failed to converge

[PolenP]

Hi! I would like to ask how to possible trouble shoot this? I believe I have good coverage for my 2.9Gb diploid genome. The histo file are from the 150bp pe short reads. Both histo from jellyfish and meryl are giving me the same failed to converge problem.

I believe the coverage is not the problem since the first graph is showing peak at 40? Tried it as well with kmer max coverage at 10000, 1000000, and 9000000 and I keep getting the same result.

This is from jellyfish histo

and this is from meryl histo

The graphs are made from the website.
I'd appreciate your help. Thank you!

[Timothy Rhyker Ranallo-Benavidez]

Can you please attach the histogram file so I can troubleshoot. Thanks.

…

On Thu, Nov 10, 2022, 4:57 AM PolenP ***@***.***> wrote: Hi! I would like to ask how to possible trouble shoot this? I believe I have good coverage for my 2.9Gb diploid genome. The histo file are from the 150bp pe short reads. Both histo from jellyfish and meryl are giving me the same failed to converge problem. I believe the coverage is not the problem since the first graph is showing peak at 40? Tried it as well with kmer max coverage at 10000, 1000000, and 9000000 and I keep getting the same result. This is from jellyfish histo [image: 2022-11-10_19-56_sp_buf_jf] <https://user-images.githubusercontent.com/92421984/201052819-f41d334e-5061-4e5a-8bf2-561f2dd67488.png> and this is from meryl histo [image: 2022-11-10_19-56_sp_buf_meryl] <https://user-images.githubusercontent.com/92421984/201053649-cb99c4bb-6bd6-464a-bb04-1e0358d5f023.png> The graphs are made from the website. I'd appreciate your help. Thank you! — Reply to this email directly, view it on GitHub <#88>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE3K6PIDO6GOXD5SOM7GGSTWHTBI7ANCNFSM6AAAAAAR4LW2AM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[PolenP]

Thank you very much!

sp_reads_.zip

[Timothy Rhyker Ranallo-Benavidez]

Hello, we recommend using version 2 of genomescope from www.genomescope.org/genomescope2.0. I tested your data and the updated model converges correctly. I would use the meryl histogram, since the jellyfish histogram you provided truncates at 10,000. (Alternatively, you can tell jellyfish to increase the max coverage). Let me know if you have any further issues.

[PolenP]

Thank you very much! Didn't notice I am using the old version of the website. Got it resolved now.