error occurred when converting the SOLID output to fastq
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/
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: yjx@rice.edu 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:
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-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
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/
___________________________________________________________ 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:
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
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
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participants (5)
-
Anton Nekrutenko -
Jennifer Jackson -
Jia-Xing Yue -
Kelly Vincent -
Mike Dufault