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related package R session crash #1

Open Sophie-DR opened 5 years ago

Sophie-DR commented 5 years ago

SNP.bi.mis.dp4.ratio.maf5perc.g9_noAqua_noRepl_geoOrd_PopYear_scaff_noHWE_LD_Hobs2_related_EC_NS_3gps.txt Dear Tim,

I am trying to run the related package and my R session keeps on crashing when I use the familysim or the compareestimators functions. I am using R 3.5.1 and RStudio v1.1.414. I updated RTools before installation. I am running on a Windows 10 PC. All relatedness estimators run fine on my data. I am attaching my input file.

Any help would be very welcome.

Sophie

timothyfrasier commented 5 years ago

Hi Sophie:

I’m sorry that you are having this problem. It is a well-known issue that arises when someone has “a lot” of loci (i.e., >100) and tries to use the familysim function (which is also called in the compareestimators function). Is that correct for your data set?

Unfortunately, fixing it would require a complete re-write of package, and I won’t have time to do that in the near future.

The only “fix” that I can give you is that there is a new R package that has much of the same functionality that may work better. It is called Demerelate and can be found here https://www.ncbi.nlm.nih.gov/pubmed/28281323.

Sincerely, Tim Frasier

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.ca http://frasierlab.ca/

On Oct 8, 2018, at 5:21 PM, Sophie-DR notifications@github.com wrote:

Dear Tim,

I am trying to run the related package and my R session keeps on crashing when I use the familysim or the compareestimators functions. I am using R 3.5.1 and RStudio v1.1.414. I updated RTools before installation. I am running on a Windows 10 PC. All relatedness estimators run fine on my data.

Any help would be very welcome.

Sophie

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Sophie-DR commented 5 years ago

Hi Timothy,

Thank you for your honest answer. Yes I have more than a thousand snps. Your solution seems like a solution. I'll try that demerelate.

I work on a flatfish and I found some relatedness values above 0.9 and some between 0.1 and 0.3. Can I deduce from that the relationship of my individuals (0.9 are somewhat clones??) without simulations? Or are there no standard expected values?

Do you see a way to account for the fact that the individuals sampled together will have a higher likelihood to be more related to each other than the rest of the individuals (in demerelate)?

Thanks for your feedback,

Sophie

On Tue, 9 Oct 2018, 19:41 timothyfrasier, notifications@github.com wrote:

Hi Sophie:

I’m sorry that you are having this problem. It is a well-known issue that arises when someone has “a lot” of loci (i.e., >100) and tries to use the familysim function (which is also called in the compareestimators function). Is that correct for your data set?

Unfortunately, fixing it would require a complete re-write of package, and I won’t have time to do that in the near future.

The only “fix” that I can give you is that there is a new R package that has much of the same functionality that may work better. It is called Demerelate and can be found here < https://www.ncbi.nlm.nih.gov/pubmed/28281323>.

Sincerely, Tim Frasier

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.ca http://frasierlab.ca/

On Oct 8, 2018, at 5:21 PM, Sophie-DR notifications@github.com wrote:

Dear Tim,

I am trying to run the related package and my R session keeps on crashing when I use the familysim or the compareestimators functions. I am using R 3.5.1 and RStudio v1.1.414. I updated RTools before installation. I am running on a Windows 10 PC. All relatedness estimators run fine on my data.

Any help would be very welcome.

Sophie

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timothyfrasier commented 5 years ago

Hi Sophie:

Good, I hope that Demerelate will work for you. I have not used it before (I just know about it), so I’m afraid that I can’t give you any advice about that.

In terms of relatedness values, you can expect high relatedness values (e.g., 0.9) from individuals who are only somewhat related, just given the variation in potential values from a particular relationships (fill sibs can actually range from 0 to 1, it is just the average expected value that is 0.5). So, I wouldn’t take any particular relatedness value at face value with respect to indicating a specific degree of relatedness.

