error occurred when converting the SOLID output to fastq

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error occurred when converting the SOLID output to fastq

Jia-Xing Yue
Hi, when I converted the solid output to fastq, the galaxy always complained the following error. Does anybody know why>>
-------------
An error occurred running this job:Traceback (most recent call last):
File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 207, in <module>
main()
File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 188, in main


Traceback (most recent call last):
  File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 207, in

    main()
  File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 188, in main
    merge_reads_qual( fr, fq, con, trim_name=options.trim_name, out='db', double_encode=options.de, trim_first_base=options.trim_first_base, min_qual=options.min_qual, table_name="f3" )
  File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 83, in merge_reads_qual
    cursor.execute('insert into %s values("%s","%s","%s")' % (table_name, defline, lines[0], qual ) )    
sqlite3.OperationalError: near "?3": syntax error

-----------
Thanks!

Jia-Xing

--
Jia-Xing Yue

Graduate Student
Ecology & Evolutionary Bio. -MS 170
Rice University
6100 Main Street
Houston TX 77005

Phone: 1-832-360-6228
E-mail: [hidden email]
Blog: http://bestrok.blogspot.com/




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Re: error occurred when converting the SOLID output to fastq

Jen Hillman-Jackson
Hello Jia-Xing,

It might be a good idea to double check the file format and FTP transfer
by reloading the data and running the tool again. Then, if the problem
is persistent, please share a link to your history containing the
original and new loaded data tool errors and we would be glad to examine
and provide feedback.

Use "Options -> Share or Publish" to generate a share link and email
back directly to me.

Hopefully we can resolve the issue quickly!

Best,

Jen
Galaxy team

On 5/26/11 7:50 AM, Jia-Xing Yue wrote:

> Hi, when I converted the solid output to fastq, the galaxy always complained the following error. Does anybody know why>>
> -------------
> An error occurred running this job:Traceback (most recent call last):
> File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 207, in<module>
> main()
> File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 188, in main
>
>
> Traceback (most recent call last):
>    File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 207, in
>
>      main()
>    File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 188, in main
>      merge_reads_qual( fr, fq, con, trim_name=options.trim_name, out='db', double_encode=options.de, trim_first_base=options.trim_first_base, min_qual=options.min_qual, table_name="f3" )
>    File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 83, in merge_reads_qual
>      cursor.execute('insert into %s values("%s","%s","%s")' % (table_name, defline, lines[0], qual ) )
> sqlite3.OperationalError: near "?3": syntax error
>
> -----------
> Thanks!
>
> Jia-Xing
>
> --
> Jia-Xing Yue
>
> Graduate Student
> Ecology&  Evolutionary Bio. -MS 170
> Rice University
> 6100 Main Street
> Houston TX 77005
>
> Phone: 1-832-360-6228
> E-mail: [hidden email]
> Blog: http://bestrok.blogspot.com/
>
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: error occurred when converting the SOLID output to fastq

Anton Nekrutenko
In reply to this post by Jia-Xing Yue
Jia-Xing:

Your input datasets are corrupted and result in this error. Specifically, you _F3 files are out of sync. One of the reads in csfasta file:

#line number    #file content
21035992 >905_1278_862_F3
21035993 T21231001202131323300311210111233230100333003123120

appears twice in the corresponding QUAL file:

#line number    #file content
21035992 >905_1278_862_F3
21035993 31 32 32 29 32 33 31 32 30 33 32 32 32 29 32 33 31 33 32 30 33 30 29 32 22 32 32 31 31 26 33 32 30 30 30 28 26 28 28 28 33 25 24 31 13 30 21 7 14 30
--
21037350 >905_1278_862_F3
21037351 31 32 32 29 32 33 31 32 30 33 32 32 32 29 32 33 31 33 32 30 33 30 29 32 22 32 32 31 31 26 33 32 30 30 30 28 26 28 28 28 33 25 24 31 13 30 21 7 14 30

which should not happen. As a result this file cannot be easily converted into fastq without explicit identifier matching. Please, check that your input csfasta and QUAL files have exactly the same number of non-comment lines.

Thanks for using Galaxy,

anton
galaxy team

PS Your _R3 files are fine.

Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



On May 26, 2011, at 10:50 AM, Jia-Xing Yue wrote:

> Hi, when I converted the solid output to fastq, the galaxy always complained the following error. Does anybody know why>>
> -------------
> An error occurred running this job:Traceback (most recent call last):
> File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 207, in <module>
> main()
> File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 188, in main
>
>
> Traceback (most recent call last):
>  File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 207, in
>
>    main()
>  File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 188, in main
>    merge_reads_qual( fr, fq, con, trim_name=options.trim_name, out='db', double_encode=options.de, trim_first_base=options.trim_first_base, min_qual=options.min_qual, table_name="f3" )
>  File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2fastq.py", line 83, in merge_reads_qual
>    cursor.execute('insert into %s values("%s","%s","%s")' % (table_name, defline, lines[0], qual ) )    
> sqlite3.OperationalError: near "?3": syntax error
>
> -----------
> Thanks!
>
> Jia-Xing
>
> --
> Jia-Xing Yue
>
> Graduate Student
> Ecology & Evolutionary Bio. -MS 170
> Rice University
> 6100 Main Street
> Houston TX 77005
>
> Phone: 1-832-360-6228
> E-mail: [hidden email]
> Blog: http://bestrok.blogspot.com/
>
>
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>  http://lists.bx.psu.edu/


___________________________________________________________
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at usegalaxy.org.  Please keep all replies on the list by
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Indel Extraction - Deletion Information

Mike Dufault
Hi All,
 
Does anyone know if there is a way to get the deleted base information that corresponds to the "Extract indels from SAM" output?
 
The output from this tool includes the bases for insertions or "-" for deletions. I want to get the actual bases instead of the "-".
 
I assume there is a way to use the SAM file to extract the information, but if someone already has a nifty way to do it, that would be great.
 
Thanks,
Mike

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Re: Indel Extraction - Deletion Information

Kelly Vincent-2
Mike, 

There actually is not a way to get the deleted base(s) from the SAM alone, since SAM displays only the read and not the reference. 

Thanks,
Kelly


On Wed Jun 8, at 4:58 PM, Mike Dufault wrote:

Hi All,
 
Does anyone know if there is a way to get the deleted base information that corresponds to the "Extract indels from SAM" output?
 
The output from this tool includes the bases for insertions or "-" for deletions. I want to get the actual bases instead of the "-".
 
I assume there is a way to use the SAM file to extract the information, but if someone already has a nifty way to do it, that would be great.
 
Thanks,
Mike
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
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use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
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