Test simulation attempted run without progress

[heather340]

Hi! I'm running SNP data and am having problems getting it to run. I left it running for ~5 hrs yesterday and no progress was made in the run log so I stopped it. Now I keep getting an error once I restarted the GUI but the error is not defined within the run log so I'm not sure where the issue lies. Would it be possible to send my data and a model to someone to see if another set of eyes can determine where I'm making a mistake?

I used the vcf to DIYABC script to convert my file over, and made sure I had spaces instead of tabs within my SNP data file.

Data file info Sex ratio: NM=0.5NF Minimum allele frequency criterion: MAF=hudson Additional information: DIYABC_SNP_800_75 header: 'IND SEX POP A A A A A A A A A A A A A A A A A ...' Sample: 63 individuals from 5 populations Total number of loci = 1065 Available loci: 893 (note: 172 loci are filtered out based on MAF criterion)

Sample historical model:

N1 N2 N3 N4 N5 N1 N1 N1 N1 0 sample 1 0 sample 2 0 sample 3 0 sample 4 0 sample 5 t1 merge 3 5 t2 merge 2 4 t3 merge 2 3 t4 merge 2 1

Priors and conditions: Keep as Uniform N1 -> N5: min: 1000 max: 1000000

(min-max) t1 100-100000 t2 1000-1000000 t3 10000-1000000 t4 10000-1000000

Condition setting: t1<t2 t2<t3 t1<t3

Hi Heather,

Part of your issue may be that t1>t2. See the manual part 2.5.

[heather340]

Thanks @jbucholz! I fixed this but am still getting an error.

t1>t2 t2>t3 t1>t3

[jbucholz]

I would try removing your ghost populations and see if it runs. I was having issues with those as well. It doesn't look like they are getting sampled.

[gdurif]

Hi, I am currently working on the next release, that should be available in the next few days.

I did a lot of internal modifications, hopefully it will solve your problem. I'll keep you updated.

[heather340]

@gdurif Oh great! I'll look forward to the release. Thanks for keeping the program up to date.

@jbucholz A ghost population! Which population is that?

[jbucholz]

@heather340 I guess it's not a true "ghost" population bc it exists in your file, but the extra N1s in the first line of your model might be throwing things off? just a thought. Thanks @gdurif for all your hard work on this!

[gdurif]

Thanks, and sorry I am kind of two or three weeks late on my schedule for this release but it should be worth it.

[heather340]

@jbucholz Good thought, but doesn't seem like it worked. Perhaps with the update then it can be more easily sorted out... I'll hold off until then and post if needed. @gdurif You mean that things don't always work the first time as planned? 😝 Good luck with the rolling out of the release!

[gdurif]

Hi, I am really sorry, the next release was delayed to the end of June. I hope this will be ok. All apologies for the trouble.

[heather340]

Hi @gdurif - that's fine! However, I'm finishing my dissertation this summer and this analysis is the very last thing that I'm waiting to add to it. Would you have any time to take a look at my prior issue in light of the current version? I was hoping to have at least a first run completed by the end of the month!

[gdurif]

@heather340 I will be away from office for a week but I will try to look into it when I get back.

[heather340]

Perfect! Next week works better for me as well. Thank you!!

On Jun 14, 2021, at 11:35 AM, gdurif @.***> wrote:

@heather340 https://github.com/heather340 I will be away from office for a week but I will try to look into it when I get back.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/diyabc/diyabcGUI/issues/103#issuecomment-860782740, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKKYHXEQOGECUG7J3T3TA6DTSYOVDANCNFSM46A5DSFQ.

[Belenarias]

Hi all, Is there any update about this issue?

My dataset is SNPs, 6 populations and 1907 snps. I have a similar problem, in my case after a minute since start the run, came up with "issues in run" (GUI platform). In R came up this error: [1] "diyabc run" Running \ /Library/Frameworks/R.framework/Versions/3.6/Resources/library/diyabcGUI/bin/diyabc-RF-macos-v1.1.24 \ -p /var/folders/c4/s8btkkx97l3_vn1nyqmzfn_40000gn/T//RtmpyoW2ZO/diyabc_rf27b046d5441f/ -R -m -g 50 \ -r 1000 -t 8 [1] "diyabc run process" PROCESS 'diyabc-RF-macos-v1.1.24', running, pid 12841. [1] "diyabc simu run exit status: -11"

I'm new in DIYABC but after different attempts (reduce my datasets, different scenarios) using the GUI platform, the error came up. I'm not sure if is something with my computer (macOS Big Sur version 11.4) or something with my input file (I used the vcf2diyabc.py script to convert my vcf).

Looking forward any suggestion/update

[heather340]

Hi @Belenarias - I was just going to check in today so you beat me to it. No, no progress so far. It looks like the new version is not quite out yet, but I really hope that it will solve both of our issues!

[Belenarias]

Hi @heather340, I gave a new try this morning using different MAF values and the problem continue, no simulations. I'll appreciate any update with this issue, I do need to do this analysis!

[gdurif]

Hi @Belenarias @heather340 I am still working on this and it got delayed again, I am really sorry. But hopefully the new release should be ready soon (a matter of days, I will keep you updated. Best

[jbucholz]

Hi @Belenarias I struggled with this at first but I was able to get DIYABC up and running for all my analyses. I will say if your populations are not in order in your VCF that you want for your scenarios, your scenarios will fail (for example I had 3 sampling locations in my file that were organized by site, but those sites were in alphabetical order in my VCF, not all lumped together). Once I realized this, and practiced with the toy data for setting conditions, I was able to run all my models pretty seamlessly.

