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Old 12-28-2010, 11:22 PM   #1
gfmgfm
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Location: il

Join Date: Jun 2010
Posts: 64
Default 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?
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Old 12-28-2010, 11:38 PM   #2
gfmgfm
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Location: il

Join Date: Jun 2010
Posts: 64
Default

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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