Tools fail on fastq files imported from certain Get Data tools -- Workaround: adjust metadata assignment

Question: Tools fail on fastq files imported from certain Get Data tools -- Workaround: adjust metadata assignment

4 months ago by

molsen1 • 0 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.

sra fastqsanger.gz galaxy ebi fastqsanger • 358 views

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modified 4 months ago by Jennifer Hillman Jackson ♦ 25k • written 4 months ago by molsen1 • 0

what galaxy are you using?

ADD REPLY • link written 4 months ago by Martin Čech ♦♦ 4.9k

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 REPLY • link written 4 months ago by molsen1 • 0

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 REPLY • link written 4 months ago by Martin Čech ♦♦ 4.9k

4 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

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