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I ran the METABOLIC-G.pl script and some errors in error file and log file. So, no figures generated. Could you please have a look and give me some suggestions on how to avoid these errors?
error code:[2025-01-09 20:45:18] The Prodigal annotation is running...
[2025-01-09 21:11:41] The Prodigal annotation is finished
mkdir: cannot create directory ‘/data/home/database/metabolic-result/nosz-carried/intermediate_files/Hmmsearch_Outputs’mkdir: cannot create directory ‘/data/home/database/metabolic-result/nosz-carried/intermediate_files/Hmmsearch_Outputs’: File exists
: File exists
[2025-01-10 08:38:24] The hmmsearch is running with 50 cpu threads...
[2025-01-10 21:42:59] The hmmsearch is finished
[2025-01-12 16:43:00] The hmm hit result is calculating...
[2025-01-12 16:43:04] Generating each hmm faa collection...
[2025-01-12 16:44:19] Each hmm faa collection has been made
[2025-01-12 16:44:19] The KEGG module result is calculating...
[2025-01-13 18:42:51] The KEGG identifier (KO id) result is calculating...
[2025-01-13 18:44:45] The KEGG identifier (KO id) seaching result is finished
[2025-01-13 18:44:45] Searching CAZymes by dbCAN2...
[2025-01-13 22:16:15] dbCAN2 searching is done
[2025-01-13 22:16:16] Searching MEROPS peptidase...
[2025-01-13 23:34:48] MEROPS peptidase searching is done
Error: 1:102: unexpected '/'
1: options("repos"=c(CRAN="https://mirrors.pku.edu.cn/CRAN/","The Comprehensive R Archive Network",http:/
^
Execution halted
Error: 1:102: unexpected '/'
1: options("repos"=c(CRAN="https://mirrors.pku.edu.cn/CRAN/","The Comprehensive R Archive Network",http:/
^
Execution halted
mv: cannot stat 'METABOLIC_result.xlsx': No such file or directory
mv: cannot stat 'METABOLIC_result.xlsx': No such file or directory
[2025-01-13 23:34:51] METABOLIC table has been generated
[2025-01-13 23:34:51] Drawing element cycling diagrams...
Error: 1:102: unexpected '/'
1: options("repos"=c(CRAN="https://mirrors.pku.edu.cn/CRAN/","The Comprehensive R Archive Network",http:/
^
Execution halted
Error: 1:102: unexpected '/'
1: options("repos"=c(CRAN="https://mirrors.pku.edu.cn/CRAN/","The Comprehensive R Archive Network",http:/
^
Execution halted
mv: cannot stat '/data/home/database/metabolic-result/nosz-carried/Output/draw_biogeochem_cycles': No such file or directory
mv: cannot stat '/data/home/database/metabolic-result/nosz-carried/Output/draw_biogeochem_cycles': No such file or directory
rm: cannot remove '/data/home/database/metabolic-result/nosz-carried/Output'rm: cannot remove '/data/home-wujw/database/metabolic-result/nosz-carried/Output': No such file or directory
: No such file or directory
[2025-01-13 23:35:27] Drawing element cycling diagrams finished
METABOLIC-G was done, the total running time: 98:50:09 (hh:mm:ss)
running code: perl METABOLIC-G.pl -in-gn /data/home/database/metabolic-result/sequence1 -o /data/home/database/metabolic-result/nosz-carried -cpu 50
What should I do ? Thanks.
The text was updated successfully, but these errors were encountered:
Dear METABOLIC support team,
I ran the METABOLIC-G.pl script and some errors in error file and log file. So, no figures generated. Could you please have a look and give me some suggestions on how to avoid these errors?
error code:[2025-01-09 20:45:18] The Prodigal annotation is running...
[2025-01-09 21:11:41] The Prodigal annotation is finished
mkdir: cannot create directory ‘/data/home/database/metabolic-result/nosz-carried/intermediate_files/Hmmsearch_Outputs’mkdir: cannot create directory ‘/data/home/database/metabolic-result/nosz-carried/intermediate_files/Hmmsearch_Outputs’: File exists
: File exists
[2025-01-10 08:38:24] The hmmsearch is running with 50 cpu threads...
[2025-01-10 21:42:59] The hmmsearch is finished
[2025-01-12 16:43:00] The hmm hit result is calculating...
[2025-01-12 16:43:04] Generating each hmm faa collection...
[2025-01-12 16:44:19] Each hmm faa collection has been made
[2025-01-12 16:44:19] The KEGG module result is calculating...
[2025-01-13 18:42:51] The KEGG identifier (KO id) result is calculating...
[2025-01-13 18:44:45] The KEGG identifier (KO id) seaching result is finished
[2025-01-13 18:44:45] Searching CAZymes by dbCAN2...
[2025-01-13 22:16:15] dbCAN2 searching is done
[2025-01-13 22:16:16] Searching MEROPS peptidase...
[2025-01-13 23:34:48] MEROPS peptidase searching is done
Error: 1:102: unexpected '/'
1: options("repos"=c(CRAN="https://mirrors.pku.edu.cn/CRAN/","The Comprehensive R Archive Network",http:/
^
Execution halted
Error: 1:102: unexpected '/'
1: options("repos"=c(CRAN="https://mirrors.pku.edu.cn/CRAN/","The Comprehensive R Archive Network",http:/
^
Execution halted
mv: cannot stat 'METABOLIC_result.xlsx': No such file or directory
mv: cannot stat 'METABOLIC_result.xlsx': No such file or directory
[2025-01-13 23:34:51] METABOLIC table has been generated
[2025-01-13 23:34:51] Drawing element cycling diagrams...
Error: 1:102: unexpected '/'
1: options("repos"=c(CRAN="https://mirrors.pku.edu.cn/CRAN/","The Comprehensive R Archive Network",http:/
^
Execution halted
Error: 1:102: unexpected '/'
1: options("repos"=c(CRAN="https://mirrors.pku.edu.cn/CRAN/","The Comprehensive R Archive Network",http:/
^
Execution halted
mv: cannot stat '/data/home/database/metabolic-result/nosz-carried/Output/draw_biogeochem_cycles': No such file or directory
mv: cannot stat '/data/home/database/metabolic-result/nosz-carried/Output/draw_biogeochem_cycles': No such file or directory
rm: cannot remove '/data/home/database/metabolic-result/nosz-carried/Output'rm: cannot remove '/data/home-wujw/database/metabolic-result/nosz-carried/Output': No such file or directory
: No such file or directory
[2025-01-13 23:35:27] Drawing element cycling diagrams finished
METABOLIC-G was done, the total running time: 98:50:09 (hh:mm:ss)
running code: perl METABOLIC-G.pl -in-gn /data/home/database/metabolic-result/sequence1 -o /data/home/database/metabolic-result/nosz-carried -cpu 50
What should I do ? Thanks.
The text was updated successfully, but these errors were encountered: