7/dist-packages/qiime/check_id_map.py", line 97, in check_mapping_file
    added_demultiplex_field, strip_quotes=False, suppress_stripping=True)
  File "/usr/local/lib/python2.7/dist-packages/qiime/check_id_map.py", line 182, in process_id_map
    added_demultiplex_field)
  File "/usr/local/lib/python2.7/dist-packages/qiime/check_id_map.py", line 822, in check_header
    desc_ix, bc_ix, linker_primer_ix, added_demultiplex_field)
  File "/usr/local/lib/python2.7/dist-packages/qiime/check_id_map.py", line 888, in check_header_required_fields
    if (header[curr_check] != header_checks[curr_check] and
IndexError: list index out of range

TonyWalters

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Nov 24, 2020, 11:57:24 AM11/24/20
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Hello,

The standard disclaimer: QIIME1 is no longer being updated, and we'd advise moving to QIIME2.

See:


The metadata mapping files are very similar between the versions, so you might check your format here:
http://qiime.org/documentation/file_formats.html#metadata-mapping-files

And you can download an example mapping file here:
http://qiime.org/_static/Examples/File_Formats/Example_Mapping_File.txt

I would guess that you have an invalid formatted mapping file. It needs to be tab-delimited text file (not, for example, an excel formatted .xlsx file ).

I'd recommend comparing the example mapping file above and your mapping file in a plain text editor to see if the formatting is correct and you have the correct headers.

--Tony
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