Hi Milane,

I was trying to run fineRADstructure on my data and got some C++ related errors that I don't understand. Here is what I did:

1. I installed fineRADstructure using conda & bioconda channel.
2. Because I called variants with freebayes instead of Stacks/pyrad, I used Stacks' populations module (v2.0) to convert my vcf to radpainter format.
3. I run RADpainter and finestructure as suggested on your website. RADpainter finished successfully, while the MCMC step of finestructure terminated with error (I used bash -x):

+ finestructure -x 100000 -y 100000 -z 1000 r123_newrbmcl100_fb_vfq20dp10gq20_2_snps.p.haps_chunks.out r123_newrbmcl100_fb_vfq20dp10gq20_2_snps.p.haps_chunks.mcmc.xml
################################################### 100%
################################################### 100%
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
fineRADstructure.sh: řádek 5: 22975 Neúspěšně ukončen (SIGABRT)        finestructure -x 100000 -y 100000 -z 1000 ${1}_chunks.out ${1}_chunks.mcmc.xml

*p.haps_chunks.out was produced by RADpainter.
I tried this on two different machines with the same error:

• First I run it on a cluster with PBS system, using one node with 80 cores and 192 GB RAM. After it failed I read the website of finestructure, where they report problems with PBS, so I decided to run it on other machine.
• Second I run it on a single node without PBS, that has 64 cores and 1 TB of RAM. It was used by other users and processes, but I still had more than half of the cores and memory available.
  I put these specs here as I found that memory could be related to the error.

BTW my dataset has 150 samples and the input filtered VCF before processing by stacks had 400k SNPs.

Thanks for any help

Jan

Hi,

I am running Stacks2fineRAD using the population haplotype file produced by 'population' program in RAD. Then I come across this error, is it a bug?
Code:
python Stacks2fineRAD.py -i /wrk/cuiwang/DONOTREMOVE/amphibian_project300/data/Fejervarya_multistriata/ipyrad/popmappop/stacks/populations.haplotypes.tsv -n 4 -m 20

Error message:
Traceback (most recent call last):
File "Stacks2fineRAD.py", line 70, in
num_snp_list.append(len(list(alleles_set)[0]))
IndexError: list index out of range

Thanks,
Cui

Hello Dr Milan,

First of all, thank you for such a useful, easy and fast tool.

I am sorry in advance if I missed something, but after searching I couldn't find information about this.

I was wondering, how does the software order the individuals in the matrix?

Also, is it possible to reorder the individuals in the matrix manually?

Cheers,

Valéria Marques

Hello,
I am having some issues with the step of assigning individuals to populations.
I had to install the conda fineRADstructure version because I do not have root access, so that may be part of the problem.
I first converted my stacks populations output file (in .tsv format) using the script provided, Stacks2fineRAD.py with the parameters n= 10 and m=50. Everything worked fine until I ran the line:

finestructure -x 100000 -y 100000 -z 1000 ./rats/populations.haplotypes.tsv.fineRADpainter.lociFilt.samples50%missFilt_chunks.out ./rats/populations.haplotypes.tsv.fineRADpainter.lociFilt.samples50%missFilt_chunks.mcmc.xml

First, it did not recognize the values for -x and -y so I took them out. Then, it gave me the error of "invalid data". I used the hack mentioned in a previous question on the forum and ran the following code:

fs fs -X -Y -z 1000 ./rats/populations.haplotypes.tsv.fineRADpainter.lociFilt.samples50%missFilt_chunks.out ./rats/populations.haplotypes.tsv.fineRADpainter.lociFilt.samples50%missFilt_chunks.mcmc.xml

However, after a few seconds of running, I keep getting the following error and can't seem to find any help online.

free(): double free detected in tcache 2bash: line 9: 55886 Aborted (core dumped) fs fs -X -Y -z 1000 ./rats/populations.haplotypes.tsv.fineRADpainter.lociFilt.samples50%missFilt_chunks.out ./rats/populations.haplotypes.tsv.fineRADpainter.lociFilt.samples50%missFilt_chunks.mcmc.xml

I would greatly appreciate any help, thank you!

Hello! Like several others, I've had some issues with the tree building component of the software. I had previously received the Lgamma error described in an earlier post. After running the git pull command, I no longer receive this Lgamma error, but instead, I receive a segmentation fault. Has anyone encountered or resolved this error? Thank you!

In a linux environment, I'm able to calculate the coancestry matrix but when trying to assign individuals to populations with the ./finestructure command I get 'Invalid file!' Any suggestions?

