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.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?