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NancyZxll / temperate-phage-active-prophage-detection

detect temperate phage (active prophage) in assembled bacterial genome sequences
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Problems with installing and running TemPhD. #2

Open NorthonColt opened 8 months ago

NorthonColt commented 8 months ago

I tried to install and run TemPhD on a linux server with the following sepcifications:

  1. When I try to install the TemPhD tool using the command conda install -c lwbuct temphd it returns the error found in the attached _temphd_installerror.txt file. temphd_install_error.txt

  2. After installing the TemPhD tool using the alternative method, downloading and building the specified bacterial database, and running the temperate phage detection process on the provided test files as specified in the readme, the program returns with the error attached in the _temphd_xml_simple_error.txt__ file. This error indicates that the XML/Simple module might be missing and need to be installed. temphd_xml_simple_error.txt

  3. After installing the XML/Simple module, and trying to run TemPhD on the same testing data again, it returned the error seen in the attached _temphd_bio_rooterror.txt file. This indicates that there is a problem with the Bio::Root::Version module, the installation of this module failed on multiple errors. temphd_bio_root_version_error.txt

I would like to kindly ask for your help to solve these problems because right now I can't run and use TemPhD for prophage detection. Your help is much appreciated, and I thank you for it in advance.

Best regards, Márton Réti

NancyZxll commented 7 months ago

Hi Reti, It seems that the prokka wasn't installed successfully. You can try to install prokka first and to see whether can run prokka successfully.

On Sun, Feb 25, 2024 at 3:23 AM Márton Réti @.***> wrote:

I tried to install and run TemPhD on a linux server with the following sepcifications:

I would like to kindly ask for your help to solve these problems because right now I can't run and use TemPhD for prophage detection. Your help is much appreciated, and I thank you for it in advance.

Best regards, Márton Réti

— Reply to this email directly, view it on GitHub https://github.com/NancyZxll/temperate-phage-active-prophage-detection/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADKXUCO6JS6R544NNDMPEH3YVI42HAVCNFSM6AAAAABDYHGSL2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGE2TENBVGI4DQMQ . You are receiving this because you are subscribed to this thread.Message ID: @.*** com>

NorthonColt commented 7 months ago

Hello!

Thanks for the response. Unfortunately, I was not able to solve the described issues in my environment so I tried again starting from a completely fresh Ubuntu virtual machine on Google Cloud. I successfully managed to install all the specified dependencies, and I also succeeded in installing TemPhD with the described alternative installation method (as the method using conda still did not work). However, I got the attached log and errors when running TemPhD on the specified testing data, and it could not detect any phage sequences. temphd_test_error.txt Unfortunately, I could not solve theses issues, even after many attempts and I would be grateful if you could help me. I wonder if you could send me a container with a working installation of TemPhD and all its dependencies? It would be highly appreciated. Thank you for your help in advance.

Best regards, Márton Réti