Hi!Firstly, i want to extend my appreciation to you for your fineradstructue so i can detect genetic
structure of my data via haplotype information
However, i meet a sample problem that the file of -F & initialpopfile is the same thing? My data have populations tag, and i want to the software to distinguish it and when it running it use these populations tag to Improve accuracy . So . what i can do to add population tag file：-F or initialpopfile. And ,what the difference between these 2 file?
Thank you very much and i look forward to hearing from you soon!

Hi Milan,
I am having issue with drawing co ancestry matrix using your fineradstructureplot.R script.
The issue is following:

datamatrix<-dataraw[fullorder,fullorder]
Error in dataraw[fullorder, fullorder] : subscript out of bounds
I am using R version 3.6.1 inside conda, as earlier with R-4.2 also same issue occurred.
Please suggest me the possible solution for plotting.
Thanks,
Lomous

Hi,

I used edgardomortiz/fineRADstructure-tools to change my ipyrad files to finRADstructure compatible files. I am able to calculate the co-ancestry matrix without issue, but when I use the chunk.out file it generates I get the error "Invalid file!". I have attached my chunks.out file, I do not see any errors in it.

Thanks,
Megan

spinosa_dnasp52.alleles.min2.finerad_chunks.out.zip

Hi,

I'm trying to install fineRADstructure and after running the ./configure, when I run make I get this error:

collect2: error: ld returned 1 exit status Makefile:610: recipe for target 'finestructure' failed make: *** [finestructure] Error 1

Do you know why?

Thanks in advance!

Hi Millanek,

I just installed fineRADstructure and am trying to convert my stacks haplotype.tsv using Stacks2fineRAD.py.

So what I did is simple python Path/to/Stacks2fineRAD.py -h

However I got this error:

Traceback (most recent call last):
File "/programs/fineRADstructure/Stacks2fineRAD.py", line 6, in
from sklearn.decomposition import PCA as sklearnPCA
ImportError: No module named sklearn.decomposition

Any ideas or suggestions are most welcome! Thank you very much!

Best regards,
Han Xiao

Hello! I used https://github.com/edgardomortiz/fineRADstructure-tools to make my ipyrad files suitable for fineRADstructure. I installed through conda.
I ran RADpainter and it seems to have worked fine. When I try to use the output file (INPUT_chunks.out) in finestructure, it keeps throwing this error: Invalid data. Expected a number but received -nan... do you need to use -X and -Y?)
I have added the X and Y flags, and I still get the same error. Is there anything else that I can try?
Thanks in advance!

Update: I found that the RADpainter output file had produced one row that had an NA in each cell. Strange, because the column for that sample looked normal. I removed the sample and it seems to be running in finestructure now. But, I am curious to know how that happened!

Hi,
I'm working with on Linux and I have problem with fineRADstructure installation.

Everything seems to work for the first steps. I do :
./configure
make
It returns : "/bin/sh: aclocal-1.14: command not found"
So i do :
aclocal
autoconf
automake -a

Then :
./configure
make

It finally prints this error :
collect2: error: ld returned 1 exit status
make: *** [Makefile:645: finestructure] Error 1

I don't understand from where this comes from.
Is there anyone that knows how to fix this ?

Thanks in advance,

I have a preliminary data set, which was run through the ipyrad pipeline without a reference genome. I used the alleles.loci outputfile with fineRADstructure-tools, following their recommendations. I have attached the file here fineradtools_converted.txt, since I am not sure if this is the issue. I will be using a reference genome in the future, but I am attempting some comparative analyses with this small data set first.

Any ways, I run step 1 and 2 fine, at least I think so. Step 2 does not give me any arguments other than that it has finished...

like so:

################################################### 100%
################################################### 100%

So I assume this has run correctly?

Yet, when I run step 3 I keep getting outputs like this:

################################################### 100%
Lgamma error: z=-8.37464e+08
terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >'
Aborted (core dumped)

and

################################################### 100%
Lgamma error: z=-2.47596e+08
terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >'
Aborted (core dumped)

The only thing different I can tell is that the Lgamma error changes... Perhaps it is related to the missingness output from step 1. I have a few samples that are well above 0.50 that I thought were supposed to be filtered out. I thought fineRADstructure-tools was supposed to clean up missing data... It certainly reduced my data set...

