---------------------------- Original Message ---------------------------- Subject: Re: [galaxy-user] error occurred when converting the SOLID output to fastq From: "Jia-Xing Yue" yjx@rice.edu Date: Wed, June 8, 2011 5:48 pm To: "Anton Nekrutenko" anton@bx.psu.edu --------------------------------------------------------------------------
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: yjx@rice.edu 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: yjx@rice.edu Blog: http://bestrok.blogspot.com/
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anton＠bx.psu.edu