NCBI FCS GX fails (but used to run)

usegalaxy.org support
,
1

Hi, I am running NCBI FCS GX and I get a fail each time, but no reasons (“fatal error: exit code 1 ()”). The fasta file I am running it on works for other processes, so this seems like its not badly formatted or anything, and previously NCBI FCS GX worked for other fasta files. So has something changed in the last week or so? Thanks in advance

2

This tool had some issues recently at UseGalaxy.org so I am wonder where you are using it?

To complicate it, we just did an update on the ORG server, so that could be another factor if that is where you are working.

Would you be able to share a small history with an example of the failure? I’ll also start up my small test case as another check.

Thanks for reporting the issue and we can follow up more! :slight_smile:

3

Update: This is now confirmed, and we are working on the solution. More feedback soon! :hammer_and_wrench:

cc @delphinel

4

thank you :slight_smile: yes its on .org

5

Update

Apologies! I forgot to link this back. 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

Hope this helps or that everyone saw the other post already! :rocket: