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Hi,
I've encountered today a possible bug while parsing HMMER3 text output. In some rare cases HMMER appends additional lines below line indicating the end of results section ('//'). In such case p…
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Following https://github.com/tseemann/prokka/blob/master/README.md#github
Prokka was downloaded on 2017-02-21 using:
cd $HOME
git clone https://github.com/tseemann/prokka.git
ls prokka
…
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Last time we looked at this, PyPy's reimplementation of NumPy was very incomplete - missing things like linear algebra support - but they have been making steady improvement, see http://buildbot.pypy.…
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Hi Jon,
I encountered an issue when installing the funannotate database.
I got the error message "Error: File fuOG_4.5.hmm does not appear to be in a recognized HMM format."
Iran the command one …
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Hi,
As mentioned in my comment in issue #820 , I'm not able to run `Tests/test_KDTree.py` or the related class in the `Bio` folder.
Following @peterjc suggestion, I've run the `python setup.py i…
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I downloaded a custom HMM database for use with Prokka (specifically, the TIGR database), and subsequently ran `hmmpress` and `--setupdb` on it before running Prokka; however, the job does not complet…
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Hi!
I have been using hmmer (mainly hmmsearch) for the past couple months and have been looking at its MPI performance. I was wondering if there was any specific reason for the value given to the MAX…
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When I run MGE_Scan_nonLTR_v2 on linux command line using this call:
`run_MGEScan.pl -genome=scafs/ -data=output/ -hmmerv=3 -program=N 2>mgescan.stderr 1>mgescan.stdout`
it gives many lines of …
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IN01909053
To run a topology predictor called OCTOPUS, which is part of TOPCONS2 and requires installing all of it.
It also requires a 212G dataset.
https://github.com/ElofssonLab/TOPCONS2
http://w…
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Hi Sean,
Just spotted a minor issue. We've used a multi-hmm to search a bunch of genomes with either nhmmer or hmmsearch. When we use "-A" we get some lovely Stockholm alignments, but it'd be handy t…