Hi Gilgi,

If you read the beginning of the fastq_groomer.py file, you can see that this script takes 5 mandatory arguments (input_filename, input_type, output_filename, output_type, force_quality_encoding) and an optional argument (summarize_input):

    input_filename = sys.argv[1]
    input_type = sys.argv[2]
    output_filename = sys.argv[3]
    output_type = sys.argv[4]
    force_quality_encoding = sys.argv[5]
    summarize_input = sys.argv[6] == 'summarize_input'
    if force_quality_encoding == 'None':
        force_quality_encoding = None

Your problem is likely that you provided only 4 arguments.

In my eyes, the FASTQ tools lack two things that can be an issue when running the script through the command line: 1/ There is no help manual that describes what the tools does and what arguments it takes 2/ The scripts do not check that the mandatory arguments were provided by the user


On 02/01/11 16:34, Dave Clements, GMOD Help Desk wrote:
I am forwarding your question to the Galaxy Dev list, which is the
best place to ask this type of question.

Dave C

On Tue, Dec 28, 2010 at 11:27 PM,<gilgi.friedlan...@weizmann.ac.il>  wrote:

I am trying to run locally the fastq_groomer.py

My command:

python /usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py seq.txt 
illumina seq_out.txt sanger

seq.txt is a fastq file with Illumina qualities.

I get the following error:

Traceback (most recent call last):
File "/usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py", line 37, 
if __name__ == "__main__": main()
File "/usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py", line 10, in 
force_quality_encoding = sys.argv[5]
IndexError: list index out of range

Does anyone know what the problem is?

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