Open TimSkvortsov opened 9 years ago
Hello,
This is by design; Prokka is used if you are running in isolate (-I) mode or running iMetAMOS ( initPipeline -W imetamos), but not on a metagenome. Given that Prokka we can run in a metagenomic setting (--metagenome), I will switch this over to a feature request.
If you are enabling Prokka on a metagenomic dataset I recommend adding the (--metagenome) parameter to the command-line options.
Hello treangen,
Thank you for clarifying the situation with Prokka, and sorry for reporting this as an issue, I was just confused by the fact that Prokka was indicated as a genecaller in the manual, but MetAMOS refused to use it.
Hello, I am facing the same problem. May I please get a detailed resolution to get prokka to work with my data.
Thank you
hi aabood,
I am facing the same problem.
to clarify, you would like to use Prokka on a metagenomic sample? If so, this is still not supported in MetAMOS and is currently marked as a feature request.
May I please get a detailed resolution to get prokka to work with my data.
Prokka can be used in MetAMOS if you are running in isolate (-I) mode or running iMetAMOS ( initPipeline -W imetamos), but not on a metagenome. Unfortunately I don't think we'll be able to get to this anytime soon.
As a workaround, you could run Prokka outside of MetAMOS on the assembled contigs. Alternatively, if you have experience with Python, you could try to add Prokka support to your local MetAMOS install; if you are enabling Prokka on a metagenomic dataset, you will need to add the '--metagenome' parameter to the command-line options.
Thank you for your response. I will take your advice and perform Prokka externally.
On Tue, May 31, 2016 at 12:42 PM, Todd J Treangen notifications@github.com wrote:
hi aabood,
I am facing the same problem.
to clarify, you would like to use Prokka on a metagenomic sample? If so, this is still not supported in MetAMOS and is currently marked as a feature request.
May I please get a detailed resolution to get prokka to work with my data.
Prokka can be used in MetAMOS if you are running in isolate (-I) mode or running iMetAMOS ( initPipeline -W imetamos), but not on a metagenome. Unfortunately I don't think we'll be able to get to this anytime soon.
As a workaround, you could run Prokka outside of MetAMOS on the assembled contigs. Alternatively, if you have experience with Python, you could try to add Prokka support to your local MetAMOS install; if you are enabling Prokka on a metagenomic dataset, you will need to add the '--metagenome' parameter to the command-line options.
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Whenever I try to select Prokka as a tool for finding ORFs, MetAMOS uses FragGeneScan. After reviewing the code of
runPipeline
,findorfs.py
andfindscforfs.py
I found out that prokka is not on the list of the supported genecallers and thus cannot be used for ORFs search:supported_genecallers = ["fraggenescan","metagenemark","glimmermg"]
After addition of
"prokka"
to the list of genecallers, MetAMOS started to use it. Why was Prokka excluded from this list in the first place?