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genescf / GeneSCF

Gene Set Clustering based on Functional annotation
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Unable to run geneSCF on linux #1

Closed yxu405 closed 4 years ago

yxu405 commented 4 years ago

When I ran geneSF using this command, it gives me this error message. Command: ./geneSCF -m=normal -i=test/annotation.tsv -o=test/output/ -t=sym -db=GO_MF -bg=20000 --plot=yes -org=goa_human Message: processing in 'normal' mode started....Sun May 24 08:41:35 PDT 2020 => Finished retriving database... => Calculating statistics... Note:Only KEGG and Geneontology supports multiple organisms (GeneSCF-xx/org_codes_help). If you choose REACTOME/NCG database please specify organism as 'Hs'. Currently REACTOME and NCG in GeneSCF only supports Human (Hs). GO_MF last updated 2017-07-07 14:04 nohup: redirecting stderr to stdout

Run successful. Check your output directory test/output/

Parameters used:

Organism: Human/Homo sapiens background genes: 20000 Identitiy: Gene Symbol Database used: GO_MF Output file: test/output/annotation.tsv_GO_MF_functional_classification.tsv WARNING: Your output is not sorted with P-val/FDR.

Author: Santhilal Subhash santhilal.subhash@gu.se GeneSCF elapse time 6 seconds Sun May 24 08:41:41 PDT 2020 finished processing

Furthermore, because I saw your previous post about the getting such error could due to database not being updated. Then, I tried using this command to update the database. Command:./prepare_database -db=[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME] -org=[hsa] Message: KEGG: command not found GO_CC: command not found REACTOME]: command not found GO_MF: command not found GO_BP: command not found

Please help! Thank you so much for your time

decodebiology commented 4 years ago

Will you please provide your sample input file?

yxu405 commented 4 years ago

Sure! Screen Shot 2020-05-24 at 11 27 25 AM

These are the annotations I obtained from the GO website

decodebiology commented 4 years ago

Hi,

Listed identifiers ae protein/peptide IDs. GeneSCF only accepts Gene symbol (HGNC) or Entrez gene IDs.

Example:

'A0A023HHK9' can be given as either 'TET1' (HGNC) or '80312' (Entrez).

yxu405 commented 4 years ago

I know this is an easy question to ask, I am pretty new at using this, but is there any way that I can convert this list of annotations to gene IDs? The list I obtained from, QuickGo, wouldn't show me the gene IDs in group; as I had to click in one by one.

decodebiology commented 4 years ago

You must convert 'UniProt Accession' to 'Gene Symbols' or 'Entrez Gene ID' or 'HGNC symbols'. Check out if this helps, https://www.biostars.org/p/283347/

Good luck.

decodebiology commented 4 years ago

I will be closing this issue now. You are welcome to contact me for future queries.