Re: [galaxy-dev] galaxy command line error (fasq_grromer.py)
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?
-- ===> PLEASE KEEP RESPONSES ON THE LIST <=== http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/Help_Desk_Feedback
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?
-- ===> PLEASE KEEP RESPONSES ON THE LIST <=== http://gmod.org/wiki/GMOD_Americas_2011 http://gmod.org/wiki/GMOD_News http://gmod.org/wiki/Help_Desk_Feedback _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
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?
Hi Looks like the argument list should be longer. Marina
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?
-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
participants (4)
-
Dannon Baker -
Dave Clements, GMOD Help Desk -
Florent Angly -
Marina Gourtovaia