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
Best,
Florent
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:
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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