azat-badretdin
commented
2 months ago Thank you for your report, user @XMUykyz !
I understand your frustration, but the only way is to restart update as recommended. We also have from time to time internet problems in our testing of PGAP.
If this happens too often, this must be related to your local internet setup and needs to be addressed with your local system specialists
Describe the bug I occasionally have connection problems when executing commands, but sometimes I can successfully start updating, but after downloading some files, it always reports an error, it has been repeated many times, it is the same situation, I have seen others have similar situations, but I still have not found an effective solution.
Command：./pgap.py --update &> a1.log a1.log
be9dcf07eb22: Retrying in 1 second 9fcdf5fda447: Verifying Checksum 9fcdf5fda447: Download complete b9c6f0d7f0b3: Verifying Checksum b9c6f0d7f0b3: Download complete be9dcf07eb22: Verifying Checksum be9dcf07eb22: Download complete read tcp 192.168.1.105:47000->104.16.97.215:443: read: connection reset by peer Downloading (as needed) Docker image ncbi/pgap:2024-07-18.build7555 None Traceback (most recent call last): File "/data/shenhx/code/pgap-new/./pgap.py", line 1123, in main params = Setup(args) ^^^^^^^^^^^ File "/data/shenhx/code/pgap-new/./pgap.py", line 630, in init self.update() File "/data/shenhx/code/pgap-new/./pgap.py", line 782, in update raise Exception(f'installation of some or all of components failed. Please remove {self.data_path}, {self.install_dir}/test_genomes, {self.test_genomes_path} directories and try again.') Exception: installation of some or all of components failed. Please remove /data/shenhx/code/PGAP_Input/input-2024-07-18.build7555, /data/shenhx/code/PGAP_Input/test_genomes, /data/shenhx/code/PGAP_Input/test_genomes-2024-07-18.build7555 directories and try again.
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