[heather340]

Thanks @jbucholz for the tip! I do feel like this may have been part of the issue and fixed this. However, I still haven't been able to get it going, but it does run for a few more seconds. I'm open to more suggestions if you see anything that sticks out to you in the below info:

R console: [1] "diyabc simu run exit status: 1"

End of the log:

...
locus=891   OK=2
locus=892   OK=2
scenario 1   (1)
    nevent=9   nne0=9
    nsamp =5   npop=9   popmax=9
    nparam=9    nparamvar=9
    samp/refsamp 1    time_sample = 0
    samp/refsamp 2    time_sample = 0
    samp/refsamp 3    time_sample = 0
    samp/refsamp 4    time_sample = 0
    samp/refsamp 5    time_sample = 0
    events:
    0   samp   pop=1
    0   samp   pop=2
    0   samp   pop=3
    0   samp   pop=4
    0   samp   pop=5
    19942   merge  pop=2   pop1=1
    46609   merge  pop=2   pop1=3
    56540   merge  pop=2   pop1=4
    94607   merge  pop=3   pop1=5
    histparam:
    name=N1   val=425563   category=0
    name=N2   val=168825   category=0
    name=N3   val=117224   category=0
    name=N4   val=978111   category=0
    name=N5   val=71317   category=0
    name=t1   val=94607   category=1
    name=t2   val=56540   category=1
    name=t3   val=46609   category=1
    name=t4   val=19942   category=1
    nparamvar = 9
 paramvar : 425563   168825   117224   978111   71317   94607   56540   46609   19942   
   nconditions=3
t1  >  t2
t2  >  t3
t1  >  t3

sOK[ipart] = 1654
Total number of simulated loci : 44650

fermeture du fichier /var/folders/zk/npmr9sn5449_3cd0mccfq45m0000gn/T//RtmpLgY1Bq/diyabc_rfaefa59585447/reftableRF.bin taille=20

[heather340]

@jbucholz @Belenarias @gdurif I think we are making progress! After reorganizing my file and removing my population 5, I was able to get one of my scenarios successfully simulated. However, I'm still having issues with the other scenarios and keep getting error messages.

This one worked: N1 N2 N3 N4 N1 N1 N1 0 sample 1 0 sample 2 0 sample 3 0 sample 4 t1 merge 2 3 t2 merge 4 1 t3 merge 4 2

and these two did not work: **Scenario 2 [BAD] N1 N2 N3 N4 N1 N1 N1 0 sample 1 0 sample 2 0 sample 3 0 sample 4 t1 merge 2 3 t2 merge 2 4 t3 merge 1 2

**Scenario 3 [BAD] N1 N2 N3 N4 N1 N1 N1 0 sample 1 0 sample 2 0 sample 3 0 sample 4 t1 merge 3 2 t2 split 4 3 1 r1 t3 merge 3 1

verification de l'integrite de la table de reference fichier/var/folders/zk/npmr9sn5449_3cd0mccfq45m0000gn/T//RtmpvJBjuq/diyabc_rf1233d2b997712/reftableRF.bin nrec = 100 nrecscen[0] = 100 nparam[0] = 7 nstat = 130 1 scenario(s) 50 100 fichier reftable OK

dans rt.readheader this->filerefscen = /var/folders/zk/npmr9sn5449_3cd0mccfq45m0000gn/T//RtmpvJBjuq/diyabc_rf1233d2b997712/reftabscen.txt nparam[0] = 7 debut de sethistparamname nparamut=0 nscenarios=2 avant la boucle des scenarios nscenarios =2 scenario 0 scenario[i].nparam=7 nparamvar=7 scenario 1 scenario[i].nparam=7 nparamvar=7 PROBLEME scenario 1 nparam=-805306368 nparamvar=7 nmutparam=0

Do you have any ideas on why they might not work? Does it matter in which order I put the merges and splits?

[heather340]

@jbucholz @Belenarias @gdurif I think we are making progress! After reorganizing my file and removing my population 5, I was able to get one of my scenarios successfully simulated. However, I'm still having issues with the other scenarios and keep getting error messages. ....

Do you have any ideas on why they might not work? Does it matter in which order I put the merges and splits?

Or perhaps I am doing something else incorrectly: Adding more than one scenario resulted in errors, but simulating each scenario independently worked fine. Maybe the new version will correct this issue ;)

[Belenarias]

Hi all! sorry for my late reply. @jbucholz many thanks for your tip..it helped me a lot! @heather340 thanks for your updates, you give me hope to keep trying with the program. My update, I'm still stuck in the simulation runs, but I think I found the potential issue. My snps vcf file was converted with the python script, using MAF=Hudson (also try with 0.05 and 0.01, remaining the problem)once I tried to run the simulation the "debut" come up with an unusual results: from 1179 loci, 728 from them were monomorphic loci and in somehow the program needs to rewrite the binary file (details below):

purge of 728 monomorphic loci Observed PPL = 61.8249% end of purge of monomorphs sexratio = 0.5 after the 'processing' of the snps rewrite to binary file /var/folders/c4/s8btkkx97l3_vn1nyqmzfn_40000gn/T//RtmpMG6ZWx/diyabc_rf376c411e8c65/snps_med_poporder_renam_5ind.snp.bin ecribin this-> ssize [0] [0] = 10 ecribin this-> ssize [0] [1] = 10 ecribin this-> ssize [0] [2] = 10 ecribin this-> ssize [0] [3] = 10 ecribin this-> ssize [0] [4] = 10 ecribin this-> ssize [0] [5] = 10 end of ecribin open file /var/folders/c4/s8btkkx97l3_vn1nyqmzfn_40000gn/T//RtmpMG6ZWx/diyabc_rf376c411e8c65/snps_med_poporder_renam_5ind.snpbin.txt OK after maf nloc = 1179 after the second line binary file replay smaf = hudson's algorithm THIS-> MAF = 0 sexratio = 0.5 nloc = 1179 nsample = 6 type 0 catexist = 1 type 1 catexist = 0 type 2 catexist = 0 type 3 catexist = 0 type 4 catexist = 0 type 0 10 10 10 10 10 10 this-> maf = 0 in libin this-> locus [0] .haplosnp [0] [0] = 1 end of binary file reading

@heather340 @jbucholz @gdurif have you got these monomorphic loci in your simulation runs? Do you think it might be the issue in my simulations? I'm confusing about this point, all my data is autosome (A) and it seems the converted script reject polymorphism when is not biallelic (some of my loci are 0/0 but I found many others 0/1. Is there any other way to convert vcf to diyabc? (script used is here: https://github.com/loire/vcf2DIYABC.py)

Just in case, I selected a subset from my snps (20 loci) using MAF=Hudson and again some of them came up us monomorphic (8) but at least I was able to run 600 simulation with one scenario (1000 simulations were set initially). No idea what is going on with my input file so any help/template/example will be very useful!

