Closed marcosbarbeitos closed 1 year ago
Should be fixed in the new commit.
Hello, the fix worked, however, there is a typo in assemble_wrapper.py, line 101. It should be "megahit_core_no_hw_accel" and not "megahit_core_no_hwaccel". I corrected the typo in my local copy and it worked.
There is an additional typo in the Github page, it should be "./MitoFlex.py load-modules" and not "./MitoFlex.py load_modules".
Cheers!
Em qua., 10 de mai. de 2023 às 01:11, Li Junyu @.***> escreveu:
Should be fixed in the new commit.
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-- Marcos S. Barbeitos
Departamento de Zoologia - Sala 360 Setor de Ciências Biológicas Universidade Federal do Paraná Caixa Postal 19020 Curitiba, PR 81531-980 Brazil
Phone: (55 41) 3361-1634
I also ran into trouble trying to generate the Circos plot. I was able to get it to work using an older version cloned from https://github.com/node/circos/
MitoFlex was developed 3 or 4 years ago. It's been a long time since I last worked on mitogenomes. I'll fix it soon.
By the way, may I ask what Circos version you're using? I thought the Circos version in environment.yml should work fine (v0.69.8), or maybe older machines will need an older version to work properly?
Yep, my bad. I got version 0.52-4 from https://github.com/vigsterkr/circos, where Google took me when I was looking for the program.
I thought I had found the fix in an older version (0.69-3) because of the ancient commit dates in the node I pulled it from, but did not realize that the version I had was even older.
I always go for the Conda installation, but the line in MitoFlex GitHub's page is:
conda create -n {environment name here} --file requirements.txt
when I believe it should be:
conda create -n {environment name here} --file environment.yaml
I tried this latter option but it complained about not being able to parse the file. So I decided to go old school.
If you'd allow me one last question, I am trying to assemble mitochondrial genomes from ezRAD data collected from scleractinian corals.
I should therefore use Cnidarian as "required_taxa" and "clade" in the *config.py, but there is no "Cnidarian.hmm" file.
I set "disable_taxa" to True, but it will still look for Cnidarian.hmm.
Commenting out "required_taxa" and "clade" resulted in errors.
I wonder if it is possible to run the pipeline with no reference *.hmm file.
Perhaps enabling "use_hmmer" in *config.py would be the way to go?
If needed, I can put together a Cnidarian (or Scleractinian) HMM file using hmmbuild or something, but I'd rather not walk this extra mile. :-)
Thanks again!
Em sex., 12 de mai. de 2023 às 04:39, Li Junyu @.***> escreveu:
By the way, may I ask what Circos version you're using? I thought the Circos version in environment.yml should work fine (v0.69.8), or maybe older machines will need an older version to work properly?
— Reply to this email directly, view it on GitHub https://github.com/Prunoideae/MitoFlex/issues/14#issuecomment-1545314585, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4TMDFN4L57BDEPUFNI4BK3XFXSMNANCNFSM6AAAAAAX33JKEU . You are receiving this because you authored the thread.Message ID: @.***>
-- Marcos S. Barbeitos
Departamento de Zoologia - Sala 360 Setor de Ciências Biológicas Universidade Federal do Paraná Caixa Postal 19020 Curitiba, PR 81531-980 Brazil
Phone: (55 41) 3361-1634
MitoFlex tries to find Cnidarian.hmm
because --clade Cnidarian
is specified.
It will try to use the clade-specific HMM file specified by --clade
(check out /profile/CDS_HMM/*.hmm
for a list of available HMM files) to ensure accuracy in identification. Disabling taxa only removes the need for a fasta file in /profile/MT_database
.
Hello, I have just pulled Mitoflex into an older Dell R900 server running Scientific Linux (= RHEL 7) and I am currently trying to test it using
test_config.py
. I keep getting the following message:I am using Megahit v1.2.9.
Any help will be greatly appreciated!
Best wishes,
Marcos