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AnantharamanLab / METABOLIC

A scalable high-throughput metabolic and biogeochemical functional trait profiler
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METABOLIC_result.xlsx cannot be opened #8

Closed Thexiyang closed 4 years ago

Thexiyang commented 4 years ago

Hi Thanks for the nice tool! When dealing with many genomes, e..g 300, the produced METABOLIC_result.xlsx cannot be opened, saying this file is corrupt and cannot be opened. For dealing with 2 or 3 genomes, it works well. What could be the issue? Thanks!

patriciatran commented 4 years ago

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?

Thexiyang commented 4 years ago

Microsoft office 365 ProPlus. For the running log, there is no error message.

PandengWang commented 4 years ago

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

patriciatran commented 4 years ago

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.

patriciatran commented 4 years ago

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!