Open smurdock-UVic opened 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.
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.
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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.
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 Guppy is outdated (python2) and guppy3 doesn't seem to work with EukCC.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