[Fwd: Re: error occurred when converting the SOLID output to fastq]

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

[Fwd: Re: error occurred when converting the SOLID output to fastq]

Anton Nekrutenko
---------------------------- Original Message ----------------------------
Subject: Re: [galaxy-user] error occurred when converting the SOLID output
to fastq
From:    "Jia-Xing Yue" <[hidden email]>
Date:    Wed, June 8, 2011 5:48 pm
To:      "Anton Nekrutenko" <[hidden email]>
--------------------------------------------------------------------------

Dear Anton,

Thank you very much! I re-uploaded the input file  this Monday and galaxy
now can work well with the data. I guess the corrupted input file is due
to some problem when I uploaded them via FTP software at the first time.
:)

Best regards,

Sincerely,
Jia-Xing
--
Jia-Xing Yue

Graduate Student
Putnam Lab
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/



On Jun 8, 2011, at 3:40 PM, Anton Nekrutenko wrote:

> 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/
>
>






___________________________________________________________
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/