Comments (5)
Hi everyone, this was due to the Perl module which doesn't work well on all systems. In our most recent version (which we will update soon), we use R's openxlsx package to generate the Excel file instead. We'll post here again when the new version is available, and if any of you could test it out and see if that solves your issue, that would be great. Stay tuned! Thank you.
from metabolic.
Hi! Just updating you to let you know our latest METABOLIC version has been updated with the R script to generate the spreadsheet which solves the issue. We also generate individual TSV files for each spreadsheet. Thanks!
from metabolic.
Hi! Can you tell us more details about which program and version you are using the view the xlsx file? Can you see in if any error was output to the log when the xlsx were created in the 300 genomes run, and compare to the log in the 2-3 genomes run?
from metabolic.
Microsoft office 365 ProPlus. For the running log, there is no error message.
from metabolic.
I used the lastest version (I dowloaded this tool one week ago), BUT I encontered the same problem. My genome number is 215.
Belows are the log:
[2020-06-11 09:19:19] Drawing element cycling diagrams finished
mkdir: cannot create directory ‘Anaerolineales_pick987_metabolic/’: File exists
[2020-06-11 10:03:31] The Prodigal annotation is running...
[2020-06-11 10:05:13] The Prodigal annotation is finished
[2020-06-11 10:06:02] The hmmsearch is running with 15 cpu threads...
[2020-06-11 12:29:11] The hmmsearch is finished
[2020-06-11 12:30:07] The hmm hit result is calculating...
[2020-06-11 12:30:08] Generating each hmm faa collection...
[2020-06-11 12:30:09] Each hmm faa collection has been made
[2020-06-11 12:30:09] The KEGG module result is calculating...
[2020-06-11 14:27:43] The KEGG identifier (KO id) result is calculating...
[2020-06-11 14:27:50] The KEGG identifier (KO id) seaching result is finished
[2020-06-11 14:27:50] Searching CAZymes by dbCAN2...
[2020-06-11 15:05:24] dbCAN2 searching is done
[2020-06-11 15:05:24] Searching MEROPS peptidase...
[2020-06-11 15:47:02] MEROPS peptidase searching is done
[2020-06-11 15:47:09] METABOLIC table has been generated
[2020-06-11 15:47:09] Drawing element cycling diagrams...
Loading required package: shape
[2020-06-11 15:47:20] Drawing element cycling diagrams finished
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Related Issues (20)
- Output_energy_flow/Energy_plot/network.plot.pdf': No such file or directory HOT 1
- Not a bug/ only a question
- (Question) Can you give it proteins instead of genomes?
- Possibly wrong link for MEROPS in run_to-setup.sh HOT 1
- Should the arrow of Step8: Nitrite ammonification start from nitrate or nitrite? HOT 1
- What are values in Sequential_Transformation_input_2 based on?
- How to get access to test google drive files? HOT 2
- The gtdbtk module throws an error: 'EXCEPTION: OSError MESSAGE: [Errno 12] Cannot allocate memory‘ when running METABOLIC-C.pl. HOT 2
- Running 7000+MAGs, no progress after Prodigal HOT 3
- Bio::Perl instalation HOT 1
- Access to test filés in google drive HOT 2
- The result files "All_gene_collections_mapped.depth.txt" ,"Functional_network_figures" are empty. HOT 2
- Can metabolic used for annotation of virus genome? HOT 2
- cannot locate statistic/descriptive.pm in for metabolic-c.pl line 40
- Perl version conflict when installing via YAML
- Hi @patriciatran, Mrtabolic-c was unsuccessful in producing All_gene_collections_mapped.depth.txt documents
- WHY only 1 CPU when hmmsearch HOT 1
- Issues installing required R packages HOT 1
- Sulfite oxidation/Sulfate Reduction
- Cannot allocate memory
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