Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Unable to install embplant_pt, and embplant_mt #129

Closed
Nbpgr-Nbpgr opened this issue Jan 12, 2022 · 3 comments
Closed

Unable to install embplant_pt, and embplant_mt #129

Nbpgr-Nbpgr opened this issue Jan 12, 2022 · 3 comments

Comments

@Nbpgr-Nbpgr
Copy link

Dear Sir,
I have run the get_organelle_from_reads.py command in Ubuntu terminal, but command can not run and throw some installing error.
This is an error
env1) user@user:~$ get_organelle_from_reads.py -1 S-alatum_R1.fastq.gz -2 S-alatum_R2.fastq.gz -o plastome_output -F embplant_pt -R 10

############################################################################
ERROR: default embplant_pt,embplant_mt database not added yet!

Install it by: get_organelle_config.py -a embplant_pt,embplant_mt
or
Install all types by: get_organelle_config.py -a all

Please help me to install embplant_mt and embplant_pt or all
i have tried so many times but failed to install, when i try to install show one more error i.e Bowtie2 is not available, but Bowtie2 is already exist.
Therefore, i requested to solve my problem as soon as possible.
Regards,

Mukesh Kumar

@Kinggerm
Copy link
Owner

Those who complained that they had bowtie2 but still got the Bowtie2 is not available error usually had not really tried running it. #85 and #102 are where you should read solutions and post follow-ups before opening this new issue.

I will close this issue unless your issue is different from available issues. In that case, please provide the following info:

  1. Which GetOrganelle version
  2. How you installed GetOrganelle
  3. More running environment info

@Nbpgr-Nbpgr
Copy link
Author

Sir,
As per your need related details are given below:-

  1. Conda version is 4.11.0 and Python version is 3.7.11
  2. My GetOrganelle version is GetOrganelle v1.7.5
  3. I am install GetOrganelle through conda and running environment info is Ubuntu 18.04.6 LTS, Processor is Intel® Xeon(R) Silver 4216 CPU @ 2.10GHz × 64

@Kinggerm
Copy link
Owner

Kinggerm commented Feb 1, 2022

What did you get if you type in bowtie2 --help through terminal?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants