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Question: Fasta dataset contains non-ATCGN characters and fails with FastQC
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gravatar for jay
9 months ago by
jay • 20
jay • 20 wrote:

Hi,

I am getting this error on job submission. it is just a subset of the error. Not all files gives me this error. How to resolve this?

File "/opt/galaxy-user/galaxy-17.09-github/.venv/lib/python2.7/site-packages/MySQLdb/connections.py", line 208, in unicode_literal return db.literal(u.encode(unicode_literal.charset)) UnicodeEncodeError: 'latin-1' codec can't encode character u'\u2018' in position 117: ordinal not in range(256)
fasta content fastqc datatype dataset • 345 views
ADD COMMENT • link •
modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by jay • 20

Are you using quotation marks in those file names?

ADD REPLY • link modified 9 months ago • written 9 months ago by skhan • 40

Hi, The filename doesn't have quotation marks

ADD REPLY • link written 8 months ago by jay • 20
1
gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This looks like an input formatting problem.

  1. Make sure the input is nucleotide content and not protein (amino acids).
  2. Check the fasta content for non-ATCGN content. IUPAC characters will cause problems.
  3. Ensure the datatype assigned is correct. Note that fastqsanger, fastq, fasta, fastqsanger.gz, fastq.gz, fasta.gz are all distinct datatypes - and must match the input datatype compression (if used).

Support FAQs: https://galaxyproject.org/support/#troubleshooting

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson ♦ 25k
1

Thanks Jennifer the file contains invalid charaters

ADD REPLY • link written 8 months ago by jay • 20
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