[Error] Docker exited with rc = 1

[namho4577]

[Error] Docker exited with rc = 1

[azat-badretdin]

Thank you for your report, user @namho4577 !

Your command line says:

./pgap.py -r -o E_coli_result9 -g $HOME/.pgap/test_genomes/MG37/input.yaml -s 'Escherichia coli' --ignore-all-errors

When you are using -g option it requires a FASTA file, not a YAML file.

[namho4577]

Then what code should I write for the yaml file? iOS용 Outlook<https://aka.ms/o0ukef> 다운로드

…

________________________________ 보낸 사람: Azat Badretdin ***@***.***> 보낸 날짜: Saturday, May 4, 2024 5:57:13 PM 받는 사람: ncbi/pgap ***@***.***> 참조: charmantflower ***@***.***>; Mention ***@***.***> 제목: Re: [ncbi/pgap] [Error] Docker exited with rc = 1 (Issue #301) Closed #301<#301> as completed. — Reply to this email directly, view it on GitHub<#301 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BHIG5NIERWDCYFASUIQZ7CTZASPGTAVCNFSM6AAAAABHGS4JZ6VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJSG4YDGOBTGY2DENQ>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[azat-badretdin]

If you would like to continue using YAML file replace -s and -g parameters with YAML file.

So this:

./pgap.py -r -o E_coli_result9 -g $HOME/.pgap/test_genomes/MG37/input.yaml -s 'Escherichia coli' --ignore-all-errors

will become this

./pgap.py -r --ignore-all-errors -o E_coli_result9 $HOME/.pgap/test_genomes/MG37/input.yaml