To kick off the introductions:
π I'm James - I'm one of the instructors of the workshop π. I'm currently based in Leipzig Germany, where I'm shared as a post-doc between the Leibniz Institute for Natural Product Research and Infection Biology - Hans KnΓΆll Institute, and the Max Planck Institute for Evolutionary Anthropology (Germans really like long institute names for some reason...)
I don't actually work on environmental DNA - in fact my original background wasn't in biology but rather archaeology - but from my PhD I've been applying and developing ancient metagenomics techniques to dental calculus from ancient humans, Neandertals, and Chimps/Gorillas.
However many of the concepts and methods overlap very much! So one component of my postdoc has been trying to improve the quality (and user experience) of running standard metagenomic pipelines through the nf-core initiative, and other aspects of bioinformatic analyses. Another component of my postdoc has been establishing and running the SPAAM summer school, some of the material you have already been sent as pre-reading for the workshop you will be attendingin a couple of weeks π.
*Thread Reply:* If you're installing into a conda environment, then conda it should install the right version of python.
Which step are you stuck on?
*Thread Reply:* Hey James, I'm stuck on 'conda env create -f denovo-assembly.yml'. It keeps failing to solve the environment. I have sent a screenshot of error message I get in the main chat (can't figure out how to attach here sorry!). Here is also an extract of this rather unruly string further detailing the problems: 'Solve for environment specs The following packages are incompatible ββ pin-1 is installable and it requires β ββ python 3.11.** , which can be installed; ββ pydamage is not installable because it requires ββ matplotlib-base but there are no viable options ββ matplotlib-base [2.1.2|2.2.3|2.2.4|2.2.5] would re quire β ββ python >=2.7,<2.8.0a0 , which conflicts with an y installable versions previously reported; ββ matplotlib-base [2.1.2|2.2.3|...|3.3.4] would requ ire β ββ python >=3.6,<3.7.0a0 , which conflicts with an y installable versions previously reported; ββ matplotlib-base [2.1.2|2.2.3|...|3.5.3] would requ ire β ββ python >=3.7,<3.8.0a0 , which conflicts with an y installable versions previously reported; ββ matplotlib-base [2.2.4|2.2.5|...|3.7.3] would requ ire β ββ python >=3.8,<3.9.0a0 , which conflicts with an y installable versions previously reported; ββ matplotlib-base [2.2.5|3.3.2|...|3.8.2] would requ ire β ββ python >=3.9,<3.10.0a0 , which conflicts with a ny installable versions previously reported; ββ matplotlib-base [3.4.3|3.5.0|...|3.8.2] would requ ire β ββ python >=3.10,<3.11.0a0 , which conflicts with any installable versions previously reported; ββ matplotlib-base [3.6.1|3.6.2|...|3.8.0] would requ ire β ββ pillow >=6.2.0 but there are no viable options β ββ pillow [6.2.0|6.2.1] would require β β ββ python >=2.7,<2.8.0a0 , which conflicts w ith any installable versions previously reported; β ββ pillow [6.2.0|6.2.1|...|8.3.2] would require β β ββ python >=3.6,<3.7.0a0 , which conflicts w ith any installable versions previously reported; β ββ pillow [6.2.0|6.2.1|...|9.2.0] would require β β ββ python >=3.7,<3.8.0a0 , which conflicts w ith any installable versions previously reported;'
*Thread Reply:* Hey James, just for your reference, here is the entire error message I get: (base) [duxburyl@rosalind-01 denovo-assembly]$ conda env create -f denovo-assembly.yml Retrieving notices: ...working... done Channels:
- conda-forge
- bioconda
- defaults Platform: linux-64 Collecting package metadata (repodata.json): done Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- conda-forge::visidata
- bioconda::samtools
- bioconda::pydamage
- bioconda::prokka
- bioconda::metabat2
- bioconda::megahit
- bioconda::maxbin2
- conda-forge::k8
- bioconda::gunc
- bioconda::fastp
- bioconda::diamond
- bioconda::concoct
- bioconda::checkm-genome
- bioconda::bowtie2
- bioconda::bioawk
Current channels:
- https://conda.anaconda.org/conda-forge/linux-64
- https://conda.anaconda.org/bioconda/linux-64
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/r/linux-64
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/bioconda
- https://conda.anaconda.org/conda-forge
- https://conda.anaconda.org/conda-forge
To search for alternate channels that may provide the conda package you're looking for, navigate to
<https://anaconda.org>
and use the search bar at the top of the page.
