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krasileva-group / plant_rgenes

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db_description.txt file is not working for species which have no annotation on public database #11

Open ttolessa opened 4 years ago

ttolessa commented 4 years ago

@krasileva, I was trying to run the script "K-parse_Pfam_domains_NLR-fusions-v2.2.pl" to extract NLR and NLR-IDs from unannotated species. I have tried editing it for few such species and run it but gives empty outputs with no error report. I wonder if there is any means of using this species description input for unannotated species.

Kind regards, Tamene

Lsz-20 commented 1 year ago

The same question. Have you solved it yet?

krasileva commented 1 year ago

Hello, Have you tested the scripts with sample datasets provided here? If the sample datasets runs fine, and your species of interest does not, there might be two types of issues: 1) input formatting (I'd check the metadata file first as it might not be finding same species names in the metadata file vs file names) 2) there might be no -IDs.

Let me know if you still have the same issue while running the sample data. You can also email me your sample input kseniak@berkeely.edu and I am happy to help troubleshoot and update the scripts to produce error messages to help people in the future.

best wishes,

Ksenia

Lsz-20 commented 1 year ago

Hello, Have you tested the scripts with sample datasets provided here? If the sample datasets runs fine, and your species of interest does not, there might be two types of issues:

  1. input formatting (I'd check the metadata file first as it might not be finding same species names in the metadata file vs file names)
  2. there might be no -IDs.

Let me know if you still have the same issue while running the sample data. You can also email me your sample input kseniak@berkeely.edu and I am happy to help troubleshoot and update the scripts to produce error messages to help people in the future.

best wishes,

Ksenia

Thanks for your apply. I seem to find the error in the provided ‘2.2.pl' file, the file name cannot not retrieved and I modified it to work correctly.