Dear METABOLIC team,
When I ran METABOLIC 2nd, it generated results successfully but it has some problems: I cannot find MW score Excel file and network plot. Can you please help me find solutions. Below is my history in Ubuntu
(METABOLIC_v4.0) min@Workstation:/mnt/e/DA/shallow_shotgun/METABOLIC$ perl METABOLIC-C.2nd_run.pl -in-gn /mnt/e/DA/shallow_shotgun/genome_bins_2nd_test -r /mnt/e/DA/shallow_shotgun/raw_reads/Sl_read_pairs.txt
-o /mnt/e/DA/shallow_shotgun/function_annotation_2nd_test -rt metaG -st illumina -t 64 -p meta -2nd-run true -2nd-run-suffix MW_score_tax_genus -depth-file All_gene_collections_mapped.depth.txt -tax genus
[2025-06-23 15:41:44] Skip Prodigal running for a 2nd run
[2025-06-23 15:42:10] Skip hmmsearch running for a 2nd run
[2025-06-23 16:03:57] Skip printing out each hmm faa collection
[2025-06-23 16:03:57] Skipe doing the KEGG module result calculating
[2025-06-23 16:03:57] Skip doing the KEGG identifier (KO id) result calculating
[2025-06-23 16:03:57] Skip searching CAZymes by dbCAN2
[2025-06-23 16:03:57] Skip searching MEROPS peptidase
[2025-06-23 16:03:57] Skip generating METABOLIC table
[2025-06-23 16:03:57] Drawing element cycling diagrams...
mkdir: cannot create directory ‘/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/METABOLIC_Figures_Input.MW_score_tax_genus’: File exists
Many thanks for your effort and I look forward to hearing from you soon
mkdir: cannot create directory ‘/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/METABOLIC_Figures_Input.MW_score_tax_genus/Nutrient_Cycling_Diagram_Input’: File exists
mkdir: cannot create directory ‘/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/METABOLIC_Figures.MW_score_tax_genus’: File exists
[2025-06-23 16:04:52] Drawing element cycling diagrams finished
[2025-06-23 16:04:52] Drawing metabolic handoff diagrams...
[2025-06-23 16:04:59] Drawing metabolic handoff diagrams finished
[2025-06-23 16:04:59] Drawing energy flow chart...
mv: cannot stat '/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/Output_energy_flow/Energy_plot/network.plot.pdf': No such file or directory
[2025-06-23 16:05:02] Drawing energy flow chart finished
[2025-06-23 16:05:02] Calculating MW-score ...
mkdir: cannot create directory ‘/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/MW-score_result.MW_score_tax_genus’: File exists
[2025-06-23 16:05:04] Calculating MW-score is done
METABOLIC-C was done, the total running time: 00:23:20 (hh:mm:ss)
Dear METABOLIC team,
When I ran METABOLIC 2nd, it generated results successfully but it has some problems: I cannot find MW score Excel file and network plot. Can you please help me find solutions. Below is my history in Ubuntu
(METABOLIC_v4.0) min@Workstation:/mnt/e/DA/shallow_shotgun/METABOLIC$ perl METABOLIC-C.2nd_run.pl -in-gn /mnt/e/DA/shallow_shotgun/genome_bins_2nd_test -r /mnt/e/DA/shallow_shotgun/raw_reads/Sl_read_pairs.txt
-o /mnt/e/DA/shallow_shotgun/function_annotation_2nd_test -rt metaG -st illumina -t 64 -p meta -2nd-run true -2nd-run-suffix MW_score_tax_genus -depth-file All_gene_collections_mapped.depth.txt -tax genus
[2025-06-23 15:41:44] Skip Prodigal running for a 2nd run
[2025-06-23 15:42:10] Skip hmmsearch running for a 2nd run
[2025-06-23 16:03:57] Skip printing out each hmm faa collection
[2025-06-23 16:03:57] Skipe doing the KEGG module result calculating
[2025-06-23 16:03:57] Skip doing the KEGG identifier (KO id) result calculating
[2025-06-23 16:03:57] Skip searching CAZymes by dbCAN2
[2025-06-23 16:03:57] Skip searching MEROPS peptidase
[2025-06-23 16:03:57] Skip generating METABOLIC table
[2025-06-23 16:03:57] Drawing element cycling diagrams...
mkdir: cannot create directory ‘/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/METABOLIC_Figures_Input.MW_score_tax_genus’: File exists
Many thanks for your effort and I look forward to hearing from you soon
mkdir: cannot create directory ‘/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/METABOLIC_Figures_Input.MW_score_tax_genus/Nutrient_Cycling_Diagram_Input’: File exists
mkdir: cannot create directory ‘/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/METABOLIC_Figures.MW_score_tax_genus’: File exists
[2025-06-23 16:04:52] Drawing element cycling diagrams finished
[2025-06-23 16:04:52] Drawing metabolic handoff diagrams...
[2025-06-23 16:04:59] Drawing metabolic handoff diagrams finished
[2025-06-23 16:04:59] Drawing energy flow chart...
mv: cannot stat '/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/Output_energy_flow/Energy_plot/network.plot.pdf': No such file or directory
[2025-06-23 16:05:02] Drawing energy flow chart finished
[2025-06-23 16:05:02] Calculating MW-score ...
mkdir: cannot create directory ‘/mnt/e/DA/shallow_shotgun/function_annotation_2nd_test/MW-score_result.MW_score_tax_genus’: File exists
[2025-06-23 16:05:04] Calculating MW-score is done
METABOLIC-C was done, the total running time: 00:23:20 (hh:mm:ss)