Error type : "Error in xtmp >= 1 && xtmp <= end_for_mean : 'length = 61065' in coercion to 'logical(1)'"

[simleopold]

Hi,

I generated a histo file (7347 obs) and when I try to use findGSE I always receive this error message :
Error in xtmp >= 1 && xtmp <= end_for_mean :
'length = 61065' in coercion to 'logical(1)'

I don't understand where it comes from.

Thanks,

[HeQSun]

Hi, would it be possible to share the histo file?

[simleopold]

Hi, yes sure
19mer_out.histo.zip

[HeQSun]

Hi, yes sure 19mer_out.histo.zip

There was no issue with the histo file. Can you show me the cmd that you used?

I assumed the data is from a heterozygous diploid genome, and you sequenced the genome with 12x per haplotype genome.
19mer_out_user_data.pdf

[simleopold]

Here is the cmd I used :
findGSE(histo = "19mer_out.histo", sizek=19, outdir="findGSE_test")

[HeQSun]

Here is the cmd I used : findGSE(histo = "19mer_out.histo", sizek=19, outdir="findGSE_test")

the species of interest looks like heterozygous diploid. So you should set up exp_hom=30.

[fuckCZJ]

similar error:

Error in xtmp >= 1 && xtmp <= end_for_mean :
'length = 4536' in coercion to 'logical(1)'

[HeQSun]

similar error:

Error in xtmp >= 1 && xtmp <= end_for_mean : 'length = 4536' in coercion to 'logical(1)'

Can you share your histo file?

[fuckCZJ]

kmer21.zip

[HeQSun]

kmer21.zip

Similarly, you should set up exp_hom=100.

kmer21_usr2.pdf

[HeQSun]

@simleopold , could you try a different version of R?

[simleopold]

Sure, I will try

[simleopold]

I still have the problem, I wanted to know the runtime for my histo file. Do you know it ?

By the way I wanted to thank you for the pdf.

[HeQSun]

I still have the problem, I wanted to know the runtime for my histo file. Do you know it ?

By the way I wanted to thank you for the pdf.

Should be around 1-2 mins.