Create Conda Environment Exception

[liangjinsong]

Hi, I occurred errors when running the test command (snakemake -s test/Snakefile --use-conda --reason --cores 1 -p), could you please help me figure out the reason? Thank you in advance. It seems the file directory "/home/taoyechen/software/PathoFact/rules/AMR/../../envs/VirSorter.yaml" is wrong.

(PathoFact) taoyechen@HUAWEI:~/software/PathoFact$ snakemake -s test/Snakefile --use-conda --reason --cores 1 -p
Building DAG of jobs...
Executing subworkflow pathofact.
Building DAG of jobs...
Creating conda environment envs/VirSorter.yaml...
Downloading remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /home/taoyechen/software/PathoFact/rules/AMR/../../envs/VirSorter.yaml:
Collecting package metadata (repodata.json): ...working... done

[samnooij]

Dear Liang, thank you for your interest in this repository. First, I need to apologize that this is an inactive project and I have very little time to work on it. Anyway, I tried to replicate your error and noticed that this repo does not have a test directory, so it is impossible to run that command using this 'PathoFact' only. Are you sure you are contacting the right repo? You might have been working with the original PathoFact, which can be found here: https://gitlab.lcsb.uni.lu/laura.denies/PathoFact If you are using both, I'd like to know exactly how you set up your PathoFact so that I can try and find the error. The path (/home/taoyechen/software/PathoFact/rules/AMR/../../envs/VirSorter.yaml) seems to be correct. I do not see a problem there.

[Chenhaoyuanakk]

I have the same question, but I think the problem is that when it creates the virsorter environment, some packages installed in conda conflict with each other. As mentioned here: https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/issues/97 May I ask your conda version?

Dear Liang, thank you for your interest in this repository. First, I need to apologize that this is an inactive project and I have very little time to work on it. Anyway, I tried to replicate your error and noticed that this repo does not have a test directory, so it is impossible to run that command using this 'PathoFact' only. Are you sure you are contacting the right repo? You might have been working with the original PathoFact, which can be found here: https://gitlab.lcsb.uni.lu/laura.denies/PathoFact If you are using both, I'd like to know exactly how you set up your PathoFact so that I can try and find the error. The path (/home/taoyechen/software/PathoFact/rules/AMR/../../envs/VirSorter.yaml) seems to be correct. I do not see a problem there.

[liangjinsong]

Hi, thank you for your discussion, the version of conda in my server is 22.9.0

梁金松 LIANG Jinsong

手机(Mobile Phone):+86-18565801115 广东省深圳市南山区桃源街道深圳大学城哈尔滨工业大学校区，518055 School of Civil & Environmental Engineering, Harbin Institute of Technology, Shenzhen 518055, China ---- Replied Message ---- | From | @.> | | Date | 1/11/2023 15:47 | | To | @.> | | Cc | Liang @.> , @.> | | Subject | Re: [samnooij/PathoFact] Create Conda Environment Exception (Issue #1) |

I have the same question, but I think the problem is that when it creates the virsorter environment, some packages installed in conda conflict with each other. As mentioned here: https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/issues/97 May I ask your conda version?

Dear Liang, thank you for your interest in this repository. First, I need to apologize that this is an inactive project and I have very little time to work on it. Anyway, I tried to replicate your error and noticed that this repo does not have a test directory, so it is impossible to run that command using this 'PathoFact' only. Are you sure you are contacting the right repo? You might have been working with the original PathoFact, which can be found here: https://gitlab.lcsb.uni.lu/laura.denies/PathoFact If you are using both, I'd like to know exactly how you set up your PathoFact so that I can try and find the error. The path (/home/taoyechen/software/PathoFact/rules/AMR/../../envs/VirSorter.yaml) seems to be correct. I do not see a problem there.

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[xuanxuan69]

#

嗨，感谢您的讨论，我的服务器中的 conda 版本是 22.9.0 梁金松 梁劲松 手机（手机）：+86-18565801115 广东省深圳市南山区桃源街道深圳大学城哈尔滨工业大学校区，518055 哈尔滨工业大学土木与环境工程学院， 深圳 518055 ----回复消息---- |来自 |@.> | |日期 |2023/1/11 15：47 | |至 |@.> | |抄送 |梁@.> ， @.> | |主题 |回复：[samnooij/PathoFact] 创建 Conda 环境异常 （问题 #1） | 我有同样的问题，但我认为问题是当它创建 virsorter 环境时，安装在 conda 中的一些包相互冲突。正如这里提到的：https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/issues/97 我可以问你的康达版本吗？ 亲爱的梁，感谢您对这个存储库的关注。首先，我需要道歉，这是一个不活跃的项目，我几乎没有时间去做。无论如何，我试图复制您的错误并注意到此存储库没有测试目录，因此仅使用此“PathoFact”无法运行该命令。您确定您正在联系正确的存储库吗？您可能一直在使用原始的PathoFact，可以在这里找到：https://gitlab.lcsb.uni.lu/laura.denies/PathoFact 如果您同时使用两者，我想知道您如何设置PathoFact，以便我可以尝试找到错误。路径（/home/taoyechen/software/PathoFact/rules/AMR/../../envs/VirSorter.yaml）似乎是正确的。我看不出那里有问题。 — 直接回复此电子邮件，在 GitHub 上查看或取消订阅。 您收到此消息是因为您创作了线程。消息 ID：@.>

I have the same problem. Has the issue been resolved? I would like to know how to resolve it. My conda version is 23.5.2，I am unable to access your email or contact you through email. If possible, please contact me at my email address: 1006195443@qq.com

[nguyenwang2602]

I also have problems when i'm trying to test the pipline if its working. I also use the command "snakemake -s test/Snakefile --use-conda --reason --cores 1 -p" to check the working ability of the pipeline and then a recieved the same issue above I'm looking forward for yours answers