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WGLab / DeepRepeat

An accurate repeat detection from Nanopore data using deep learning and image techniques
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No sequencing summary file found using docker execution #9

Closed fanavarro closed 1 year ago

fanavarro commented 1 year ago

Hi, I am trying to use DeepRepeat through docker, so I have followed the instructions in the readme to do that.

Nonetheless, I am receiving an error indicating the following:

Error happen!
     data/LSA-2022-0019/test/sequencing_summary.txt does not exist. Should specified by --summary_file.

Actually, I am setting the summary file by using --summary_file option. The file exists, so I can do "cat data/LSA-2022-0019/test/sequencing_summary.txt" to see its content.

I am wondering if this issue could be related to Docker. Should I include the file inside the docker container? Or is it fine to have it in my filesystem?

Thanks beforehand!

fanavarro commented 1 year ago

I am answering myself after reading other issue... Yes, I have to map my working directory into the container when running the docker command. Something like:

docker run -v "MY_WORK_DIR":/workspace/ --rm genomicslab/deeprepeat:0.1.3 python DeepRepeat.py Detect

And then specify the parameters by assuming the root "/workspace".

liuqianhn commented 1 year ago

@fanavarro Glad that you solved the issue. Yes, you need to map local folder to docker folder.