Re: galaxy command line error (fasq_grromer.py)

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Re: galaxy command line error (fasq_grromer.py)

Dave Clements, GMOD Help Desk-3
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,  <[hidden email]> 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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Re: galaxy command line error (fasq_grromer.py)

Dannon Baker
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,  <[hidden email]> 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
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Re: galaxy command line error (fasq_grromer.py)

Florent Angly
In reply to this post by Dave Clements, GMOD Help Desk-3
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,<[hidden email]>  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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Re: galaxy command line error (fasq_grromer.py)

Marina Gourtovaia
In reply to this post by Dave Clements, GMOD Help Desk-3
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,<[hidden email]>  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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