[gdurif]

Hi @Belenarias @heather340,

Could you paste here the content of the file header.txt (or headerRF.txt) that is created by the GUI before calling the diyabc software (i.e. when you click on Validate before clicking on Simulate). It should be available either by saving your project (Save button at the botom of the page), or in the project temp dir that is printed in the R console (if you are using the GUI within R directly).

Regarding the conversion from VCF to DIYABC format, I do not know, I will try to get some information and get back to you.

[heather340]

@Belenarias you are also motivating me! Sorry you're having trouble with monomorphic loci now.

Thanks @gdurif for being willing to take a look: below I have my headerRF.txt. I included the first three scenarios that I will be testing. I have also attached my SNP file (as .txt) DIYABC_800_75p.recode_NEW_reduced.DIYABC.txt

DIYABC_800_75p.recode_NEW_reduced.DIYABC.snp
8 parameters and 130 summary statistics

3 scenarios: 8 8 8
scenario 1 [0.33333] (7)
N1 N2 N3 N4 N1 N1 N1
0 sample 1 
0 sample 2
0 sample 3
0 sample 4
t1 merge 2 3
t2 merge 4 1
t3 merge 4 2
scenario 2 [0.33333] (7)
N1 N2 N3 N4 N1 N1 N1 
0 sample 1 
0 sample 2
0 sample 3
0 sample 4
t1 merge 2 3
t2 merge 2 4
t3 merge 1 2
scenario 3 [0.33333] (8)
N1 N2 N3 N4 N1 N1 N1
0 sample 1 
0 sample 2
0 sample 3
0 sample 4
t1 merge 3 2
t2 split 4 3 1 r1
t3 merge 3 1

historical parameters priors (8,3)
N1 N UN[1000,1000000,0,0]
N2 N UN[1000,1000000,0,0]
N3 N UN[1000,1000000,0,0]
N4 N UN[1000,1000000,0,0]
t1 T UN[100,100000,0,0]
t2 T UN[1000,1000000,0,0]
t3 T UN[10000,1000000,0,0]
r1 A UN[0.05,0.95,0,0]
t1>t2
t2>t3
t1>t3
DRAW UNTIL

loci description (1)
635 <A> G1 from 1

group summary statistics (130)
group G1 (130)
ML1p 1 2 3 4
ML2p 1.2 1.3 1.4 2.3 2.4 3.4
ML3p 1.2.3 1.2.4 1.3.4 2.3.4
HWm 1 2 3 4
HWv 1 2 3 4
HBm 1.2 1.3 1.4 2.3 2.4 3.4
HBv 1.2 1.3 1.4 2.3 2.4 3.4
FST1m 1 2 3 4
FST1v 1 2 3 4
FST2m 1.2 1.3 1.4 2.3 2.4 3.4
FST2v 1.2 1.3 1.4 2.3 2.4 3.4
NEIm 1.2 1.3 1.4 2.3 2.4 3.4
NEIv 1.2 1.3 1.4 2.3 2.4 3.4
AMLm 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.3.4 3.1.4 4.1.3 2.3.4 3.2.4 4.2.3
AMLv 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.3.4 3.1.4 4.1.3 2.3.4 3.2.4 4.2.3
FST3m 1.2.3 1.2.4 1.3.4 2.3.4
FST3v 1.2.3 1.2.4 1.3.4 2.3.4
FST4m 1.2.3.4
FST4v 1.2.3.4
F3m 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.3.4 3.1.4 4.1.3 2.3.4 3.2.4 4.2.3
F3v 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.3.4 3.1.4 4.1.3 2.3.4 3.2.4 4.2.3
F4m 1.2.3.4 1.3.2.4 1.4.2.3
F4v 1.2.3.4 1.3.2.4 1.4.2.3

