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genescf / GeneSCF

Gene Set Clustering based on Functional annotation
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Error: Illegal division by zero at List.pl line 599, <IN2> chunk 1 #4

Closed golrokh51 closed 4 years ago

golrokh51 commented 5 years ago

command line: ./geneSCF -m=normal -i=/Users/.../.../geneID_list.txt -t=gid -o=simple1_CSF.txt -db=GO_all -p=yes -bg=24850 -org=mgi

ERROR: processing in 'normal' mode started....Fri 9 Nov 2018 17:31:39 EST => Finished retriving database... => Calculating statistics... find: -printf: unknown primary or operator 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_all last updated Illegal division by zero at /Users/.../.../geneSCF-master-source-v1.1-p2/class/lib/List/Vectorize/lib/List.pl line 599, chunk 1. Fri 9 Nov 2018 17:31:40 EST finished processing

decodebiology commented 5 years ago

Which operating system are you using ?

Requirement: GeneSCF only works on Linux system, it has been successfully tested on Ubuntu, Mint,Cent OS and Windows 10 bash (>version 1607). Other distributions of Linux might work as well.

Usually this error occurs,

1) When you use unsupported operating system.

2) When none of your genes in the list matches with database

3) When the database is not formatted/downloaded properly. Try ’prepare_database’ module to update the database.

4) Or the list/database is prepared with textedit (Mac) or notepad (windows). The input list/database must be prepared using Linux terminal or Linux supported text editor (example, Gedit).

decodebiology commented 5 years ago

Since you did not respond back. I assume above comment answered you query. I am closing this issue now. Thanks for using GeneSCF.

chuddy-ibk commented 1 year ago

hi there. (i post here because i cannot submit a new issue somehow)

I have tried following code from the GeneSCF directory and get following error:

$ bash geneSCF -m=normal -i=/home/chuddy/Documents/GeneSCF-1.1-p3.beta/test/H0.list -t=sym -o=/home/chuddy/Documents/GeneSCF-1.1-p3.beta -db=GO_all -p=yes -bg=20000 -org=goa_human processing in 'normal' mode started....Thu Apr 27 21:17:10 CEST 2023 => Finished retriving database... => Calculating statistics... find: '/home/chuddy/Documents/GeneSCF-1.1-p3.beta/class/lib/db/goa_human/GO_all_sym.txt': No such file or directory 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_all last updated Error opening in database file at /home/chuddy/Documents/GeneSCF-1.1-p3.beta/class/functional_class3.pl line 136. Thu Apr 27 21:17:10 CEST 2023 finished processing

Same error as with my own gene ID list (changed everything so i though i try the established one but get this error. Then I also tried KEGG for mouse and ended up with nothing so i tried again the test data from the geneSCF list and following appeared:

$ bash geneSCF -m=normal -i=/home/chuddy/Documents/GeneSCF-1.1-p3.beta/test/H0.list -t=sym -o=/home/chuddy/Documents/GeneSCF-1.1-p3.beta -db=KEGG -p=yes -bg=20000 -org=hsa processing in 'normal' mode started....Thu Apr 27 21:20:41 CEST 2023 => 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). KEGG last updated 2022-07-25 21:32 Example input types

gid | sym 100616456 miRNA 3885 CDS 10699 CDS 6654 CDS 100616273 miRNA 1667 CDS 143244 CDS 113218485 miRNA 8153 CDS 1106 CDS => Retreving gene list for hsa from KEGG sh: 1: cannot create /home/chuddy/Documents/GeneSCF-1.1-p3.beta/mapping/DB/H0.list_gene_list.txt: Directory nonexistent curl: (23) Failure writing output to destination => Mapping user list Error opening in file at /home/chuddy/Documents/GeneSCF-1.1-p3.beta/class/scripts/mappingIDS.pl line 7. sh: 1: cannot create /home/chuddy/Documents/GeneSCF-1.1-p3.beta/mapping/H0.list_input_list.txt: Directory nonexistent Note: There were 0 genes mapped from 139 user provided unique genes (0 %) Please cross-check your gene identifier.Thu Apr 27 21:20:59 CEST 2023 finished processing

So what could be the issue? I use an established test gene set. created the GO folder in the SFC directory for the output. Please help.

Cheers.