filter.py no such file or directory
Closed this issue · 5 comments
Hello, the following are my codes; The filter.py worked smoothly but I am encountering issues with predict.py:
docker run -it --rm -v /home/sealight1999/ASC_lifted/rmzero/history/all_bam/:/pikachu -w /varnet kiranchari/varnet:latest /bin/bash -c "git pull; python predict.py --sample_name AS_02N --normal_bam /pikachu/AS_02N_BQSR.bam --tumor_bam /pikachu/AS_02T_BQSR.bam --processes 2 --output_dir /pikachu/ --reference /pikachu/VarNet/GRCh38_no_alt.fna --path_to_positions_to_predict /pikachu/VarNet/
The error says fatal: Not a git repository (or any of the parent directories): .git
python: can't open file 'predict.py': [Errno 2] No such file or directory.
What could be the problem? thank you!
@Heather1999 If you downloaded the docker image again, please update the working directory to -w /VarNet in your command as the code directory was changed. The example docker command in the README has also been changed accordingly.
Thank you for your swift reply; So I did changed the N to capital letter but still getting the same error:
code:
docker run -it --rm -v /home/sealight1999/ASC_lifted/rmzero/history/all_bam/:/pikachu -w /varNet kiranchari/varnet:latest /bin/bash -c "git pull; python predict.py --sample_name AS_02N --normal_bam /pikachu/AS_02N_BQSR.bam --tumor_bam /pikachu/AS_02T_BQSR.bam --processes 2 --output_dir /pikachu/ --reference /pikachu/VarNet/GRCh38_no_alt.fna --path_to_positions_to_predict /pikachu/VarNet/"
error:
fatal: Not a git repository (or any of the parent directories): .git
python: can't open file 'predict.py': [Errno 2] No such file or directory
It should be -w /VarNet, both V and N should be capitalized
Ah! Don't know how I missed that. Issue fixed, thank you so much!