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AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
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mv: cannot stat '/home/adm/dingyi/metabolicC/Output_energy_flow/Energy_plot/network.plot.pdf': No such file or directory #191

Open yi-dingg opened 3 months ago

yi-dingg commented 3 months ago

Hello, When I use METABOLIC/METABOLIC-C.2nd_run.pl, I get the following error message. File "All_gene_collections_mapped.depth.217pc.txt " and "MW-score_result.txt" are empty. Looking forward to your response. [2024-07-29 12:19:12] Skip Prodigal running for a 2nd run [2024-07-29 12:45:12] Skip hmmsearch running for a 2nd run [2024-07-29 16:15:37] Skip printing out each hmm faa collection [2024-07-29 16:15:37] Skipe doing the KEGG module result calculating [2024-07-29 16:15:37] Skip doing the KEGG identifier (KO id) result calculating [2024-07-29 16:15:37] Skip searching CAZymes by dbCAN2 [2024-07-29 16:15:37] Skip searching MEROPS peptidase [2024-07-29 16:15:37] Skip generating METABOLIC table [2024-07-29 16:15:37] Drawing element cycling diagrams... [2024-07-30 00:42:59] Drawing element cycling diagrams finished [2024-07-30 00:42:59] Drawing metabolic handoff diagrams... [2024-07-30 00:43:37] Drawing metabolic handoff diagrams finished [2024-07-30 00:43:37] Drawing energy flow chart... mv: cannot stat '/home/adm/dingyi/metabolicC/Output_energy_flow/Energy_plot/network.plot.pdf': No such file or directory mv: cannot stat '/home/adm/dingyi/metabolicC/Output_energy_flow/Energy_plot/network.plot.pdf': No such file or directory [2024-07-30 00:43:47] Drawing energy flow chart finished [2024-07-30 00:43:47] Calculating MW-score ... [2024-07-30 00:44:21] Calculating MW-score is done METABOLIC-C was done, the total running time: 12:25:09 (hh:mm:ss)

My command is: nohup perl /home/adm/software/METABOLIC/METABOLIC-C.2nd_run.pl -in-gn /home/adm/dingyi/bins_rename -r /home/adm/dingyi/217pc_reads_path.txt -o /home/adm/dingyi/metabolicC -2nd-run true -2nd-run-suffix 217pc -t 30 &> 217_2nd_run.out &

patriciatran commented 2 months ago

Hi, the script to make the energy flow chart is here: https://github.com/AnantharamanLab/METABOLIC/blob/master/draw_metabolic_Sankey_diagram.R Do you know if the input files Energy_flow_input <- userprefs[1] # Path to to Energy_flow_input.txt , a file named Energy_flow_input.txt is present in one of your output folders?