Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.
GNU General Public License v3.0
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nextPolish on Docker #67

Open marco91sol opened 3 years ago

marco91sol commented 3 years ago

Describe the bug Hi,

I ran nextPolish on docker. Firstly, I used the docker pull pvstodghill/nextpolish. Later, I ran the following command: docker run --ulimit nofile=64000:64000 -u $(id -u) -v /mnt/mrc/CS:/nextPolish_wd pvstodghill/nextpolish nextPolish ./run.cfg.nextpolish

Error message Emulate Docker CLI using podman. Create /etc/containers/nodocker to quiet msg. Traceback (most recent call last): File "/opt/NextPolish/nextPolish", line 511, in main(args) File "/opt/NextPolish/nextPolish", line 337, in main log = plog(log_file) File "/opt/NextPolish/lib/kit.py", line 56, in plog fileHandler = logging.FileHandler(path, mode='w') File "/usr/lib/python2.7/logging/init.py", line 920, in init StreamHandler.init(self, self._open()) File "/usr/lib/python2.7/logging/init.py", line 950, in _open stream = open(self.baseFilename, self.mode) IOError: [Errno 13] Permission denied: '/mnt/pid1.log.info'

How can I solve this issue?

moold commented 3 years ago

Hi, I do not familiar with docker, so you can follow here to have a try.