I may just run Stacks in the future, since I will be getting some paired end reads as opposed to this preliminary data set I have. But for the time being, I wonder if there is anything I can do to resolve this? I see that there was another person who had a similar issue but their question did not get resolved.

I appreciate your time!

ignore

Hi Milan,

I could run the software. Now using the scripts from this page to draw a plot in R:
https://github.com/millanek/fineRADstructure/blob/master/fineRADstructurePlot.R

However I got stuck. The code gives error at this point:

_> tdend<-myapetodend(ttree,factor=1)
is.binary.tree() is deprecated; using is.binary() instead.

is.binary.tree() will be removed soon: see ?is.binary and update your code._

Apparently it is related to ape version, and I need to update the code. But which code should I update? I can't see any "is.binary" in R code supplied. A little tip would help a lot!

Best,
Yeserin.

Good morning,
I am having a problem installing fineRADstructure in ubuntu 17.10.
Following the instructions in fineRADstructure I get this error after make:

make
CDPATH="${ZSH_VERSION+.}:" && cd . && aclocal-1.14 -I m4 -I ./eigen/
/bin/bash: aclocal-1.14: command not found
Makefile:559: recipe for target 'aclocal.m4' failed
make: *** [aclocal.m4] Error 127

I have aclocal-1.15 and automake-1.15 installed on my computer.

I checked online what could I do and finally I did this:

autoreconf --force --install
aclocal: warning: couldn't open directory 'm4': No such file or directory
configure.ac:17: installing 'config/compile'
Makefile.am: error: required file './NEWS' not found
parallel-tests: installing 'config/test-driver'
autoreconf: automake failed with exit status: 1

I created the ./NEWS file and run autoreconf again

autoreconf
aclocal: warning: couldn't open directory 'm4': No such file or directory

I created an empty directory called m4 and this time autoreconf worked, but after running ./configure and make i got this error:

make
...
In file included from state.cpp:4:0:
/usr/include/c++/7/bits/locale_facets_nonio.tcc: In member function ‘_InIter std::__cxx11::time_get<_CharT, _InIter>::_M_extract_name(std::__cxx11::time_get<_CharT, _InIter>::iter_type, std::__cxx11::time_get<_CharT, _InIter>::iter_type, int&, const _CharT**, std::size_t, std::ios_base&, std::ios_base::iostate&) const’:
rng.h:12:18: error: expected unqualified-id before ‘(’ token
#define min(a,b) ((a) <= (b) ? (a) : (b))
^
/usr/include/c++/7/bits/locale_conv.h: In member function ‘bool std::wbuffer_convert<_Codecvt, _Elem, _Tr>::_M_conv_get()’:
rng.h:12:18: error: expected unqualified-id before ‘(’ token
#define min(a,b) ((a) <= (b) ? (a) : (b))
^
rng.h:12:18: error: expected unqualified-id before ‘(’ token
#define min(a,b) ((a) <= (b) ? (a) : (b))
^
Makefile:762: recipe for target 'finestructure-state.o' failed
make: *** [finestructure-state.o] Error 1

I am a novice in this so I don't really know what else I can do. I installed fineRADstructure in my mac and I didn't have any kind of problems.
Any help will be welcomed

Marisa

Hi all,

I'm a new user of R and need some help to correctly plot my finestructure. I'm trying to reorder the position of my different individuals in the plots and even though I am able to get plots, I don't know what to change in the script to do that.

Is there a file or line in the script I would need to change in order for the plot to have the order of populations I want to?

I attached the file I want to change. I need the group in the center with the highest co-ancestry levels to be on the bottom left side of the plot.

Thanks!
Diego

Dear Milan,

A while ago I could progress in drawing the results of fineradstructure analysis using fineRADstructurePlot.R. But as I remember it took hours to find the correct versions of R packages.

Unfortunately, I had to reinstall R to my PC again. And all the previous packages are gone. Now, the latest R (v 4.2) or probably XML doesn't work. This code gives an error:

mcmcxml<-xmlTreeParse(mcmcfile) ## read into xml format
Error: XML content does not seem to be XML: ''

mcmcfile used to work before. So, something must be off with the R packages.

Could you please kindly write which versions of R, XML, and ape do I need? This will help a lot.

Best wishes,
Yeserin.

I'm getting an error when running the first step ('paint') on the stickleback example matrix. For each line of the input file, an error message appears saying the allele is not found. Here are the last 7 lines:

/INPUT_RAD_FILE.txt: line 19842: CC: not found
/INPUT_RAD_FILE.txt: line 19843: TC: not found
/INPUT_RAD_FILE.txt: line 19844: CC: not found
/INPUT_RAD_FILE.txt: line 19845: GT: not found
/INPUT_RAD_FILE.txt: line 19846: GT: not found
/INPUT_RAD_FILE.txt: line 19847: GT: not found
/INPUT_RAD_FILE.txt: line 19848: GT: not found

Any suggestions?

Trying to install on an Apple M1 processor and getting the following error message after issuing the 'make' command. Any help is appreciated.

g++ -DPACKAGE_NAME="fineRADstructure" -DPACKAGE_TARNAME="fineradstructure" -DPACKAGE_VERSION="0.3.1" -DPACKAGE_STRING="fineRADstructure\ 0.3.1" -DPACKAGE_BUGREPORT="[email protected]" -DPACKAGE_URL="" -DPACKAGE="fineradstructure" -DVERSION="0.3.1" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -DHAVE_POW=1 -DHAVE_SELECT=1 -DHAVE_SQRT=1 -DHAVE_STRCHR=1 -DHAVE_STRTOUL=1 -I. -I/opt/homebrew/Cellar/gsl/2.7/include -O3 -Wall -mfpmath=sse -msse -msse2 -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -lgsl -lgslcblas -Wall -g -O2 -MT finestructure-safegetline.o -MD -MP -MF .deps/finestructure-safegetline.Tpo -c -o finestructure-safegetline.o test -f 'safegetline.cpp' || echo './'safegetline.cpp
clang: warning: -lgsl: 'linker' input unused [-Wunused-command-line-argument]
clang: warning: -lgslcblas: 'linker' input unused [-Wunused-command-line-argument]
clang: warning: argument unused during compilation: '-msse' [-Wunused-command-line-argument]
clang: warning: argument unused during compilation: '-msse2' [-Wunused-command-line-argument]
error: unknown FP unit 'sse'
make: *** [finestructure-safegetline.o] Error 1

Hi, I'm trying to analyse my data (reference mapped SNP data produced using Stacks 2.3e) using fineRADstructure, but am encountering this error:

#convert Stacks .haplotypes.tsv file to .fineRADstructure input
Stacks2fineRAD.py -i alba-ori-pass1-p11-r50-c.haplotypes.tsv -n 1 -m 30

Traceback (most recent call last):
File ".//Stacks2fineRAD.py", line 70, in
num_snp_list.append(len(list(alleles_set)[0]))
IndexError: list index out of range

I'm not sure which exact version of fineRADstructure I have installed, but it was installed using gitclone on 18th December 2018 (current version?). I recently had no problem running this command and rest of the program using Stacks 1.4 denovo assembled SNP data.

Happy to share the input haplotype.tsv file or my copy of Stacks2fineRAD.py with anyone, if this helps.

Thanks!

My haplotype file looks like this:

