Open simleopold opened 7 months ago
Hi, would it be possible to share the histo file?
Hi, yes sure 19mer_out.histo.zip
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
Here is the cmd I used : findGSE(histo = "19mer_out.histo", sizek=19, outdir="findGSE_test")
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.
similar error:
Error in xtmp >= 1 && xtmp <= end_for_mean : 'length = 4536' in coercion to 'logical(1)'
similar error:
Error in xtmp >= 1 && xtmp <= end_for_mean : 'length = 4536' in coercion to 'logical(1)'
Can you share your histo file?
@simleopold , could you try a different version of R?
Sure, I will try
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.
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.
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?
Sure, I'll try
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
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
I got the same error back
'length = 5' in coercion to 'logical(1)'
in a polyploid withhet_peak_pos for het fitting: 33
and setexp_hom = 67
it works fine in mac with same commands
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: @.***>
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: @.***>
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.
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?
I got the same error back
'length = 5' in coercion to 'logical(1)'
in a polyploid withhet_peak_pos for het fitting: 33
and setexp_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.
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,