Screening assembled genomes for contamination using NCBI FCS workflow not working

[Dibya]

Sequence analysis / Screening assembled genomes for contamination using NCBI...

I was trying to run this workflow using galaxy to check contaminants in my draft assembly fasta file but I got the error and could not run this workflow. It looks like the format of my fasta file is not right. How do we format our fasta file to run this workflow?

[jennaj]

Hi @Dibya

Thanks for linked the tutorial but to help we would need to see your data and how you are using the workflow, plus the exact errors. We can still help if you would like to generate the history share link and post that back in a reply. Or, if you solves this, let us know!

But in general, your inputs can be compared to the formats of the example data? For this workflow that is just a fasta file of an assembled genome. Fasta format is very common and if you search the tool panel you’ll find tools that can help to summarize and perform various QA and statistical summaries as a way to confirm the format.

XRef → How to get faster help with your question

[Dibya]

Hi team,

Thank you for your email. Here is the bug I get while running the workflow. I tried the help wizard, and it doesn’t help as well. I keep getting the same error.

Thank you.

[jennaj]

Hi @Dibya

Thanks for posting back the bug report page, very helpful!

Please try switching to use current version of the tool. Exactly where to make the change in the workflow is in the screenshots. Please let us know if you need more help with this and if it works!

@jennaj

The solution here is to update the tutorial workflow, or your own workflow, or your direct run, to use the most current version of the NCBI FCS tool when working a UseGalaxy.org or any other server where you may be having problems.

We might be able to correct the older version but it isn’t a priority. Full details are in here if you aren’t sure how to do this (screenshots, FAQs) → Correcting errors with NCBI FCS GX Foreign Contamination Screening assembled genomes

[Dibya]

Thank you for your email. Does that mean I need to run the tools individually and not use the workflow?

Thank you.

[jennaj]

Hi @Dibya

You won’t need to do that, you can use the workflow, you’ll just need to update it. See the topic I linked. I included a screenshot that shows exactly where to find the tool form Versions menu in the workflow editor. It is the same as a tool form, but the editor is new to some people, so I though it might be helpful.

Here, I’ll copy it

this

@jennaj

We might be able to correct the older version but it isn’t a priority. Full details are in here if you aren’t sure how to do this (screenshots, FAQs) → Correcting errors with NCBI FCS GX Foreign Contamination Screening assembled genomes

Points to

@jennaj

What to do

If you are working at UseGalaxy.org (where I was testing) the most current version is Galaxy Version 0.5.5+galaxy1 for three of the tools included, and the adaptor tool didn’t change and is still at Galaxy Version 0.5.0+galaxy0.

I was able to simply update the tool version in the GTN workflow, save, and run without any complicated changes to the parameters. This works about the same as the tool form directly. Open the workflow in the editor, click on the tool, modify the version(s), double check parameters are OK (new params, defaults), save, and run.

• FAQ: Changing the tool version

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Please give that a try and let us know if you need more help!

You should give this a try too. Learning how to make small modifications to workflows is really important. Tools change over time, servers may host slightly different versions (as in this case), you may want to use a different reference genome at some point in some workflow, or you may want to extract and create your own. These are really powerful and once you explore it you’ll see it is pretty much like a history but flattened out all at once. Really nice for planning your steps, too.

Let us know how this works!