Error for FASTQ Trimmer by column.
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 ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).
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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participants (2)
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Jennifer Jackson -
Xu, Jianpeng