galaxy command line error

gfmgfm · 12-28-2010, 11:22 PM

I am trying to run locally the fastq_groomer.

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 knows what could be the problem?

gfmgfm · 12-28-2010, 11:38 PM

Please ignore.

I got the error because I had missed parameters.

If anyone is interested, the correct command should be:

python /usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py seq.txt illumina seq_out.txt sanger ascii dont_summarize_input

for more details see:
http://gmod.827538.n3.nabble.com/que...td1171208.html

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12-28-2010, 11:22 PM	#1
gfmgfm Member Location: il Join Date: Jun 2010 Posts: 64	galaxy command line error I am trying to run locally the fastq_groomer. 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 knows what could be the problem?

12-28-2010, 11:38 PM	#2
gfmgfm Member Location: il Join Date: Jun 2010 Posts: 64	Please ignore. I got the error because I had missed parameters. If anyone is interested, the correct command should be: python /usr/local/src/galaxy-central/tools/fastq/fastq_groomer.py seq.txt illumina seq_out.txt sanger ascii dont_summarize_input for more details see: http://gmod.827538.n3.nabble.com/que...td1171208.html