ggplot build error

[susheelbhanu]

Hi,

I'm running a grid single command as follows and get the following error:

grid single -r . -e fastq -o grid_output -g ../B12_maxbin.001.contigs.fa-fixed.fa -n 2

Loading required package: proto
Warning message:
no DISPLAY variable so Tk is not available
Warning: Ignoring unknown aesthetics: outfit
Error in if (zero_range(as.numeric(limits))) { :
  missing value where TRUE/FALSE needed
Calls: ggplot_build ... <Anonymous> -> f -> <Anonymous> -> f -> <Anonymous> -> f
Execution halted

Any thoughts on why this is occuring?

Thank you!

[aemiol]

Hi, It seems the genome coverage in that sample is zero or too low.

Cheers, Tunde

[susheelbhanu]

Hi Tunde,

How is the genome coverage calculated? Because I used a different coverage estimation method, and according to it, the same is 12X.

Could you please clarify?

Thanks!

[aemiol]

Could you confirm that majority of your contigs have coverage > 0?

[susheelbhanu]

Hi,

Please see attached the contigs coverage file.

Thank you! B12_maxbin.001.contigs.fa.txt

[aemiol]

Hi,

Please see attached the contigs coverage file.

Thank you! B12_maxbin.001.contigs.fa.txt

Hi, it is not clear what the columns are in the attached file. What are they? I assume the 2nd column is contig length. Right?

[susheelbhanu]

yeah sorry.. the 2nd is length and the 3rd the coverage per contig

[aemiol]

Is there a way you can send across the fastq file and in question and also the genome?

[susheelbhanu]

Thanks.. i'm on a train at the moment, so will send them to you Wednesday, if that's ok?! thanks again for the help!

[aemiol]

Thanks.. i'm on a train at the moment, so will send them to you Wednesday, if that's ok?! thanks again for the help!

Sure. Send it whenever you are ready