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A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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MetAMOS 1.5rc3 - impossible to use Prokka to find ORFs #167

Open TimSkvortsov opened 9 years ago

TimSkvortsov commented 9 years ago

Whenever I try to select Prokka as a tool for finding ORFs, MetAMOS uses FragGeneScan. After reviewing the code of runPipeline, findorfs.py and findscforfs.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?

treangen commented 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.

TimSkvortsov commented 9 years ago

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.

aabood commented 8 years ago

Hello, I am facing the same problem. May I please get a detailed resolution to get prokka to work with my data.

Thank you

treangen commented 8 years ago

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.

aabood commented 8 years ago

​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.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/marbl/metAMOS/issues/167#issuecomment-222747304, or mute the thread https://github.com/notifications/unsubscribe/AOrA2TV5epm_Kb91nQXAFEi6OoA4zwDmks5qHGTkgaJpZM4C4FYj .

Abdullah "Arby" Abood MS Student | Graduate Teaching Assistant ​ Richards' Lab | 111 Jordan Hall Clemson University ​

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