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@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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