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.

[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.

Could you git again from the repo, re-install, and run it again?

[simleopold]

Sure, I'll try

[wozixing]

Hello,

I generated a histo file by jellyfish and when I try to use findGSE I always receive this error message :
Error in genome_size_summary != 0 && genome_size_summary2 != 0 :
'length = 5' in coercion to 'logical(1)'

Here is the cmd I used :
findGSE(histo = "kmer21.histo", sizek = 21, exp_hom = 100, outdir = "outputdir")
Kmer_21.zip

Thanks

[dozhun]

I got the same error back 'length = 5' in coercion to 'logical(1)' in a polyploid with het_peak_pos for het fitting: 33 and set exp_hom = 67

[dozhun]

I got the same error back 'length = 5' in coercion to 'logical(1)' in a polyploid with het_peak_pos for het fitting: 33 and set exp_hom = 67

it works fine in mac with same commands

[HeQSun]

Okay. I will check this tomorrow.Best,HequanOn 15. Jan 2024, at 22:44, dozhun ***@***.***> wrote: I got the same error back 'length = 5' in coercion to 'logical(1)' in a polyploid with het_peak_pos for het fitting: 33 and set exp_hom = 67 it works fine in mac with same commands —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[HeQSun]

could you pls uload the histo fike as well?Best,HequanOn 15. Jan 2024, at 23:06, dozhun ***@***.***> wrote: I got the same error back 'length = 5' in coercion to 'logical(1)' in a polyploid with het_peak_pos for het fitting: 33 and set exp_hom = 67 —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you modified the open/close state.Message ID: ***@***.***>

[dozhun]

could you pls uload the histo fike as well?Best,HequanOn 15. Jan 2024, at 23:06, dozhun @.> wrote: I got the same error back 'length = 5' in coercion to 'logical(1)' in a polyploid with het_peak_pos for het fitting: 33 and set exp_hom = 67 —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you modified the open/close state.Message ID: @.>
hifi_cell4.k35.jf.histo.txt

thanks for your help， The kmer size used is 35.

[HeQSun]

Could you git again from the repo, re-install, and run it again?

Hello,

I generated a histo file by jellyfish and when I try to use findGSE I always receive this error message : Error in genome_size_summary != 0 && genome_size_summary2 != 0 : 'length = 5' in coercion to 'logical(1)'

Here is the cmd I used : findGSE(histo = "kmer21.histo", sizek = 21, exp_hom = 100, outdir = "outputdir") Kmer_21.zip

Thanks

There was a related bug which showed up probably due to recent update of R version.

Now it should have been fixed.

Could you git findGSE again from the repo, re-install, and test the new version?

[HeQSun]

I got the same error back 'length = 5' in coercion to 'logical(1)' in a polyploid with het_peak_pos for het fitting: 33 and set exp_hom = 67

it works fine in mac with same commands

There was a bug. I think now it is fixed. Please re-try after installing the updated code.