-Tim

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.ca http://frasierlab.ca/

On Oct 9, 2018, at 4:27 PM, Sophie-DR notifications@github.com wrote:

Hi Timothy,

Thank you for your honest answer. Yes I have more than a thousand snps. Your solution seems like a solution. I'll try that demerelate.

I work on a flatfish and I found some relatedness values above 0.9 and some between 0.1 and 0.3. Can I deduce from that the relationship of my individuals (0.9 are somewhat clones??) without simulations? Or are there no standard expected values?

Do you see a way to account for the fact that the individuals sampled together will have a higher likelihood to be more related to each other than the rest of the individuals (in demerelate)?

Thanks for your feedback,

Sophie

On Tue, 9 Oct 2018, 19:41 timothyfrasier, notifications@github.com wrote:

Hi Sophie:

I’m sorry that you are having this problem. It is a well-known issue that arises when someone has “a lot” of loci (i.e., >100) and tries to use the familysim function (which is also called in the compareestimators function). Is that correct for your data set?

Unfortunately, fixing it would require a complete re-write of package, and I won’t have time to do that in the near future.

The only “fix” that I can give you is that there is a new R package that has much of the same functionality that may work better. It is called Demerelate and can be found here < https://www.ncbi.nlm.nih.gov/pubmed/28281323>.

Sincerely, Tim Frasier

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.ca http://frasierlab.ca/

On Oct 8, 2018, at 5:21 PM, Sophie-DR notifications@github.com wrote:

Dear Tim,

I am trying to run the related package and my R session keeps on crashing when I use the familysim or the compareestimators functions. I am using R 3.5.1 and RStudio v1.1.414. I updated RTools before installation. I am running on a Windows 10 PC. All relatedness estimators run fine on my data.

Any help would be very welcome.

Sophie

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nlv209 commented 4 years ago

Hi Timothy, I am not sure this is the same issue that Sophie was having with familysim since my dataset is 130 individuals genotyped at 19 microsatellite loci (so certainly not 100's of loci).
But when I try to run familysim I get the error pasted below, any idea what is happening here? (am using R 3.6.1 on a Macbook Pro). Any help is much appreciated!! Nikki

caught segfault address 0x18, cause 'memory not mapped' Traceback:

  1. familysim(input$freqs, 100)

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace

timothyfrasier commented 4 years ago

Hi Nikki:

That sounds strange. Could you send me your file(s) and exact commands, and I can see if I can figure out what the issue is.

-Tim

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.camailto:timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.cahttp://frasierlab.ca

On Oct 3, 2019, at 4:25 PM, nlv209 notifications@github.com<mailto:notifications@github.com> wrote:

Hi Timothy, I am not sure this is the same issue that Sophie was having with familysim since my dataset is 130 individuals genotyped at 19 microsatellite loci (so certainly not 100's of loci). But when I try to run familysim I get the error pasted below, any idea what is happening here? (am using R 3.6.1 on a Macbook Pro). Any help is much appreciated!! Nikki

caught segfault address 0x18, cause 'memory not mapped' Traceback:

  1. familysim(input$freqs, 100)

Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace

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nlv209 commented 4 years ago

Thanks Tim, Attached is my input file. Also FYI, running the coancestry command works fine. Red.txt

Nikki

timothyfrasier commented 4 years ago

Hi Nikki:

Very interesting. It runs fine on my computer (a “Late 2013” Macbook Pro running R v3.5.0), and your data set is smaller than the example file that comes with related.

My guess (hope) is that there is just something weird with your commands. A wayward space or other character can cause huge problems. I’ve attached the exact code that worked on my compute. Can you try copying and pasting that (once in the correct working directory) and see if that works?

