8000 error: "Cannot open file locus.84.sample.txt for appending." · Issue #185 · bpp/bpp · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

error: "Cannot open file locus.84.sample.txt for appending." #185

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Open
svedwards opened this issue Jun 20, 2023 · 3 comments
Open

error: "Cannot open file locus.84.sample.txt for appending." #185

svedwards opened this issue Jun 20, 2023 · 3 comments

Comments

@svedwards
Copy link
svedwards commented Jun 20, 2023 •
edited
Loading

Hello -

I've been trying to analyze a moderate data set of ~2500 loci across 5 species, just using the speciestree = 0 mode. The alignments seem to read in well but I am getting an error of "Cannot open file locus.84.sample.txt for appending...". I think this is referring to the among-locus rate variation files, but I still seem to get the error when I put locusrate=0 in the ctl file. I also am using a custom set of substitution models but when I change the ctl file to simply using HKY for everything (as below) I still get the error. I'll attach the ctl file and the substitution model and imap files but the alignments themselves are 89M - can put them on a download site if you'd like to see them. Locus 84 itself seems fine otherwise - will paste it's line below as well.

83 | HKY | 34 | 1016 | 13 | 40 | Empirical ACGT 0.32 0.19 0.24 0.26
84 | HKY | 34 | 1045 | 74 | 71 | Empirical ACGT 0.28 0.18 0.20 0.34
85 | HKY | 34 | 1003 | 3 | 38 | Empirical ACGT 0.25 0.20 0.17 0.38

....

2486 | HKY | 34 | 1001 | 6 | 29 | Empirical ACGT 0.30 0.20 0.18 0.32
2487 | HKY | 34 | 1024 | 53 | 55 | Empirical ACGT 0.27 0.25 0.26 0.23
2488 | HKY | 34 | 1008 | 12 | 50 | Empirical ACGT 0.21 0.29 0.29 0.21
2489 | HKY | 34 | 1003 | 9 | 45 | Empirical ACGT 0.30 0.22 0.19 0.29

Parsing map file... Done
Cannot open file locus.84.sample.txt for appending...
sj_2489_subst_models.csv
SJ_all_imac.txt
SJ_all_ctl.txt
@ziheng-yang
Copy link
Collaborator
ziheng-yang commented Jun 20, 2023 •
edited
Loading

Hi Scott,
i think this is an issue with the program trying to open too many files. tomas had an earlier post #181: on the number of open files.

you can also check whether supressing the locus-specific output makes any difference:
print = 1 0 0 0 *

if your species are closely related, say, within 30 myrs of divergence for birds or mammals, or if your sequences are within 10% of divergences, say, i suggest that you use JC and forget about HKY.
the substitution model is used to correct for multiple hits, and when sequences are close, the model does not matter. this should be obvious, but we also did simulations where the data were simulated under gtr+g and analyzed using jc, and the results were fine.

tauprior = invgamma 3 0.002
your tau prior has the prior mean 0.001, which means 1 difference per kb from the root of the species tree to the present time. if that is a reasonable prior, your species are very close, so there is no problem with using JC. as you know in the 1980s or 1990s, people were using the infinite-sites model for closely related species such as human chimp gorilla. the difference between JC and GTR+G is even smaller. forget about model test.
best wishes,
ziheng

@svedwards
Copy link
Author
svedwards commented Jun 20, 2023 •
edited
Loading

Hi Ziheng,

Thanks for these quick comments. From Tomas's earlier post#181 it's not clear what can be done on mac OSX. So I will just try on our cluster. I was running it on my mac just to check to see if it worked.

Good points about the substitution models. Of course, I was just trying to be fancy :). Actually, thanks to your point, I realize I have set the tau prior too small. In gene trees (different from tau of course) I typically see ~0.005- 0.01 substitutions to the root, not 0.001. So I will change the prior.

Thanks again.

Scott

@svedwards
Copy link
Author

Actually, I think changing the print line fixed the issue in my case. Thanks!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@ziheng-yang @svedwards
0