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EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
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Unlisted and outdated dependency #25

Open smurdock-UVic opened 2 years ago

smurdock-UVic commented 2 years ago

Hi there,

Just tried installing and using EukCC but it says there is a missing dependency (guppy), which I don't even see listed as a EukCC dependency. Guppy is outdated (python2) and guppy3 doesn't seem to work with EukCC.

Admittedly, I am a biologist with limited command line experience, so I may just be missing something really simple since it seems to work for others. Advice appreciated.

-Sheryl

openpaul commented 2 years ago

Hi, guppy should be installed together with pplacer. Did you install pplacer?

If that does not solve the issue let me know, I will look into it, as this of course should not happen.

smurdock-UVic commented 2 years ago

I did find the pplacer fix and the guppy problem is solved. Still can't get anything to work though. Now it seems metaEuk isn't working.

21-10-2021 14:37:47: #################################### 21-10-2021 14:37:47: Set sequence type to DNA 21-10-2021 14:37:58: Doing a first pass placement in the base database 21-10-2021 14:37:58: Searching for marker genes in base database 21-10-2021 14:37:58: Hmmsearch failed, check logfile /home/Sheryl/EMw1/EukConcoct/EukCC/workdir/hmm/placement/base/hmmsearch.stdout (base) @.*** EukCC]# cat /home/Sheryl/EMw1/EukConcoct/EukCC/workdir/hmm/placement/base/hmmsearch.stdout

Error: Sequence file /home/Sheryl/EMw1/EukConcoct/EukCC/workdir/metaeuk/18_metaeuk_cleaned.faa is empty or misformatted

On Thu, Oct 14, 2021 at 2:05 AM Paul @.***> wrote:

Hi, guppy should be installed together with pplacer. Did you install pplacer?

If that does not solve the issue let me know, I will look into it, as this of course should not happen.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Finn-Lab/EukCC/issues/25#issuecomment-943161861, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALTPY5LSOWRSZEDECJZMW6TUG2MOFANCNFSM5F6LLRZA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

openpaul commented 2 years ago

Glad we could solve the first issue.

Could it be that metaEuk crashed and created an empty file?

How does the file /home/Sheryl/EMw1/EukConcoct/EukCC/workdir/metaeuk/18_metaeuk_cleaned.faa look like.

You can relaunch metaeuk by simply removing the malformed .faa file and restart EukCC. it should then rerun the needed steps automatically.