[Gmod-help] Re: [galaxy-dev] galaxy command line error (fasq_grromer.py)

[Dannon Baker]

There are two more parameters that the fastq groomer requires, force_quality_encoding and summarize_input.

Try this:
python /usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py seq.txt illumina seq_out.txt sanger None summarize_input

force_quality_encoding can be 'None', 'ascii', or 'decimal'.  When this parameter is set to 'None', the groomer automatically uses the source encoding.
summarize_input	 can be 'summarize_input'  or 'dont_summarize_input'

-Dannon

On Jan 2, 2011, at 10:34 AM, 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.friedlander at weizmann.ac.il> wrote:
>> 
>> Hi,
>> 
>> 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, in <module>
>> if __name__ == "__main__": main()
>> File "/usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py", line 10, in main
>> force_quality_encoding = sys.argv[5]
>> IndexError: list index out of range
>> 
>> Does anyone know what the problem is?
>> 
> 
> 
> 
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