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: y...@rice.edu
> Blog: http://bestrok.blogspot.com/
> 
> 
> 
> 
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