Question: Tools fail on fastq files imported from certain Get Data tools -- Workaround: adjust metadata assignment
0
gravatar for molsen1
4 weeks ago by
molsen10
molsen10 wrote:

When logged into Galaxy I went to the ENA website and forwarded a bunch of fastqc files to my account. All imported as fastqc.gz. I am unable to run fast qc on these files. I get an error. Any help would be appreciated.

ADD COMMENTlink modified 26 days ago by Jennifer Hillman Jackson25k • written 4 weeks ago by molsen10

what galaxy are you using?

ADD REPLYlink written 4 weeks ago by Martin Čech ♦♦ 4.8k

I am using version 18.05. Specifically the error message I recieved was Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/galaxy-repl/main/jobdir/020/086/20086398/_job_tmp -Xmx7g -Xms256m I get this message on fastq files imported from multiple studies on ENA so it seems like it is a common problem. I attempted running trimmomatic on the fastq files and it will not run that tool either

Thanks for any information you can provide.

ADD REPLYlink written 4 weeks ago by molsen10

The actual exception you are getting is uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@' which indicates that your file is in a wrong format I think.

ADD REPLYlink written 4 weeks ago by Martin Čech ♦♦ 4.8k
0
gravatar for Jennifer Hillman Jackson
26 days ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The root issue has to do with a current problem with certain Get Data tools. Details here: https://github.com/galaxyproject/galaxy/issues/6334 and https://github.com/galaxyproject/galaxy/issues/6472

To workaround the problem until fixed, please reassign the datatype to be "fastqsanger.gz" for your fastq inputs. The data is compressed but is not being labeled that way in the metadata -- we'll be fixing that. Please follow the tickets above for updates.

How to change metadata is in the Galaxy FAQs: https://galaxyproject.org/support/

  • How do I find, adjust, and/or correct metadata? https://galaxyproject.org/support/metadata/
  • Or, if your accession is at NCBI, the tool NCBI SRA Tools > Download and Extract Reads in FASTA/Q format from NCBI SRA can be used instead. That tool sets the metadata correctly depending on the output datatype selected on the form.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 26 days ago by Jennifer Hillman Jackson25k
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