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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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Problem with nohup snippy-core #76

Closed manuss11 closed 5 years ago

manuss11 commented 5 years ago

Hello!

I was learning about Nullarbor with that https://discourse.climb.ac.uk/t/nullarbor-tutorial-automated-bacterial-sequence-mapping-variant-calling-mlst-assignation-and-resistance-screening/32 TUTORIAL, but when I am going to run the last command to compare a group of samples that are more closely related, it doesn't run.

This is the command: nohup snippy-core --prefix shigellaflexgroup Sample1/Sample1 Sample10/Sample10 Sample11/Sample11 Sample12/Sample12 Sample2/Sample2 Sample3/Sample3 Sample4/Sample4 Sample5/Sample5 Sample6/Sample6 Sample7/Sample7 Sample8/Sample8 Sample9/Sample9 &

And the error is: nohup: ignoring input and appending output to 'nohup.out'

I really do not understand why the name of the sample appears repeated. What is the necessary input?

I would really appreciate your help

Regards

tseemann commented 5 years ago

Firstly, I did not write that tutorial, and it may be for Nullarbor 1.x and not the current series.

Secondly, nohup is not an error. That message is telling you that snippy-core is now running in the background, and its output is being put into the nohup.out file instead of printing to the screen.

The sample names are doubled because of the way Nullarbor 1.x used to work. That is no longer the case.