-Tim

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.camailto:timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.cahttp://frasierlab.ca

On Oct 6, 2019, at 3:13 PM, nlv209 notifications@github.com<mailto:notifications@github.com> wrote:

Thanks Tim, Attached is my input file. Also FYI, running the coancestry command works fine. Red.txthttps://github.com/timothyfrasier/related/files/3694708/Red.txt

Nikki

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genotypes = readgenotypedata("Red.txt") relatedness = coancestry(genotypes$gdata, wang = 1) sim = familysim(genotypes$freqs, 100)

nlv209 commented 4 years ago

Hi Tim, I tried cutting and pasting what you sent and still got the same error. So the coancestry command works, but not the familysim. I tried re-installing R (v 3.6.1), the diylib files, and even RStudio(1.2.5001) to no avail. The good news is that I have it working on a PC now, so I can move forward on that. Also, just FYI, on either a PC (following Windows Instructions) or on a Mac (following Mac instructions) I could never get related to install through RStudio. But on both platforms I could get it to work using R directly (no problems on PC, but Mac has issue described previously with familysim). I am happy to provide more details on the RStudio errors I got with each if you are interested. Nikki

timothyfrasier commented 4 years ago

Hi Nikki:

I’m sorry about all this. I think as R, RStudio, and the MAC OS change, related is getting more and more out of synch, and I have not had time to update it. I’m glad you are getting it to work on a Windows machine. I will likely spend some time updating related in the new year.

-Tim

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.camailto:timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.cahttp://frasierlab.ca

On Oct 7, 2019, at 8:30 PM, nlv209 notifications@github.com<mailto:notifications@github.com> wrote:

Hi Tim, I tried cutting and pasting what you sent and still got the same error. So the coancestry command works, but not the familysim. I tried re-installing R (v 3.6.1), the diylib files, and even RStudio(1.2.5001) to no avail. The good news is that I have it working on a PC now, so I can move forward on that. Also, just FYI, on either a PC (following Windows Instructions) or on a Mac (following Mac instructions) I could never get related to install through RStudio. But on both platforms I could get it to work using R directly (no problems on PC, but Mac has issue described previously with familysim). I am happy to provide more details on the RStudio errors I got with each if you are interested. Nikki

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ejames26 commented 4 years ago

Hey Tim,

I am having the same problem. I am trying to analyse a set of data for a project to determine the relatedness thresholds (full-sib, half-sib and unrelated). The entire Rstudio crashes as soon as I try the command input <- readgenotypedata("gtd2.txt") sim <- familysim(input$freqs, 100)

Any suggestions would be great as I cannot move forward until I sort this. I have attached the data to the post to look at. I assume it crashes because I have so many loci? gtd2.txt

timothyfrasier commented 4 years ago

Hi:

Yes, this is due to the number of loci that you have. I’m afraid that I wrote related, and the familysim function in particular, quite a while ago, and was thinking about microsatellite loci rather than large SNP panels. This is a known issue, and I hope to deal with it in the future. However, I don’t know when that will be.

In the meantime, there is another R package that has much the same functionality. It is called Demerelate, and the paper describing it can be found herehttps://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12666 I hope that it can do what you need.

Sincerely, Tim Frasier

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.camailto:timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.cahttp://frasierlab.ca

On Dec 29, 2019, at 10:16 PM, ejames26 notifications@github.com<mailto:notifications@github.com> wrote:

Hey Tim,

I am having the same problem. I am trying to analyse a set of data for a project to determine the relatedness thresholds (full-sib, half-sib and unrelated). The entire Rstudio crashes as soon as I try the command input <- readgenotypedata("gtd2.txt") sim <- familysim(input$freqs, 100)

Any suggestions would be great as I cannot move forward until I sort this. I have attached the data to the post to look at. I assume it crashes because I have so many loci? gtd2.txthttps://github.com/timothyfrasier/related/files/4008823/gtd2.txt

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cansuplati commented 4 years ago

Hi Tim,

I was wondering if it is possible to run the code of family-sim outside of R. For example, does your family-sim software do this simulation? Is there a manual file somewhere for it?

