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carolzhou / multiPhATE

Throughput PhATE processing of draft or finished phage genomes
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hmm search results not included in phate_sequenceAnnotation_main.gff #10

Closed thr44pw00d closed 4 years ago

thr44pw00d commented 5 years ago

Hi, I'm not sure if this is intended... I run multiphate using phanotate for gene calling, and for annotation only pvogs_hmm. I get hits from the hmm search, which are saved in the directory PipelineOutput/mydir/HMM/Protein/. However, these hits are not included in the file phate_sequenceAnnotation_main.gff. Would there be a way to include them there?

Thank you!

carolzhou commented 5 years ago

Please send me your config file, your phate_sequenceAnnotation_main.out and .gff files.

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On Oct 21, 2019, at 8:20 AM, thr44pw00d notifications@github.com wrote:



Hi, I'm not sure if this is intended... I run multiphate using phanotate for gene calling, and for annotation only pvogs_hmm. I get hits for the proteins of my genome, which are saved in the directory PipelineOutput/test2/HMM/Protein/. However, these hits are not included in the file phate_sequenceAnnotation_main.gff. Would there be a way to include these hits there?

Thank you!

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thr44pw00d commented 5 years ago

multiphate.zip

carolzhou commented 5 years ago

The hmm search results should now appear in the gff-formatted output.

thr44pw00d commented 4 years ago

Great, it worked, thanks a lot!