ericjove
commented
7 months ago Please attempt the following:
Option 1: Completely delete and reinstall PGAP.
Open your terminal. Execute the command rm -rf ~/.pgap to delete the PGAP directory. This command removes the .pgap directory and all of its contents.
Reinstall PGAP: Follow the instructions on the https://github.com/ncbi/pgap/wiki/Quick-Start page to download and install the latest version of PGAP.
Option 2: Set the Environment Variable for PGAP_INPUT_DIR.
In your terminal, set PGAP_INPUT_DIR to a new location using: For Linux/macOS EG: export PGAP_INPUT_DIR=/path/to/new/directory
Ensure the path you choose is different from the current PGAP installation directory (~/.pgap) as this will force a fresh installation of pgap.
Reinstall PGAP: Follow the same Quick Start instructions for PGAP installation (https://github.com/ncbi/pgap/wiki/Quick-Start). The script should use the new directory set by PGAP_INPUT_DIR.
After completing either Option 1 or Option 2, try running the PGAP command again to see if the issue has been resolved.
Unset Proxy Variables (if the issue persists):
If the error continues, execute these commands to remove any proxy settings:
unset http_proxy
unset https_proxy
unset HTTP_PROXY
unset HTTPS_PROXYRetry running PGAP:
Please let me know if you have any continued issues.
When I m trying to run pgap annotation using following command "./pgap.py -r -o test_result -g ASM2732v1.annotation.nucleotide.1.fasta -s 'Mycoplasma genitalium G37'" It is throwing error like below: PGAP version 2023-10-03.build7061 is up to date. <urlopen error [Errno 104] Connection reset by peer> Failed to update ./pgap.py, ignoring Something has gone wrong, please manually download: https://github.com/ncbi/pgap/raw/prod/scripts/pgap.py What is this error about?