scenario N1 N2 N3 N4 t1 t2 t3 r1    ML1p_1        ML1p_2        ML1p_3        ML1p_4       ML2p_1.2      ML2p_1.3      ML2p_1.4      ML2p_2.3      ML2p_2.4      ML2p_3.4     ML3p_1.2.3    ML3p_1.2.4    ML3p_1.3.4    ML3p_2.3.4      HWm_1         HWm_2         HWm_3         HWm_4         HWv_1         HWv_2         HWv_3         HWv_4        HBm_1.2       HBm_1.3       HBm_1.4       HBm_2.3       HBm_2.4       HBm_3.4       HBv_1.2       HBv_1.3       HBv_1.4       HBv_2.3       HBv_2.4       HBv_3.4       FST1m_1       FST1m_2       FST1m_3       FST1m_4       FST1v_1       FST1v_2       FST1v_3       FST1v_4      FST2m_1.2     FST2m_1.3     FST2m_1.4     FST2m_2.3     FST2m_2.4     FST2m_3.4     FST2v_1.2     FST2v_1.3     FST2v_1.4     FST2v_2.3     FST2v_2.4     FST2v_3.4      NEIm_1.2      NEIm_1.3      NEIm_1.4      NEIm_2.3      NEIm_2.4      NEIm_3.4      NEIv_1.2      NEIv_1.3      NEIv_1.4      NEIv_2.3      NEIv_2.4      NEIv_3.4     AMLm_1.2.3    AMLm_2.1.3    AMLm_3.1.2    AMLm_1.2.4    AMLm_2.1.4    AMLm_4.1.2    AMLm_1.3.4    AMLm_3.1.4    AMLm_4.1.3    AMLm_2.3.4    AMLm_3.2.4    AMLm_4.2.3    AMLv_1.2.3    AMLv_2.1.3    AMLv_3.1.2    AMLv_1.2.4    AMLv_2.1.4    AMLv_4.1.2    AMLv_1.3.4    AMLv_3.1.4    AMLv_4.1.3    AMLv_2.3.4    AMLv_3.2.4    AMLv_4.2.3   FST3m_1.2.3   FST3m_1.2.4   FST3m_1.3.4   FST3m_2.3.4   FST3v_1.2.3   FST3v_1.2.4   FST3v_1.3.4   FST3v_2.3.4   FST4m_1.2.3.4  FST4v_1.2.3.4   F3m_1.2.3     F3m_2.1.3     F3m_3.1.2     F3m_1.2.4     F3m_2.1.4     F3m_4.1.2     F3m_1.3.4     F3m_3.1.4     F3m_4.1.3     F3m_2.3.4     F3m_3.2.4     F3m_4.2.3     F3v_1.2.3     F3v_2.1.3     F3v_3.1.2     F3v_1.2.4     F3v_2.1.4     F3v_4.1.2     F3v_1.3.4     F3v_3.1.4     F3v_4.1.3     F3v_2.3.4     F3v_3.2.4     F3v_4.2.3    F4m_1.2.3.4   F4m_1.3.2.4   F4m_1.4.2.3   F4v_1.2.3.4   F4v_1.3.2.4   F4v_1.4.2.3  

[Belenarias]

Hi @heather340 I've checked your snp file, why did you used sex ratio 0.5 (NM=0.5NF)? as far I understood from the manual (key files section in Page 47 and 48) a balance sex ratio will be NM=1NF, maybe that could be the problem? Not sure but you can give a try.

@gdurif I think my input (converted vcf it's fine) but I need to remove the monomorphic loci before submitting in the program. this is suggested in the manual Page 48 paragraph "Following Hudson's (2002) criterion". Do you have any script/idea how to removed the monomorphic snps? I'm thinking give a try in PGDspider but maybe you have more experience. Maybe due to the large amount of monomorphic in my dataset the DIYABC simulation can't run. Another alternative that might affect my simulations is the Scenarios, below you can find the "headerRF.txt" for one scenario that the simulation failed. N1 is the source/native population, the others are posterior colonisation processes. Also attached is the snp file, thanks! snps_med_poporder_renamed.snp.txt

snps_med_poporder_renamed.snp 9 parameters and 572 summary statistics

1 scenarios: 12 scenario 1 [1] (9) N1 N2 N3 N4 N5 N6 0 sample 1 0 sample 2 0 sample 3 0 sample 4 0 sample 5 0 sample 6 ta merge 3 6 ta merge 4 5 ts merge 3 4 ts merge 1 2 tz merge 1 3

historical parameters priors (9,2) N1 N UN[1000,1000000,0,0] N2 N UN[10,100000,0,0] N3 N UN[10,100000,0,0] N4 N UN[10,100000,0,0] N5 N UN[10,100000,0,0] N6 N UN[10,100000,0,0] ta T UN[10,500,0,0] ts T UN[100,1500,0,0] tz T UN[1000,10000,0,0] tz>ts ts>ta DRAW UNTIL

loci description (1) 1000 G1 from 1

group summary statistics (572) group G1 (572) ML1p 1 2 3 4 5 6 ML2p 1.2 1.3 1.4 1.5 1.6 2.3 2.4 2.5 2.6 3.4 3.5 3.6 4.5 4.6 5.6 ML3p 1.2.3 1.2.4 1.2.5 1.2.6 1.3.4 1.3.5 1.3.6 1.4.5 1.4.6 1.5.6 2.3.4 2.3.5 2.3.6 2.4.5 2.4.6 2.5.6 3.4.5 3.4.6 3.5.6 4.5.6 ML4p 1.2.3.4 1.2.3.5 1.2.3.6 1.2.4.5 1.2.4.6 1.2.5.6 1.3.4.5 1.3.4.6 1.3.5.6 1.4.5.6 2.3.4.5 2.3.4.6 2.3.5.6 2.4.5.6 3.4.5.6 HWm 1 2 3 4 5 6 HWv 1 2 3 4 5 6 HBm 1.2 1.3 1.4 1.5 1.6 2.3 2.4 2.5 2.6 3.4 3.5 3.6 4.5 4.6 5.6 HBv 1.2 1.3 1.4 1.5 1.6 2.3 2.4 2.5 2.6 3.4 3.5 3.6 4.5 4.6 5.6 FST1m 1 2 3 4 5 6 FST1v 1 2 3 4 5 6 FST2m 1.2 1.3 1.4 1.5 1.6 2.3 2.4 2.5 2.6 3.4 3.5 3.6 4.5 4.6 5.6 FST2v 1.2 1.3 1.4 1.5 1.6 2.3 2.4 2.5 2.6 3.4 3.5 3.6 4.5 4.6 5.6 NEIm 1.2 1.3 1.4 1.5 1.6 2.3 2.4 2.5 2.6 3.4 3.5 3.6 4.5 4.6 5.6 NEIv 1.2 1.3 1.4 1.5 1.6 2.3 2.4 2.5 2.6 3.4 3.5 3.6 4.5 4.6 5.6 AMLm 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.2.5 2.1.5 5.1.2 1.2.6 2.1.6 6.1.2 1.3.4 3.1.4 4.1.3 1.3.5 3.1.5 5.1.3 1.3.6 3.1.6 6.1.3 1.4.5 4.1.5 5.1.4 1.4.6 4.1.6 6.1.4 1.5.6 5.1.6 6.1.5 2.3.4 3.2.4 4.2.3 2.3.5 3.2.5 5.2.3 2.3.6 3.2.6 6.2.3 2.4.5 4.2.5 5.2.4 2.4.6 4.2.6 6.2.4 2.5.6 5.2.6 6.2.5 3.4.5 4.3.5 5.3.4 3.4.6 4.3.6 6.3.4 3.5.6 5.3.6 6.3.5 4.5.6 5.4.6 6.4.5 AMLv 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.2.5 2.1.5 5.1.2 1.2.6 2.1.6 6.1.2 1.3.4 3.1.4 4.1.3 1.3.5 3.1.5 5.1.3 1.3.6 3.1.6 6.1.3 1.4.5 4.1.5 5.1.4 1.4.6 4.1.6 6.1.4 1.5.6 5.1.6 6.1.5 2.3.4 3.2.4 4.2.3 2.3.5 3.2.5 5.2.3 2.3.6 3.2.6 6.2.3 2.4.5 4.2.5 5.2.4 2.4.6 4.2.6 6.2.4 2.5.6 5.2.6 6.2.5 3.4.5 4.3.5 5.3.4 3.4.6 4.3.6 6.3.4 3.5.6 5.3.6 6.3.5 4.5.6 5.4.6 6.4.5 FST3m 1.2.3 1.2.4 1.2.5 1.2.6 1.3.4 1.3.5 1.3.6 1.4.5 1.4.6 1.5.6 2.3.4 2.3.5 2.3.6 2.4.5 2.4.6 2.5.6 3.4.5 3.4.6 3.5.6 4.5.6 FST3v 1.2.3 1.2.4 1.2.5 1.2.6 1.3.4 1.3.5 1.3.6 1.4.5 1.4.6 1.5.6 2.3.4 2.3.5 2.3.6 2.4.5 2.4.6 2.5.6 3.4.5 3.4.6 3.5.6 4.5.6 FST4m 1.2.3.4 1.2.3.5 1.2.3.6 1.2.4.5 1.2.4.6 1.2.5.6 1.3.4.5 1.3.4.6 1.3.5.6 1.4.5.6 2.3.4.5 2.3.4.6 2.3.5.6 2.4.5.6 3.4.5.6 FST4v 1.2.3.4 1.2.3.5 1.2.3.6 1.2.4.5 1.2.4.6 1.2.5.6 1.3.4.5 1.3.4.6 1.3.5.6 1.4.5.6 2.3.4.5 2.3.4.6 2.3.5.6 2.4.5.6 3.4.5.6 FSTGm 0 FSTGv 0 F3m 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.2.5 2.1.5 5.1.2 1.2.6 2.1.6 6.1.2 1.3.4 3.1.4 4.1.3 1.3.5 3.1.5 5.1.3 1.3.6 3.1.6 6.1.3 1.4.5 4.1.5 5.1.4 1.4.6 4.1.6 6.1.4 1.5.6 5.1.6 6.1.5 2.3.4 3.2.4 4.2.3 2.3.5 3.2.5 5.2.3 2.3.6 3.2.6 6.2.3 2.4.5 4.2.5 5.2.4 2.4.6 4.2.6 6.2.4 2.5.6 5.2.6 6.2.5 3.4.5 4.3.5 5.3.4 3.4.6 4.3.6 6.3.4 3.5.6 5.3.6 6.3.5 4.5.6 5.4.6 6.4.5 F3v 1.2.3 2.1.3 3.1.2 1.2.4 2.1.4 4.1.2 1.2.5 2.1.5 5.1.2 1.2.6 2.1.6 6.1.2 1.3.4 3.1.4 4.1.3 1.3.5 3.1.5 5.1.3 1.3.6 3.1.6 6.1.3 1.4.5 4.1.5 5.1.4 1.4.6 4.1.6 6.1.4 1.5.6 5.1.6 6.1.5 2.3.4 3.2.4 4.2.3 2.3.5 3.2.5 5.2.3 2.3.6 3.2.6 6.2.3 2.4.5 4.2.5 5.2.4 2.4.6 4.2.6 6.2.4 2.5.6 5.2.6 6.2.5 3.4.5 4.3.5 5.3.4 3.4.6 4.3.6 6.3.4 3.5.6 5.3.6 6.3.5 4.5.6 5.4.6 6.4.5 F4m 1.2.3.4 1.3.2.4 1.4.2.3 1.2.3.5 1.3.2.5 1.5.2.3 1.2.3.6 1.3.2.6 1.6.2.3 1.2.4.5 1.4.2.5 1.5.2.4 1.2.4.6 1.4.2.6 1.6.2.4 1.2.5.6 1.5.2.6 1.6.2.5 1.3.4.5 1.4.3.5 1.5.3.4 1.3.4.6 1.4.3.6 1.6.3.4 1.3.5.6 1.5.3.6 1.6.3.5 1.4.5.6 1.5.4.6 1.6.4.5 2.3.4.5 2.4.3.5 2.5.3.4 2.3.4.6 2.4.3.6 2.6.3.4 2.3.5.6 2.5.3.6 2.6.3.5 2.4.5.6 2.5.4.6 2.6.4.5 3.4.5.6 3.5.4.6 3.6.4.5 F4v 1.2.3.4 1.3.2.4 1.4.2.3 1.2.3.5 1.3.2.5 1.5.2.3 1.2.3.6 1.3.2.6 1.6.2.3 1.2.4.5 1.4.2.5 1.5.2.4 1.2.4.6 1.4.2.6 1.6.2.4 1.2.5.6 1.5.2.6 1.6.2.5 1.3.4.5 1.4.3.5 1.5.3.4 1.3.4.6 1.4.3.6 1.6.3.4 1.3.5.6 1.5.3.6 1.6.3.5 1.4.5.6 1.5.4.6 1.6.4.5 2.3.4.5 2.4.3.5 2.5.3.4 2.3.4.6 2.4.3.6 2.6.3.4 2.3.5.6 2.5.3.6 2.6.3.5 2.4.5.6 2.5.4.6 2.6.4.5 3.4.5.6 3.5.4.6 3.6.4.5

scenario N1 N2 N3 N4 N5 N6 ta ts tz ML1p_1 ML1p_2 ML1p_3 ML1p_4 ML1p_5 ML1p_6 ML2p_1.2 ML2p_1.3 ML2p_1.4 ML2p_1.5 ML2p_1.6 ML2p_2.3 ML2p_2.4 ML2p_2.5 ML2p_2.6 ML2p_3.4 ML2p_3.5 ML2p_3.6 ML2p_4.5 ML2p_4.6 ML2p_5.6 ML3p_1.2.3 ML3p_1.2.4 ML3p_1.2.5 ML3p_1.2.6 ML3p_1.3.4 ML3p_1.3.5 ML3p_1.3.6 ML3p_1.4.5 ML3p_1.4.6 ML3p_1.5.6 ML3p_2.3.4 ML3p_2.3.5 ML3p_2.3.6 ML3p_2.4.5 ML3p_2.4.6 ML3p_2.5.6 ML3p_3.4.5 ML3p_3.4.6 ML3p_3.5.6 ML3p_4.5.6 ML4p_1.2.3.4 ML4p_1.2.3.5 ML4p_1.2.3.6 ML4p_1.2.4.5 ML4p_1.2.4.6 ML4p_1.2.5.6 ML4p_1.3.4.5 ML4p_1.3.4.6 ML4p_1.3.5.6 ML4p_1.4.5.6 ML4p_2.3.4.5 ML4p_2.3.4.6 ML4p_2.3.5.6 ML4p_2.4.5.6 ML4p_3.4.5.6 HWm_1 HWm_2 HWm_3 HWm_4 HWm_5 HWm_6 HWv_1 HWv_2 HWv_3 HWv_4 HWv_5 HWv_6 HBm_1.2 HBm_1.3 HBm_1.4 HBm_1.5 HBm_1.6 HBm_2.3 HBm_2.4 HBm_2.5 HBm_2.6 HBm_3.4 HBm_3.5 HBm_3.6 HBm_4.5 HBm_4.6 HBm_5.6 HBv_1.2 HBv_1.3 HBv_1.4 HBv_1.5 HBv_1.6 HBv_2.3 HBv_2.4 HBv_2.5 HBv_2.6 HBv_3.4 HBv_3.5 HBv_3.6 HBv_4.5 HBv_4.6 HBv_5.6 FST1m_1 FST1m_2 FST1m_3 FST1m_4 FST1m_5 FST1m_6 FST1v_1 FST1v_2 FST1v_3 FST1v_4 FST1v_5 FST1v_6 FST2m_1.2 FST2m_1.3 FST2m_1.4 FST2m_1.5 FST2m_1.6 FST2m_2.3 FST2m_2.4 FST2m_2.5 FST2m_2.6 FST2m_3.4 FST2m_3.5 FST2m_3.6 FST2m_4.5 FST2m_4.6 FST2m_5.6 FST2v_1.2 FST2v_1.3 FST2v_1.4 FST2v_1.5 FST2v_1.6 FST2v_2.3 FST2v_2.4 FST2v_2.5 FST2v_2.6 FST2v_3.4 FST2v_3.5 FST2v_3.6 FST2v_4.5 FST2v_4.6 FST2v_5.6 NEIm_1.2 NEIm_1.3 NEIm_1.4 NEIm_1.5 NEIm_1.6 NEIm_2.3 NEIm_2.4 NEIm_2.5 NEIm_2.6 NEIm_3.4 NEIm_3.5 NEIm_3.6 NEIm_4.5 NEIm_4.6 NEIm_5.6 NEIv_1.2 NEIv_1.3 NEIv_1.4 NEIv_1.5 NEIv_1.6 NEIv_2.3 NEIv_2.4 NEIv_2.5 NEIv_2.6 NEIv_3.4 NEIv_3.5 NEIv_3.6 NEIv_4.5 NEIv_4.6 NEIv_5.6 AMLm_1.2.3 AMLm_2.1.3 AMLm_3.1.2 AMLm_1.2.4 AMLm_2.1.4 AMLm_4.1.2 AMLm_1.2.5 AMLm_2.1.5 AMLm_5.1.2 AMLm_1.2.6 AMLm_2.1.6 AMLm_6.1.2 AMLm_1.3.4 AMLm_3.1.4 AMLm_4.1.3 AMLm_1.3.5 AMLm_3.1.5 AMLm_5.1.3 AMLm_1.3.6 AMLm_3.1.6 AMLm_6.1.3 AMLm_1.4.5 AMLm_4.1.5 AMLm_5.1.4 AMLm_1.4.6 AMLm_4.1.6 AMLm_6.1.4 AMLm_1.5.6 AMLm_5.1.6 AMLm_6.1.5 AMLm_2.3.4 AMLm_3.2.4 AMLm_4.2.3 AMLm_2.3.5 AMLm_3.2.5 AMLm_5.2.3 AMLm_2.3.6 AMLm_3.2.6 AMLm_6.2.3 AMLm_2.4.5 AMLm_4.2.5 AMLm_5.2.4 AMLm_2.4.6 AMLm_4.2.6 AMLm_6.2.4 AMLm_2.5.6 AMLm_5.2.6 AMLm_6.2.5 AMLm_3.4.5 AMLm_4.3.5 AMLm_5.3.4 AMLm_3.4.6 AMLm_4.3.6 AMLm_6.3.4 AMLm_3.5.6 AMLm_5.3.6 AMLm_6.3.5 AMLm_4.5.6 AMLm_5.4.6 AMLm_6.4.5 AMLv_1.2.3 AMLv_2.1.3 AMLv_3.1.2 AMLv_1.2.4 AMLv_2.1.4 AMLv_4.1.2 AMLv_1.2.5 AMLv_2.1.5 AMLv_5.1.2 AMLv_1.2.6 AMLv_2.1.6 AMLv_6.1.2 AMLv_1.3.4 AMLv_3.1.4 AMLv_4.1.3 AMLv_1.3.5 AMLv_3.1.5 AMLv_5.1.3 AMLv_1.3.6 AMLv_3.1.6 AMLv_6.1.3 AMLv_1.4.5 AMLv_4.1.5 AMLv_5.1.4 AMLv_1.4.6 AMLv_4.1.6 AMLv_6.1.4 AMLv_1.5.6 AMLv_5.1.6 AMLv_6.1.5 AMLv_2.3.4 AMLv_3.2.4 AMLv_4.2.3 AMLv_2.3.5 AMLv_3.2.5 AMLv_5.2.3 AMLv_2.3.6 AMLv_3.2.6 AMLv_6.2.3 AMLv_2.4.5 AMLv_4.2.5 AMLv_5.2.4 AMLv_2.4.6 AMLv_4.2.6 AMLv_6.2.4 AMLv_2.5.6 AMLv_5.2.6 AMLv_6.2.5 AMLv_3.4.5 AMLv_4.3.5 AMLv_5.3.4 AMLv_3.4.6 AMLv_4.3.6 AMLv_6.3.4 AMLv_3.5.6 AMLv_5.3.6 AMLv_6.3.5 AMLv_4.5.6 AMLv_5.4.6 AMLv_6.4.5 FST3m_1.2.3 FST3m_1.2.4 FST3m_1.2.5 FST3m_1.2.6 FST3m_1.3.4 FST3m_1.3.5 FST3m_1.3.6 FST3m_1.4.5 FST3m_1.4.6 FST3m_1.5.6 FST3m_2.3.4 FST3m_2.3.5 FST3m_2.3.6 FST3m_2.4.5 FST3m_2.4.6 FST3m_2.5.6 FST3m_3.4.5 FST3m_3.4.6 FST3m_3.5.6 FST3m_4.5.6 FST3v_1.2.3 FST3v_1.2.4 FST3v_1.2.5 FST3v_1.2.6 FST3v_1.3.4 FST3v_1.3.5 FST3v_1.3.6 FST3v_1.4.5 FST3v_1.4.6 FST3v_1.5.6 FST3v_2.3.4 FST3v_2.3.5 FST3v_2.3.6 FST3v_2.4.5 FST3v_2.4.6 FST3v_2.5.6 FST3v_3.4.5 FST3v_3.4.6 FST3v_3.5.6 FST3v_4.5.6 FST4m_1.2.3.4 FST4m_1.2.3.5 FST4m_1.2.3.6 FST4m_1.2.4.5 FST4m_1.2.4.6 FST4m_1.2.5.6 FST4m_1.3.4.5 FST4m_1.3.4.6 FST4m_1.3.5.6 FST4m_1.4.5.6 FST4m_2.3.4.5 FST4m_2.3.4.6 FST4m_2.3.5.6 FST4m_2.4.5.6 FST4m_3.4.5.6 FST4v_1.2.3.4 FST4v_1.2.3.5 FST4v_1.2.3.6 FST4v_1.2.4.5 FST4v_1.2.4.6 FST4v_1.2.5.6 FST4v_1.3.4.5 FST4v_1.3.4.6 FST4v_1.3.5.6 FST4v_1.4.5.6 FST4v_2.3.4.5 FST4v_2.3.4.6 FST4v_2.3.5.6 FST4v_2.4.5.6 FST4v_3.4.5.6 FSTGm_0 FSTGv_0 F3m_1.2.3 F3m_2.1.3 F3m_3.1.2 F3m_1.2.4 F3m_2.1.4 F3m_4.1.2 F3m_1.2.5 F3m_2.1.5 F3m_5.1.2 F3m_1.2.6 F3m_2.1.6 F3m_6.1.2 F3m_1.3.4 F3m_3.1.4 F3m_4.1.3 F3m_1.3.5 F3m_3.1.5 F3m_5.1.3 F3m_1.3.6 F3m_3.1.6 F3m_6.1.3 F3m_1.4.5 F3m_4.1.5 F3m_5.1.4 F3m_1.4.6 F3m_4.1.6 F3m_6.1.4 F3m_1.5.6 F3m_5.1.6 F3m_6.1.5 F3m_2.3.4 F3m_3.2.4 F3m_4.2.3 F3m_2.3.5 F3m_3.2.5 F3m_5.2.3 F3m_2.3.6 F3m_3.2.6 F3m_6.2.3 F3m_2.4.5 F3m_4.2.5 F3m_5.2.4 F3m_2.4.6 F3m_4.2.6 F3m_6.2.4 F3m_2.5.6 F3m_5.2.6 F3m_6.2.5 F3m_3.4.5 F3m_4.3.5 F3m_5.3.4 F3m_3.4.6 F3m_4.3.6 F3m_6.3.4 F3m_3.5.6 F3m_5.3.6 F3m_6.3.5 F3m_4.5.6 F3m_5.4.6 F3m_6.4.5 F3v_1.2.3 F3v_2.1.3 F3v_3.1.2 F3v_1.2.4 F3v_2.1.4 F3v_4.1.2 F3v_1.2.5 F3v_2.1.5 F3v_5.1.2 F3v_1.2.6 F3v_2.1.6 F3v_6.1.2 F3v_1.3.4 F3v_3.1.4 F3v_4.1.3 F3v_1.3.5 F3v_3.1.5 F3v_5.1.3 F3v_1.3.6 F3v_3.1.6 F3v_6.1.3 F3v_1.4.5 F3v_4.1.5 F3v_5.1.4 F3v_1.4.6 F3v_4.1.6 F3v_6.1.4 F3v_1.5.6 F3v_5.1.6 F3v_6.1.5 F3v_2.3.4 F3v_3.2.4 F3v_4.2.3 F3v_2.3.5 F3v_3.2.5 F3v_5.2.3 F3v_2.3.6 F3v_3.2.6 F3v_6.2.3 F3v_2.4.5 F3v_4.2.5 F3v_5.2.4 F3v_2.4.6 F3v_4.2.6 F3v_6.2.4 F3v_2.5.6 F3v_5.2.6 F3v_6.2.5 F3v_3.4.5 F3v_4.3.5 F3v_5.3.4 F3v_3.4.6 F3v_4.3.6 F3v_6.3.4 F3v_3.5.6 F3v_5.3.6 F3v_6.3.5 F3v_4.5.6 F3v_5.4.6 F3v_6.4.5 F4m_1.2.3.4 F4m_1.3.2.4 F4m_1.4.2.3 F4m_1.2.3.5 F4m_1.3.2.5 F4m_1.5.2.3 F4m_1.2.3.6 F4m_1.3.2.6 F4m_1.6.2.3 F4m_1.2.4.5 F4m_1.4.2.5 F4m_1.5.2.4 F4m_1.2.4.6 F4m_1.4.2.6 F4m_1.6.2.4 F4m_1.2.5.6 F4m_1.5.2.6 F4m_1.6.2.5 F4m_1.3.4.5 F4m_1.4.3.5 F4m_1.5.3.4 F4m_1.3.4.6 F4m_1.4.3.6 F4m_1.6.3.4 F4m_1.3.5.6 F4m_1.5.3.6 F4m_1.6.3.5 F4m_1.4.5.6 F4m_1.5.4.6 F4m_1.6.4.5 F4m_2.3.4.5 F4m_2.4.3.5 F4m_2.5.3.4 F4m_2.3.4.6 F4m_2.4.3.6 F4m_2.6.3.4 F4m_2.3.5.6 F4m_2.5.3.6 F4m_2.6.3.5 F4m_2.4.5.6 F4m_2.5.4.6 F4m_2.6.4.5 F4m_3.4.5.6 F4m_3.5.4.6 F4m_3.6.4.5 F4v_1.2.3.4 F4v_1.3.2.4 F4v_1.4.2.3 F4v_1.2.3.5 F4v_1.3.2.5 F4v_1.5.2.3 F4v_1.2.3.6 F4v_1.3.2.6 F4v_1.6.2.3 F4v_1.2.4.5 F4v_1.4.2.5 F4v_1.5.2.4 F4v_1.2.4.6 F4v_1.4.2.6 F4v_1.6.2.4 F4v_1.2.5.6 F4v_1.5.2.6 F4v_1.6.2.5 F4v_1.3.4.5 F4v_1.4.3.5 F4v_1.5.3.4 F4v_1.3.4.6 F4v_1.4.3.6 F4v_1.6.3.4 F4v_1.3.5.6 F4v_1.5.3.6 F4v_1.6.3.5 F4v_1.4.5.6 F4v_1.5.4.6 F4v_1.6.4.5 F4v_2.3.4.5 F4v_2.4.3.5 F4v_2.5.3.4 F4v_2.3.4.6 F4v_2.4.3.6 F4v_2.6.3.4 F4v_2.3.5.6 F4v_2.5.3.6 F4v_2.6.3.5 F4v_2.4.5.6 F4v_2.5.4.6 F4v_2.6.4.5 F4v_3.4.5.6 F4v_3.5.4.6 F4v_3.6.4.5

@Belenarias I see, there is at least one issue with the generated headerRF.txt file, which is likely due to a bug in the GUI.

The line 1000 G1 from 1 should be 1000 <A> G1 from 1. I am really sorry, I though it was working. The (soon incoming) new release should fix this.

In the mean time, I tried to use the CLI tools (see https://diyabc.github.io/cli/) to run your example with your dataset but I am still encountering an issue with the diyabc program. I am still investigating.

[heather340]

@Belenarias thanks for noticing that - I had just put in the default as a mistake. But, it doesn't seem to have affected the issue. @gdurif thanks for being willing to take a closer look at both of our files.

[Belenarias]

@gdurif Many thanks for letting me know about the bug so quick!. I hope my dataset helps to improve the program. When do you think will be available the new release? I do need to run this analysis for a resubmission so my time is tight. Thanks for your effort and support.

[gdurif]

Hi @all, I am again really sorry for the delay, but the new version of the GUI is at least available on branch refactor_app, see PR #96

If you want to try it first hand, you can install the R package and run the app with:

devtools::install_github("diyabc/diyabcGUI", ref = "refactor_app", subdir = "R-pkg")
library(diyabcGUI)
dl_all_latest_bin()
diyabc()

It will be merged tomorrow in master and a new version of the beta release will be published.

Edit (2021/08/24): I am encountering a network issue delaying the release build (always the final step...), hopefully it will be fixed in a few hours.

[gdurif]

The new release is available.

[heather340]

Hi! I'm back to working on this project and have updated to the new release of DIYABC-RF. However, I keep having an issue in which I validate all of my parameters, but upon hitting "simulate", I receive the issue: Project is not ready. Check settings above. Any suggestions?

Thanks!

[gdurif]

Hi @heather340 Yes, there is a big problem with the latest release (see #107 #111 ). I am working on it (still totally buried in work at the moment). I will keep you updated ASAP. All my apologies Best

[heather340]

Hi @heather340 Yes, there is a big problem with the latest release (see #107 #111 ). I am working on it (still totally buried in work at the moment). I will keep you updated ASAP. All my apologies Best

So sorry to hear that it's giving you issues! Good luck with the fix.

[gdurif]

Hi, I finally found the problem, new release build is now in progress, see issue #116 for a summary about this matter.

[gdurif]

The release is out: v1.1.1-beta

[gdurif]

Fixed by https://github.com/diyabc/diyabcGUI/commit/d41201218824319bab5939e78ac2ccdff6ae13d9