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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