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Admixtools 2
#16
(04-04-2024, 07:00 PM)TanTin Wrote:
(04-04-2024, 01:21 PM)Арсен Wrote:
(03-27-2024, 09:52 PM)TanTin Wrote: I guess this is a bug in Admixtools2.  Doesn't matter what dataset we use. We should get the same or near the same results if we specify the same criteria. 
But as we see: running the same script - same options - the results are disaster.
This is only for groups statistics.
When I run F4 on individuals I get perfect and stable results.
The bug is definately in Admixtools.
Thanks for confirming that you already have seen that.

dude, teach me how to use this program, question, do I have to download heavy bam ENA files from data library sites for this? and do you need a serious, powerful processor to calculate mixtures?


There is already such topic in Eupedia. Start from there.

https://www.eupedia.com/forum/threads/ad...ows.42684/

Regarding converting converting  bam to plink format - this is another topic. It is a different process. For now try to make your software working with the already available data. (in plink bed,bim fam  format).

Thank you very much for your answer, I think I’ll figure it out in the future
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#17
(04-04-2024, 01:21 PM)Арсен Wrote: do I have to download heavy bam ENA files from data library sites for this? and do you need a serious, powerful processor to calculate mixtures?

No and no. My computer is 19 years old.
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#18
For the Admixtools2 bug again. Here is another example. Several runs for the same data, same test.


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#19
What version of AT2 are you using? Platform?, though it shouldn't matter.

sessionInfo()

[1] admixtools_2.0.0
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#20
(04-09-2024, 04:47 PM)AimSmall Wrote: What version of AT2 are you using?  Platform?, though it shouldn't matter.

sessionInfo()

[1] admixtools_2.0.0

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252 LC_NUMERIC=C                    LC_TIME=English_Canada.1252   
system code page: 65001

attached base packages:
[1] stats    graphics  grDevices utils    datasets  methods  base   

other attached packages:
[1] Hmisc_5.1-0      forcats_0.5.1    stringr_1.4.0    dplyr_1.0.7      purrr_0.3.4      readr_2.1.1      tidyr_1.1.4      tibble_3.1.6    ggplot2_3.3.5    tidyverse_1.3.1  admixtools_2.0.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.8        lubridate_1.8.0  digest_0.6.29    assertthat_0.2.1  foreach_1.5.1    utf8_1.2.2        R6_2.5.1          cellranger_1.1.0  backports_1.4.1  reprex_2.0.1      evaluate_0.14   
[12] httr_1.4.2        pillar_1.6.5      rlang_1.0.0      readxl_1.3.1      data.table_1.14.2 rstudioapi_0.13  rpart_4.1-15      checkmate_2.1.0  rmarkdown_2.11    foreign_0.8-81    htmlwidgets_1.5.4
[23] igraph_1.2.11    munsell_0.5.0    broom_0.7.11      xfun_0.29        compiler_4.1.2    modelr_0.1.8      pkgconfig_2.0.3  base64enc_0.1-3  htmltools_0.5.2  nnet_7.3-16      tidyselect_1.1.1
[34] gridExtra_2.3    htmlTable_2.4.1  codetools_0.2-18  fansi_1.0.2      crayon_1.4.2      tzdb_0.2.0        dbplyr_2.1.1      withr_2.4.3      grid_4.1.2        jsonlite_1.7.3    gtable_0.3.0   
[45] lifecycle_1.0.1  DBI_1.1.2        magrittr_2.0.2    scales_1.1.1      cli_3.1.1        stringi_1.7.6    fs_1.5.2          xml2_1.3.3        ellipsis_0.3.2    generics_0.1.1    vctrs_0.3.8     
[56] Formula_1.2-5    iterators_1.0.13  tools_4.1.2      glue_1.6.1        hms_1.1.1        fastmap_1.1.0    abind_1.4-5      colorspace_2.0-2  cluster_2.1.2    rvest_1.0.2      knitr_1.37     
[67] haven_2.4.3
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#21
So, apparently version 2.01 was released on March 3rd, 2024.

https://github.com/uqrmaie1/admixtools/r...tag/v2.0.1

You can install the packages normally, or you might consider compiling from source.

Running devtools::install_github("uqrmaie1/admixtools") will compile C++ from source code (this isn’t necessary when installing packages from CRAN with install.packages()).

https://github.com/uqrmaie1/admixtools/

Not sure if your bug is corrected here, you might be able to check the changelog.
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#22
(04-09-2024, 05:13 PM)AimSmall Wrote: So, apparently version 2.01 was released on March 3rd, 2024.

https://github.com/uqrmaie1/admixtools/r...tag/v2.0.1

You can install the packages normally, or you might consider compiling from source.

Running devtools::install_github("uqrmaie1/admixtools") will compile C++ from source code (this isn’t necessary when installing packages from CRAN with install.packages()).

https://github.com/uqrmaie1/admixtools/

Not sure if your bug is corrected here, you might be able to check the changelog.
Thanks for the help !

Except these bugs that I see at random  my Admixtools is running pretty good. I have it also installed on the second computer, so I may do another test there. And I can try to run another version in VM under Linux.
For the moment I don't want to uninstall /reinstall it here, because in general it is running fine.  Will see if the same error will reproduce under different installation.
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#23
I was able to find what is causing the bug...

As you know, Admixtools2 may work by using both plink and geno file format as  source data...
So I was running my Admixtools with plink format files (.bed .bim .fam files.)
And it seems this is what's  causing such bug.  When I did the rerun on the second computer I used other file format (.geno, .ind, .snp files)  The results are stable ,  same results on each rerun.

As soon as I changed the prefix to use  plink(.bed .bim .fam files.)  I got the same bug on the second computer as well.

Here are the final results for my last F4 tests (stable).

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#24
That's interesting....
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#25
Here are the same results, visualizing Z.


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