Hi Felix, Is this file still an issue? Or have you identified the sequences with a mismatch between the sequence and qual score length? We can always take a look, too. Just share a history link and note which dataset is giving the error. (Options -> Share or Publish). You can email just to me to keep your data private and I can share with the developers here if needed. Thanks! Jen Galaxy team On 2/16/11 6:21 AM, Felix Hammer wrote:

Hi, I'm experiencing some strange problems with the fastq groomer. Trying to groom my files I get the following error:

"Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 37, in if __name__ == "__main__": main() File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 18, in main for read_count, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 452, in __iter__ yield self.next() File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 448, in next rval.assert_sequence_quality_lengths() File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 142, in assert_sequence_quality_lengths assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len ) AssertionError: Invalid FASTQ file: quality score length (63) does not match sequence length (36)"

I've double checked the file and it should be ok. Any ideas? thx, Felix

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