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SystemsBioinformatics / cbmpy-metadraft

CBMPy Metadraft: a flexible and extensible genome-scale model reconstruction tool
https://systemsbioinformatics.github.io/cbmpy-metadraft/
GNU General Public License v3.0
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Stuck on `OS Call: perl inparanoid.pl IN DB` #17

Open JoshLoecker opened 3 months ago

JoshLoecker commented 3 months ago

Hello, I am trying to create a model of Macaca Mulatta (mmul) using MetaDraft. I have the .faa file for mmul, along with a Homo Sapien .gbff file and an SBML file (Recon3D from the BiGG database).

However, when clicking "BLAST" after loading and creating the metaproteome, I am only seeing the following lines in the python console

Work directory: /work/helikarlab/joshl/cbmpy-metadraft/data_blast/1717696531
OS call: perl inparanoid.pl IN DB

Here is a screenshot of what I am seeing

Screenshot 2024-06-06 at 1 09 32 PM

If there's anything else I can provide, please let me know! Thank you for any assistance

System: Ubuntu 20.04 (supercomputing cluster) 8 Cores 50 GB RAM

Macaca Mulatta .ffa file: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/339/765/GCF_003339765.1_Mmul_10/GCF_003339765.1_Mmul_10_protein.faa.gz Homo Sapiens .gbff file: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gbff.gz Recon3D SBML file: http://bigg.ucsd.edu/models/Recon3D

xiaobin-phd commented 2 months ago

I got the same problem, I have tested systemtest.py, every software the metadraft needed is fine, but I am still stuck at the interface running "OS call: perl inparanoid.pl IN DB" for hours，I use the "top" command and can not see any blast is running.

bgoli commented 1 month ago

I think the common problem is that MetaDraft is using the BLAST+ and not the legacy BLAST that is required by an external PERL module it uses. I realise that the use of legacy BLAST is a problem, however, there is no quick fix for this version of Metadraft. I am currently looking into developing the next version of Metadraft that will completely remove the module that is causing the problems and remove most of the currently required dependencies.

My apologies for the problems you are all experiencing, the BLAST/PERL combination has been a problem that has developed over the years and now needs a radical rewrite of some core code. While I cannot give an estimate on when the new version will be available. I will release a new version and add a comment to this thread when it is available for testing.

JoshLoecker commented 1 month ago

@bgoli no problem, thanks for the update! If there's anything else I can do to be of assistance please let me know!

xiaobin-phd commented 1 month ago

Thanks for you attention, I appreciate it.

Best regards！

xiaobin

xiaobin @.***

 

------------------ 原始邮件 ------------------ 发件人: "SystemsBioinformatics/cbmpy-metadraft" @.>; 发送时间: 2024年7月19日(星期五) 下午5:59 @.>; @.**@.>; 主题: Re: [SystemsBioinformatics/cbmpy-metadraft] Stuck on OS Call: perl inparanoid.pl IN DB (Issue #17)

Sorry for the delay in reply. I think the common problem is that MetaDraft is using the BLAST+ and not the legacy BLAST that is required by an external PERL module it uses. I realise that the use of legacy BLAST is a problem, however, there is not quick fix for this version of metadraft. I am currently looking into developing the next version of Metadraft, that will completely removed the module that is causing the problems and remove most of the currently required dependencies.

My apologies for the problems you are all experiencing, the BLAST/PERL combination has been a problem developing over the years and now needs a radical rewrite of some core code. While I cannot give an estimate on when the new version will be available. I will release a new version and add a comment to this thread when it is available.

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