Problems with analyzing fastq to fasta files using DESeq2

Question: Problems with analyzing fastq to fasta files using DESeq2

2.6 years ago by

I need help please. I uploaded Fastq converted to Fasta data to Galaxy and started the DESeq2 process. Unfortunately, I saw the following:

Fatal error: An undefined error occured, please check your input carefully and contact your administrator. Creating a generic function for 'char' from package 'base' in package 'S4Vectors' Error in data.frame(sample = basename(filename In), filename =

Any suggestions please?

rna-seq deseq2 • 979 views

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written 2.6 years ago by gbernard4673 • 0

2.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

If you are running this at http://usegalaxy.org, please submit a bug report with a link to this Biostars post and we can take a look. It is unclear if this is a cluster, tool, or input problem from this info. Thanks! Jen, Galaxy team

ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

Hello Ms. Jackson ,

I hope you are extremely well.

I am receiving red error statements for DESeq 2;Fatal error: An undefined error occured, please check your intput carefully and contact your administrator. Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors' Error in data.frame(sample = basename(filenamesIn), filename = https://usegalaxy.org/dataset/errors?id=bbd44e69cb8906b5363a7d9062b1c092 https://usegalaxy.org/datasets/bbd44e69cb8906b5363a7d9062b1c092/show_params https://usegalaxy.org/tool_runner/rerun?id=bbd44e69cb8906b5363a7d9062b1c092 https://usegalaxy.org/datasets/bbd44e69cb8906b5633b3ce3e479df20/display/?preview=True

and Uniprot; Fatal error: Exit code 1 () Traceback (most recent call last): File "/galaxy/main/shed_tools/ toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/48522382b6a4/uniprot_rest_interface/uniprot.py", line 112, in <module> args.out.write(_map(qu

I would really appreciate your assistance.

Best regards

ADD REPLY • link written 2.6 years ago by gbernard4673 • 0

Hello, This is how to submit a bug report. I did not find one yet. https://wiki.galaxyproject.org/Support#Reporting_tool_errors

From the links, the inputs do not appear to be count files (fasta instead) - so you can double check this yourself if you want, it might be quicker. How to use the tool and expected input formats are described on the tool form itself.

ADD REPLY • link modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you Ms. Jackson. I appreciate your time and efforts. Perhaps there is a problem with the file. Is it possible for you to assist me in running this data?

Best regards

ADD REPLY • link written 2.6 years ago by gbernard4673 • 0

I can help you troubleshoot if you send in a bug report - this grants me access to the actual data. All is privately shared within the core team only (not published publically).

ADD REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

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