search

isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
268 stars 48 forks source link

minimal reporting through stderr #102

Closed leleory closed 5 years ago

leleory commented 5 years ago

Hello there, When I run racon in a cluster environment (SGE) I store the STDERR in the log file to see if the run went OK. This is very useful to identify failed runs. Nevertheless due to the way racon reports it's progress the logfile (especially on bigger datasets) reaches sever GB. This is not just a storage issue, but also takes a long time to skim through the report. Can the code be enhanced, so that detailed progress is not reported, but errors would still come through? If there would be a parameter to specify minimal reporting that would be really useful. Thank you, Lel

rvaser commented 5 years ago

Hi Lel, I already have this problem reported before but did not have the time yet to update. Will do it in next couple of days.

Best regards, Robert

leleory commented 5 years ago

That is great, thanks Robert. Looking forward to it.

Lel

On 31/01/2019 09:48, Robert Vaser wrote:

Hi Lel, I already have this problem reported before but did not have the time yet to update. Will do it in next couple of days.

Best regards, Robert

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/102#issuecomment-459282177, or mute the thread https://github.com/notifications/unsubscribe-auth/AGRaQ860zCdMma89hZaMthYcNQrYgBE1ks5vIrv9gaJpZM4ab2hF.

rvaser commented 5 years ago

Implemented in latest commit (v1.3.3).

leleory commented 5 years ago

Hi Robert, It works great, thanks very much for the improvement! Lel