Question: Problems With The Groomer
0
Felix Hammer • 200 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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modified 7.7 years ago
by
Jennifer Hillman Jackson ♦ 25k
•
written
7.8 years ago by
Felix Hammer • 200
