When using docker images, ggcaller does not work well

[HirokiK0]

We heard that there were problems with installation via conda, so we used docker as recommended. However, downloading the test dataset and using the commands listed in the documents did not work. Also, no error information is output, so I have no idea what is causing the problem. Please advise.

It appears that docker images is installed correctly as --help works.

Commands used. cd test && docker run --rm -it -v $(pwd):/workdir samhorsfield96/ggcaller:latest ggcaller --refs pneumo_CL_group2.txt

[samhorsfield96]

Hi, sorry to hear you ran into issues. I have a few questions which will help me troubleshoot for you.

• Are you running on Linux or MacOS?
• Was there any output at all?
• What is the contents of 'pneumo_CL_group2.txt' and does it contain the absolute file paths to the files you are analysing?

[HirokiK0]

Thanks for the reply. I have tried two operating systems, ubuntu 20.04 and ubuntu 22.04 on wsl2.

There was no output at all.

The pneumo_CL_group2.txt is the same as the one in the test folder on github. So it only contained the file name.

I personally presume that it is a permissions issue, but changing the workdir permissions by chmod 777 had no effect. Also, building the docker image on my PC did not work.

[samhorsfield96]

Hi, I would suggest trying two things:

• Try regenerating the input.txt file for the test sequence using the command documented here, this will use absolute file paths which may be causing the issue.
• If that does not work, install ggCaller from source, documented here

Please let me know whether you still run into trouble.

[HirokiK0]

By downloading from the source, the previous error no longer occurs. Thank you very much. However, I had to re-download the file from github and run it again because of the HAMMER error that was mentioned in another question. However, this time I got the following error related to DOWNLOAD. However, I can access the following link, so it does not seem to be an internet problem. I would be happy to hear your solution. Also, since it could be an access problem, I am considering how to download the necessary files from a web browser and place the files manually. Could you please tell me where to place the files?

https://ftp.ebi.ac.uk/pub/databases/pp_dbs/ggCallerdb.tar.bz2

Building coloured compacted DBG... Generating graph stop codon index... Mapping contigs to graph... Downloading databases... Traceback (most recent call last):

urllib.error.URLError: <urlopen error [Errno 104] Connection reset by peer>

[samhorsfield96]

There could be a number of reasons for this, and unfortunately I have not been able to replicate this issue. To circumvent the download, you can navigate to the models directory where you installed ggCaller from source, and run wget https://ftp.ebi.ac.uk/pub/databases/pp_dbs/ggCallerdb.tar.bz2 to download the model database. You should then be able to run ggCaller as before.

[HirokiK0]

Test data worked fine! Thank you very much for your very courteous response!