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chrisquince / STRONG

Strain Resolution ON Graphs
MIT License
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Restarting SPAdes in STRONG with --continue option #130

Open cbreusing opened 1 year ago

cbreusing commented 1 year ago

Hi Chris,

I am running STRONG on a large metagenomic dataset and will need to restart the assembly step from a checkpoint. How do I provide this option in the config file? Is it something like optional_args: '--continue' under the assembly step?

Thank you for any advice, Corinna

Taojianchang commented 1 year ago

Hello Corina, I try to suing STRONG on my study. However, the COG database url was broken (https://strongtest.s3.climb.ac.uk/rpsblast_cog_db.tar.gz). If you have download this database, would you please transfer this database to me? much thanks!

Tao Jianchang

cbreusing commented 1 year ago

Hi Tao,

Of course. Happy to help. I have uploaded the version that I have to Google Drive HERE https://drive.google.com/file/d/1JLWTY482h9BJOqVlZpyfOlD_rJbTJAMr/view?usp=share_link.

Please let me know if you have any issues.

Thank you, Corinna

On 7. Feb 2023, at 08:42, Taojianchang @.***> wrote:

Hello Corina, I try to suing STRONG on my study. However, the COG database url was broken (https://strongtest.s3.climb.ac.uk/rpsblast_cog_db.tar.gz https://strongtest.s3.climb.ac.uk/rpsblast_cog_db.tar.gz). If you have download this database, would you please transfer this database to me? much thanks!

Tao Jianchang

— Reply to this email directly, view it on GitHub https://github.com/chrisquince/STRONG/issues/130#issuecomment-1420793415, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASNTQF67OHT4SW3BUPWCT6TWWJGNJANCNFSM6AAAAAAQDKGESY. You are receiving this because you authored the thread.

Taojianchang commented 1 year ago

Thank you very much for your help ! Now STRONG is running.

cbreusing commented 1 year ago

Great! :)

On 8. Feb 2023, at 01:30, Taojianchang @.***> wrote:

Thank you very much for your help ! Now STRONG is running.

— Reply to this email directly, view it on GitHub https://github.com/chrisquince/STRONG/issues/130#issuecomment-1422083589, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASNTQF57CGIGLYHM44O7VYTWWM4Q3ANCNFSM6AAAAAAQDKGESY. You are receiving this because you authored the thread.

StickHu commented 1 year ago

Hi Tao, I try to use STRONG on my simulated dataset. However, I can't run the STRONG straightly. Could you please share the code and pipeline used? Very Thanks.

StickHu