Failed to initiate the conda environment.

[Andyargueasae]

Hi,

I actually succeeded before in setting up the environment, but recently I changed my virtual machine because the former one will be offline for a week.

Here some errors were reported: init.txt.txt The initiation phase suffers from an error from "/home/student.unimelb.edu.au/yuhtong/andy/data/binny/conda/snakemake_env/lib/python3.8/site-packages/OpenSSL/crypto.py":

Type error: deprecated() got an unexpected keyword argument 'name'.

Is it related to the version of some package?

Andy

[Andyargueasae]

Hello Oskar,

I also found that in my server, when initiating the environment, the ./binny -i config/config.init.yaml got a problem of conda, that conda info --json got exit status 1.

It also shows:

ERROR: The install method you used for conda--probably either pip install conda or easy_install conda--is not compatible with using conda as an application. If your intention is to install conda as a standalone application, currently supported install methods include the Anaconda installer and the miniconda installer. You can download the miniconda installer from https://conda.io/miniconda.html.

[ohickl]

Hey Andy, sorry for the late reply, I was on vacation. Regarding you first problem: Is /home/student.unimelb.edu.au/yuhtong/andy/data/binny/conda/*.yaml a valid path? For the second one: Do you have conda available in your path/the snakemake env?

Best

Oskar

[ohickl]

I also saw that you opened and closed some issues concerning a change of the marker database. It could be possible, in principle, but you would have to describe in detail what markers you have and what the use case would be, so we can check, if it would make sense and/or would be feasible to attempt this.

[Andyargueasae]

Hi Oskar,

Pleasure to hear from you, well for the former questions I just solved them by myself, so no need to have any concern about that.

And speak of marker genes, as my project for my bachelor of science degree of honour focuses on finding organelle genomes especially plastids and chloroplasts from algal groups, I wish to change marker genes from checkm database to a group of hmm marker genes I created by myself (e.g.: rbcL, rpl36, psaA, psbA, atpB etc.). The total number counts up to 57 genes' hmm, so not a big database.

By mimicking the file structure that the database has, I previously successfully changed that, and made it functional through changing binny_mantis.cfg.

Yours sincerely Andy

On Wed, Aug 16, 2023 at 6:50 PM Oskar Hickl @.***> wrote:

I also saw that you opened and closed some issues concerning a change of the marker database. It could be possible, in principle, but you would have to describe in detail what markers you have and what the use case would be, so we can check, if it would make sense and/or would be feasible to attempt this.

— Reply to this email directly, view it on GitHub https://github.com/a-h-b/binny/issues/54#issuecomment-1680214390, or unsubscribe https://github.com/notifications/unsubscribe-auth/AU7UKDM3NX7I5TI3K36VI4DXVSCW7ANCNFSM6AAAAAA3JNWO6Y . You are receiving this because you authored the thread.Message ID: @.***>

[ohickl]

Hi Andy,

I am not sure it will work as you intend:

1. Are these single-copy markers? If not they probably wont be useful to tell binny how complete and/or contaminated a potential bin is, which is the primary purpose of the checkm markers used.
2. Just adding the hmms and including in the mantis annotations wont suffice, as the internal parsing likely wont match, which is why probably you get that error in #55.
3. I am unsure, if organelles or other extra-chromosomal elements provide a sufficient k-mer and/or read coverage signature to bin them with binnys approach. I never tested it. So these elements might not be separable, even if you got a working marker set that is also properly integrated in binny

Best

Oskar

[Andyargueasae]

Hi Oskar,

Thanks for the advice. Well those plastid markers are orthologous for sure, and most of them are in single-copy (they lie in the large/small single copy regions), but for some lineages, they may vary by having extra copies (but for most of the genomes, they are in single-copy).

And for the second point, umm to remove the noises from the raw structure, I deleted the line in mantis.cfg specifying database path for tigrfam, so only the checkm-pfam database (in which I put my hmms into the database folder) will be used.

For point 3, my supervisor in the university of Melbourne did some previous jobs on this. K-mer and coverage signature could help to bin extra-chromosomal elements such as mitochondrial or plastidial sequences. I also tested it on the datasets I have, some datasets can actually output the results.

Best Andy

On Tue, Aug 29, 2023 at 6:18 PM Oskar Hickl @.***> wrote:

Hi Andy,

I am not sure it will work as you intend:

1. Are these single-copy markers? If not they probably wont be useful to tell binny how complete and/or contaminated a potential bin is, which is the primary purpose of the checkm markers used.
2. Just adding the hmms and including in the mantis annotations wont suffice, as the internal parsing likely wont match, which is why probably you get that error in #55 https://github.com/a-h-b/binny/issues/55.
3. I am unsure, if organelles or other extra-chromosomal elements provide a sufficient k-mer and/or read coverage signature to bin them with binnys approach. I never tested it. So these elements might not be separable, even if you got a working marker set that is also properly integrated in binny

Best

Oskar

— Reply to this email directly, view it on GitHub https://github.com/a-h-b/binny/issues/54#issuecomment-1696982289, or unsubscribe https://github.com/notifications/unsubscribe-auth/AU7UKDPEQMUERD6DUDFTPS3XXWQUFANCNFSM6AAAAAA3JNWO6Y . You are receiving this because you authored the thread.Message ID: @.***>