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simon19891216 / GFAP

a software for annotating plant genes
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Issue about annotation with database failed #1

Closed Echoring closed 1 year ago

Echoring commented 1 year ago

Thank you for developing such owesome tool for researchers in plant.

When I tried your tool on the website (http://43.139.112.84/go-kegg-pfam-index), I found that 2-annotation with database seems works not properly. I used the example data provided, but only swissprot database successed. Selecting other 3 databases will return message Opps!.

I also tried the standalone version on our own computer as python3 GFAP.py -o {outdir} -qn {cds.fasta} -qp {pep.fasta} -aws {species} -go -kegg -pfam -cpu {cpu} -awd nr -awd swissprot -mf -atf -agf. All databases mentioned in README are downloaded and put in the database dir. However, no nr and swissprot annotation is reported. (only GO_annotate, kegg_annotate, pfam_annotate, GF_result, and a blank swissprotf_result)

(By the way, the requirement svglab==1.4.1 is not fount in pip, and the program report that it cannot found svglib module. Is this a typo?)

Looking forward to your reply.

simon19891216 commented 1 year ago

Thank you for your interest in GFAP. The issues with the Linux version are primarily caused by different versions. I have updated the files, so please download it and try again. Based on your description, I have rechecked these features, and from the results, it seems that there are no issues. The steps I take are as follows: click the “using example data” button to input data, select “protein” as the "sequence type", choose “GO” as the "annotation type", select “plant-special database” as the database, and finally, click the “annotate” button for running this function. Please try again! If there are still any usage-related issues, feel free to contact me by email or github.

simon19891216 commented 1 year ago

Furthermore, the specific information about Linux command line can be found on our GitHub website. You can download it and refer to it for usage.

Echoring commented 1 year ago

Thank you for your help. I tried again the web tool, and find that check annotation type GO and protein domains can successfully annotate, but KEGG return Opps!.

Edit: Seems the refering GitHub website about Linux command line is not given anywhere. Can you paste it here?

simon19891216 commented 1 year ago

This is a difficult question to understand. I logged into our server and checked the output logs. I found that the KEGG file has been generated and there are no error messages (as following pricture). Snipaste_2023-07-18_18-20-43 I speculate that the lack of kegg results being returned to you might be due to a slow internet connection. So, I suggest you try again, this time only using one type of functional annotation with KEGG. I apologize for the inconvenience. It’s my mistake that the usage instructions for the Linux part of GFAP are missing. Please be patient, I will upload the usage instructions to GitHub within one day. I apologize once again.

simon19891216 commented 1 year ago

the manual of GFAP has been uploaded into this account. as image

Echoring commented 1 year ago

I've tried the updated linux version. A new module chardet is imported and missing in requirements.txt. After solving this I gain satisfactory result. The web tool's KEGG annotation seems still not work for me, but anyway, the standalone version work. Thanks for your help again!