Error in installing biobakery_workflows_databases

Infrastructure and utilities bioBakery workflows
62

Hi @mallamuneer , To update the default folder location, run the config tool to update the configuration file to the location of your manually downloaded data. Replace “FOLDER” in the command below with your new folder location. Then run “$ humann_config” to confirm that the new folder is listed.

$ humann_config --update database_folders chocophlan FOLDER

That should update the location. Then try running the workflows again. Let me know how it goes!

Thanks!
Lauren

63

Hi @lauren.j.mciver
Thanks for all the help through out
I tried the humann_config command but ended up with error
I first ran this
humann_config --update database_folders chocophlan /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/humann/data/chocophlan
ERROR: Unable to add new name ( chocophlan ) to existing section ( database_folders ) to config file: /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/humann/humann.cfg
then I also tried to run this
(qiime2-2021.4) qiime2@qiime2core2021-4:~$ humann_config --update database_folders chocophlan /home/qiime2/biobakery_workflows_databases/humann/nucleotide_database/full_chocophlan.v201901_v31
ERROR: Unable to add new name ( chocophlan ) to existing section ( database_folders ) to config file: /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/humann/humann.cfg
Badly stuck, kindly suggest
Thanks and Regards

64

Hi @mallamuneer , Sorry that command had a typo from my end! It should be “nucleotide” instead of “chocophlan”. Please try:

$ humann_config --update database_folders nucleotide /home/qiime2/miniconda/envs/qiime2-2021.4/lib/python3.8/site-packages/humann/data/chocophlan

Sorry again!
Lauren

65

Hi Professor
I trust you are well
While I had problems running the workflow because of memory issues.
I got access to chpc and I successfully installed the biobakery_workflows wmgx and developed a script to launch the workflow.
When I launch the flow, it shows job submitted, but doesn’t show in the queue.

  1. I have not created an out_folder just mentioned in the name of the output folder in the script, but didn’t created it.
    I doubt may be not sure the problem is because of this.
    Please advise
    Regards Muneee
66

Sorry to hear you had memory issues. That is great to hear you are setup on a hpc! I wonder if the workflow defaults are not in sync with your grid. If you could provide any detailed error messages you are seeing that would be great.

Thanks!
Lauren

67

Dear Prof
Thank you so much for your prompt reply
I really appreciate your help
I actually had a minor error in script, I corrected it and now the workflow is running from past 2 days.
The data set is about 75 Gb, and is still running. Now my only worry is about it’s successful running.
Hope for best
Thanks and Regards

68

Thank you Prof.
The workflow again crushed, may be the database is not properly installed.
Kindly guide how to install full database on hpc.
Thanks & Regards

69

Dear Prof.
Trust you are well
I have again successfully installed the biobakery_workflow, after many issues.
Although the workflow, but the MetaPhlan didn’t identify and Taxa.
Please guide what is the reason
Regards