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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