Error Occurred When Converting The Solid Output To Fastq

Question: Error Occurred When Converting The Solid Output To Fastq

7.5 years ago by

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/solid2 fastq.py", line 207, in <module> main() File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/solid2 fastq.py", line 188, in main Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/soli d2fastq.py", line 207, in main() File "/galaxy/home/g2main/galaxy_main/tools/next_gen_conversion/soli d2fastq.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/soli d2fastq.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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modified 7.5 years ago by Anton Nekrutenko ♦ 1.7k • written 7.5 years ago by Jia-Xing Yue • 10

7.5 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD COMMENT • link written 7.5 years ago by Jennifer Hillman Jackson ♦ 25k

7.5 years ago by

Anton Nekrutenko ♦ 1.7k

Penn State

Anton Nekrutenko ♦ 1.7k 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

ADD COMMENT • link written 7.5 years ago by Anton Nekrutenko ♦ 1.7k

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

ADD REPLY • link written 7.5 years ago by Mike Dufault • 270

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

ADD REPLY • link written 7.4 years ago by Kelly Vincent • 340

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