Multiple_split_libraries Error: Positional argument detected: True

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Lara Macheriotou

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Jan 25, 2017, 4:02:26 AM1/25/17
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Hi friends of qiime,


I am trying to run the multiple_extract_barcodes.py script in the following way:


multiple_extract_barcodes.py 

-i /home/gomre/lmacheriotou/Mocks/data_raw/run2_16_12_16_all 
-o /home/gomre/lmacheriotou/Mocks/data_raw/extract_barcodes 
-p /home/gomre/lmacheriotou/Mocks/qiime_files/parameters/extract_barcodes_parameters.txt 
--paired_data True 
--read1_indicator _1.fastq 
--read2_indicator _2.fastq 
--include_input_dir_path True


I keep getting "Error in multiple_extract_barcodes.py: Positional argument detected: True". It is mentioned in the description that for --paired_data and --include_input_dir_path [default: False], therefore I assume specifying True will change this. Any wisdom on this matter?

Lara Macheriotou

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Jan 25, 2017, 4:14:16 AM1/25/17
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Sorry, title of the question is wrong, but I got the same error message when trying to run split_libraries also. 

Justine Debelius

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Jan 25, 2017, 11:59:19 AM1/25/17
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The --paired_data command does not accept an argument. If you pass the argument, that indicates you have paired data. If you do not pass the argument, then you're not dealing with paired data.

You can find the html help for this command here.

Best,
Justine

Lara Macheriotou

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Jan 26, 2017, 4:30:30 AM1/26/17
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Aha! I understand now, thank you Justine! :)
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