Hi Jianpeng,

There is a problem with your input FASTQ file (data or label) or possibly the Grooming step, but the exact problem is difficult to determine without seeing your data/processing.


I know that you are running this on a local install. Please reproduce the error on the Galaxy main instance by loading a sample of the original file, grooming, running the tool to produce the error, and then sending in a bug report (using the green bug icon). Please leave all datasets undeleted in your history.

Thanks and I will watch for your bug report,

Jen
Galaxy team


On 3/29/12 8:26 AM, Xu, Jianpeng wrote:
Hi ,

I have installed our local galaxy and I am trying to run FASTQ Trimmer
by column, but I got the error message below:

Traceback (most recent call last): File
"/data/home/galaxy/galaxy-dist/tools/fastq/fastq_trimmer.py", line 41,
in if __name__ == "__main__": main() File
"/data/home/galaxy/galaxy-dist/tools/fastq/fastq_trimmer.py", line 17,
in main for num_reads, fastq_read in enumerate( fastqReader( open(
input_filename ), format = input_type ) ): File
"/data/home/galaxy/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line
456, in __iter__ yield self.next() File
"/data/home/galaxy/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line
452, in next rval.assert_sequence_quality_lengths() File
"/data/home/galaxy/galaxy-dist/lib/galaxy_utils/sequence/fastq.py", line
209, in assert_sequence_quality_lengths assert qual_len + 1 == seq_len,
"Invalid FASTQ file: quality score length (%i) does not match sequence
length (%i with adapter base)" % ( qual_len, seq_len ) AssertionError:
Invalid FASTQ file: quality score length (100) does not match sequence
length (100 with adapter base)

What is the problem with it ?

Thanks a lot.

Jianpeng

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