Looks like the argument list should be longer.
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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