I also have more than 1000 SNPs and was trying your package for simulations. My aim is to compare dyadml and trioml specifically (since there is a high probability of selfing in our populations).

Thank you very much, Best, Cansu

timothyfrasier commented 4 years ago

Hi Cansu:

Yes, my Family-Sim program (written in C) conducts the same simulations. I’m surprised you could find it! The manual is attached. Note that I wrote both the program and the manual a loooong time ago, so some aspects of both are quite embarrassing.

There is also another R package that does much of the same things as related, but handles large data files better. It is called Demerelate and can be found herehttps://www.ncbi.nlm.nih.gov/pubmed/28281323.

I hope this helps!

-Tim

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.camailto:timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.cahttp://frasierlab.ca

On Apr 11, 2020, at 2:00 PM, cansuplati notifications@github.com<mailto:notifications@github.com> wrote:

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Hi Tim,

I was wondering if it is possible to run the code of family-sim outside of R. For example, does your family-sim software do this simulation? Is there a manual file somewhere for it?

I also have more than 1000 SNPs and was trying your package for simulations. My aim is to compare dyadml and trioml specifically (since there is a high probability of selfing in our populations).

Thank you very much, Best, Cansu Cetin

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timothyfrasier commented 4 years ago

Hi Again:

I checked, and I had attached it; but it is possible that communicating via Github doesn’t allow for attachments. Can you send me a regular email (my address is in the signature below) and I can reply to that with the attachment?

-Tim

Timothy R. Frasier Coordinator - Forensic Sciences Program Associate Professor - Department of Biology Saint Mary's University 923 Robie Street Halifax, NS B3H 3C3, Canada Email: timothy.frasier@smu.ca Tel: (902) 491-6382 www.frasierlab.ca http://frasierlab.ca/

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Hi Tim,

Thanks a lot for your answer!

I was checking citations to your package which used SNP data and saw your Family-sim software cited in one of them. I don't know much about programming or C myself. By the way, can you send the manual once more? I think it is not attached.

Thanks for the suggestion! I think Demerelate don't calculate dyadML and trioML but maybe if I could simulate the data there then I can compare/analyze them in related..

Best, Cansu

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kyraenglish commented 1 year ago

Hi Tim,

First of all, thank you so much for this useful package! I am having the same issue with not being able to run the familysim or compareestimators functions, probably because I have a large SNP dataset. I also tried Demerelate but it is no longer available because a dependency, fts, was removed from the CRAN repository (I have tried everything to install it still with no luck).

Do you happen to know of any other similar package or workaround at this time?

Thank you, Kyra

timothyfrasier commented 1 year ago

Hi Kyra:

No, I'm afraid that I don't. That doesn't mean that one doesn't exist...just that I don't know of any.

-Tim

Timothy R. Frasier Coordinator: Forensic Sciences Program Professor: Biology Saint Mary's University 923 Robie Street Halifax, Nova Scotia B3H 3C3 Canada Tel: (902) 491-6382 E-mail: @.*** frasierlab.ca

From: kyraenglish @.> Sent: Tuesday, November 22, 2022 4:32 PM To: timothyfrasier/related @.> Cc: Timothy Frasier @.>; Comment @.> Subject: Re: [timothyfrasier/related] related package R session crash (#1)

Hi Tim,

First of all, thank you so much for this useful package! I am having the same issue with not being able to run the familysim or compareestimators functions, probably because I have a large SNP dataset. I also tried Demerelate but it is no longer available because a dependency, fts, was removed from the CRAN repository (I have tried everything to install it still with no luck).

Do you happen to know of any other similar package or workaround at this time?

Thank you, Kyra

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cansuplati commented 1 year ago

Hi Kyra,

For a smaller dataset (around 2000 SNPs), I could use coancestry software to generate simulated relatives (similar to familysim). I either used allele frequencies generated using "related" software or directly genotype data.

Best, Cansu