*Thread Reply:* Ok for the time being can yuo open the environment.yml file and comment out (# at the beginning) or remove the conda-forge::k8s line
*Thread Reply:* That works for me
*Thread Reply:* I guess k8 is in thewrong place
*Thread Reply:* its been movd to bioconda
*Thread Reply:* So just replace conda-forge::k8s with bioconda::k8s
*Thread Reply:* Oh awesome - thanks James - I'll try that now π
*Thread Reply:* Woohooo it's downloading now! I love coding again hahahah
*Thread Reply:* For future reference, is it a common occurrence that packages will switch between channels?
*Thread Reply:* Oh no.. for some reason the download just froze...
*Thread Reply:* > For future reference, is it a common occurrence that packages will switch between channels? No I'm a bit confused about it
*Thread Reply:* > Oh no.. for some reason the download just froze... Wht do you men?
*Thread Reply:* False alarm - turned out it was just me being impatient and I cancelled the command halfway through it running and then tried again and then that wasn't working (I think it must have been because some of the things were already downloaded and others weren't so it was getting confused or something) - so I reinstalled miniconda and started again and now it's working! Phew! π
*Thread Reply:* Hello I'm back with another problem π
*Thread Reply:* Not sure why it isn't working but the last line seems to point towards python 2.7 being a little problematic (I feel like I shouldn't be surprised...)
*Thread Reply:* Hmm that worked for me... where did you run this command from? Were you in the newly created metamaps environment>?
*Thread Reply:* yes - i ran it from my home directory in the newly created metawrap-env
*Thread Reply:* not sure if relevant but just tried running from the /denovo-assembly directory and tried running it from my base environment - and neither of those worked either... hmmmm just another day and another problem running some code hey hahah
*Thread Reply:* Hmm I'm not sure sure then sorry... The issue looks to be there is an R version that it can't find but I don't know why it would be on yours and not my machine.
But anyway metawrap is not used in the stuff we are doing for the workshop, and I'm flying today so I won't be able to look... Therefore I suggest you just read the rest of the chapter and skip the commands that require netawrap output (iirc metawrap is one of the last sections anyway)
*Thread Reply:* Easy - no worries π Safe flight and thanks for all your help!
@channel username and passwords:
ssh ${USERNAME}@acadworkshop.uoa.cloud
https://pubmed.ncbi.nlm.nih.gov/16796549/
i dont know about you https://www.youtube.com/watch?v=AgFeZr5ptV8
https://github.com/biancamariabonucci/acad_workshop2024/blob/main/README.md
<a href="https://github.com/biancamariabonucci/acad_workshop2024">biancamariabonucci/acad_workshop2024</a>
*Thread Reply:* Thank you Mikkel, I highly appreciate it!
hey team, was thinking of going to see a circus show at the garden of unearthly delights tomorrow night (right by uni), if anyone else was keen, i was thinking of this one maybe which is like circus/comedy: https://adelaidefringe.com.au/fringetix/yuck-circus-af2024 at 7pm
*Thread Reply:* This seems super nice, count me in!
Antonio's repos are really neat and he has designed the bam-filter tool among others. https://github.com/genomewalker His focus is on ancient microbes.
we have applied some of them in this preprint. but within the next 6 months we will release a ancient DNA tool kit (with loads of tools for ancient microbes). https://www.biorxiv.org/content/10.1101/2023.06.10.544454v1
https://x.com/willovvens/status/1760400254065947047?s=46&t=dn0VpPNJ3uT7U-FbUXatPA
^ for the 6 people who confirmed! https://adelaidefringe.com.au/fringetix/yuck-circus-af2024 <- follow this link if others are keen
*Thread Reply:* @Lucinda Duxbury also volunteered, I will just bring them tomorrow morning and you can decicde who wants them more π
*Thread Reply:* iβll fight her for themβ¦ but sheβs scrappy so I suspect sheβll win
*Thread Reply:* Could do an quick-fire exam and whoever gets the most number of right answers gets the eggs π¬
*Thread Reply:* (jk I hate exams)
*Thread Reply:* I am technically a volunteer fire fighter so might be in with a fighting chance
Figure 1 has a nice visualization of the LCA
Found this restaurant and couldn't resist...
*Thread Reply:* wait, is fasta pasta an adelaide thing?
*Thread Reply:* pasta is actually just an acronym for pastAncient
*Thread Reply:* > wait, is fasta pasta an adelaide thing? > No clue, but I've seen a couple of them here now...
And @Roberta Davidson wanna make your own metromaps wiothout having to learn graphic design? Rike posted this on the nf-core slack: https://tennessine.co.uk/metro/
*Thread Reply:* Yessss!! I was actually just thinking of making one for a paper yesterday
Who is keen to go on a walk tomorrow at Horsnell Gully? Weβre sorting out car pooling https://www.parks.sa.gov.au/parks/horsnell-gully-giles-conservation-parks
*Thread Reply:* I am keen!
*Thread Reply:* Which time did you want to leave?
*Thread Reply:* that's a very Dawn-like reply π€£
*Thread Reply:* We aren't sure exactly what this means. The references with 0 coverage evenness are probably bad though...
Breadth vs Exp Breadth to show the eveness of cov for each contig
Exp breadth vs evenness of coverage with the reference length shown by colour gradient
Plot cov_eveness vs exp breadth filtered and unfiltered
The top left have low cov_eveness indicating stacking of reads in maybe conserved regions.
*Thread Reply:* ^filtered for plants
Dinn er tonight: https://spaam-community.slack.com/archives/C06HATZKXFA/p1709176608580899
}
*Thread Reply:* Sorry to hear that, I hope you feel better soon!
*Thread Reply:* I love that there is absolutely no context for this - Thom we found your glasses!!!
*Thread Reply:* Ok that makes much more sense π€£
*Thread Reply:* Thought you were just showing off your swag because why not π€£
*Thread Reply:* look honestly por que no los dos
Hey nerds, I made a start on the 'glossary of ancient metagenomics acronyms'. It's a markdown (.md) file that will go on the SPAAM GitHub when it's finished. (I think) you can fork it from my GitHub and add to it like that. Then I can approve those changes or something... I guess I will learn as I go! P.S. Does anyone know if you can sort table rows (e.g. alphabetically) in a markdown file?
<a href="https://github.com/lucindaduxbury/spaam-community.github.io">lucindaduxbury/spaam-community.github.io</a>
*Thread Reply:* sent pull request!!
*Thread Reply:* Or maybe you can make the little tutorial @Roberta Davidson π
*Thread Reply:* do i need to approve anything @Roberta Davidson - or can you access?
*Thread Reply:* That's the bit I'm not sure how to do
*Thread Reply:* I think you have to approve or merge or something
*Thread Reply:* @Lucinda Duxbury this is what you normally do when you get a pull request
*Thread Reply:* what is what you normally do?
*Thread Reply:* 1. Go to the pull request tab
- Click the one that you want to look at
- Read the opening comment on the default 'conversations ' tab to see what should be in the changes
- Click on the files tab to see all the proposed changes (red lines are original, green are the new changes/additions)
- If you have comments or want changes to the proposal you can press the green 'review' button in the top right, and leave the comment there - you can either leave a generic comment, an approval, or request changes (the latter means the PR can't be merged until the reviewer gives approval)
- Once you've given the approval, you go back to the conversations tab, and at the bottom you should see a 'merge' button
*Thread Reply:* And once it's merged, it's in your main branch and you can continuing editing but with Robbi's changes in it
*Thread Reply:* Oh sweet - thanks James! Robbi have you made any changes yet?
*Thread Reply:* Yes she has! Check the pull request tab on your fork :)
*Thread Reply:* ohhhhh i getit igetit igetit! π
*Thread Reply:* codingcodingcoding!!!
*Thread Reply:* githubgithubgithub!!!
*Thread Reply:* Thanks James!!
*Thread Reply:* What is βGlossary of Ancient Metagenomic Acronymsβ? Do you mean GAMA?
*Thread Reply:* I hear @Lucinda Duxbury screaming from here
*Thread Reply:* I hate that "GAMA" has a ring to it
*Thread Reply:* Cool! I'm on +61401669032 if you wanna Whatsapp us
https://www.nature.com/articles/d41586-024-00520-y have you guys seen/heard about this?
*Thread Reply:* https://environmental-dna.ethz.ch/research/ercledna.html
Hello all! I hope you are all well!! A couple of things, first