# Catalog Locus ID	Cnt	BA49818-p..sort	BA49819-p..sort	BA49832-p..sort	BA49838-p..sort	BA49850-p..sort	BA49852-p..sort	CS69277-p..sort	CS69279-p..sort	CS69280-p..sort	CS69281-p..sort	CS69282-p..sort	CS69283-p..sort	CS69284-p..sort	CS69290-p..sort	CS69291-p..sort	CS69292-p..sort	CS69293-p..sort	CS69320-p..sort	CS69396-p..sort	CS69419-p..sort	CS69420-L1WQC01-p..sort	CS69421-p..sort	CS69422-p..sort	CS69423-p..sort	CS69424-p..sort	CS69425-p..sort	CS69426-p..sort	CS69428-p..sort	CS69429-p..sort	CS69430-p..sort	CS69431-p..sort	CS69432-p..sort	CS69433-p..sort	CS69447-p..sort	CS69448-p..sort	CS69449-p..sort	CN70301-p..sort	CN70302-p..sort	CN70303-p..sort	CN70304-p..sort	CN70305-p..sort	CN70306-p..sort	CN70307-p..sort	CN70308-p..sort	CN70309-p..sort	CN70310-p..sort	CN70311-p..sort	CN70312-p..sort	CN70313-p..sort	CN70314-p..sort	CN70316-p..sort	CN70317-p..sort	CN70318-p..sort	CN70319-p..sort	CN70320-p..sort	OR23053-p..sort	OR23057-p..sort	OR23059-p..sort	OR23062-p..sort	OR23066-p..sort	OR23067-p..sort	OR23069-p..sort	OR23070-p..sort	OR23071-p..sort	OR23072-p..sort	OR23073-p..sort	OR23075-p..sort	OR23076-p..sort	OR23077-p..sort	OR23078-p..sort	OR23080-p..sort	OR23084-p..sort	OR23086-p..sort	OR23087-L2BQCOR-p..sort	OR23089-p..sort	OR23091-p..sort	OR23092-p..sort	OR23093-p..sort	OR23097-p..sort	OR23098-p..sort	WA78375-p..sort	WA78376-p..sort	WA78377-p..sort	WA78378-p..sort	WA78379-p..sort	WA78382-p..sort	WA78384-p..sort	WA78385-p..sort	WA78386-p..sort	WA78387-p..sort	WA78390-p..sort	WA78391-p..sort	WA78392-p..sort	WA78393-p..sort	WA78395-p..sort	WA78396-p..sort	WA78398-p..sort	WA78399-p..sort	WA78401-p..sort	WA78402-p..sort	WA78403-p..sort	WA78404-p..sort	WA78405-p..sort	WA78407-p..sort	WA7831X-p..sort	BC49559-p..sort	BC49563-p..sort	BC49596-p..sort	BC49598-p..sort	BC49619-p..sort	BC49635-p..sort	BC49637-p..sort	BC49653-L3WQC01-p..sort	BC49679-p..sort	BC49684-p..sort	BC49685-p..sort	HW75302-p..sort	HW75303-p..sort	HW75304-p..sort	HW75305-p..sort	HW75306-p..sort	HW75308-p..sort	HW75309-p..sort	HW75312-p..sort	HW75313-p..sort	HW75315-p..sort	HW75316-p..sort	HW75317-p..sort	HW75318-p..sort	HW75319-p..sort	HW75322-p..sort	HW75323-p..sort	HW75324-p..sort	HW75325-p..sort	HW75326-p..sort	HW75327-p..sort	HW75328-p..sort	HW75329-p..sort	HN11439-L2BQCHN-p..sort	HN11442-p..sort	HN11458-p..sort	HN11459-p..sort	HN11460-p..sort	HN11464-p..sort	HN11465-p..sort	HN11466-p..sort	HN11467-p..sort	HN11468-p..sort	HN11469-p..sort	HN11470-p..sort	HN11471-p..sort	HN11472-p..sort	HN11473-p..sort	HN11474-p..sort	HN11476-p..sort	HN11477-p..sort	HN11478-p..sort	HN11479-p..sort	HN12058-p..sort	HN12059-p..sort	HN12060-p..sort	HN12061-p..sort	HN12062-p..sort	HN12063-p..sort	JP88802-p..sort	JP88805-p..sort	JP88807-p..sort	JP88808-p..sort	JP88809-p..sort	JP88811-p..sort	JP88812-p..sort	JP88813-p..sort	JP88814-p..sort	JP88818-p..sort	JP88819-p..sort	JP88820-p..sort	JP88822-p..sort	JP88823-p..sort	JP88824-p..sort	JP88825-p..sort	JP88827-p..sort	JP88828-p..sort	JP88829-p..sort	JP88830-p..sort	JP88831-p..sort	JP88835-p..sort	PH11948-p..sort	PH11950-p..sort	PH11954-p..sort	PH11958-p..sort	PH11981-p..sort	PH11983-p..sort	PH11986-L1WQC02-p..sort	PH11988-p..sort	PH11993-p..sort	PH11994-p..sort	PH11996-p..sort	PH11997-p..sort	PH12001-p..sort	PH12003-p..sort	PH12005-p..sort	PH12008-p..sort	PH12009-p..sort	PH12013-p..sort	PH12014-p..sort	PH12015-p..sort	PH12018-p..sort	PH12027-p..sort	PH12034-p..sort	PH12035-p..sort	PH12036-p..sort	TS00001-p..sort	TS00002-p..sort	TS00003-p..sort	TS00004-p..sort	TS00005-p..sort	TS00006-p..sort	TS00007-p..sort	TS00008-p..sort	TS00009-p..sort	TS00010-p..sort	TS00011-p..sort	TS00012-p..sort	TS00013-p..sort	TS00014-p..sort	TS00015-p..sort	TS00016-p..sort	TS00017-p..sort	TS00019-p..sort	TS00020-p..sort	TS00023-p..sort	TS00024-p..sort
25	230	G/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	-	G/G	A/G	A/G	G/G	G/G	G/G	A/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	A/A	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/A	G/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	A/G	G/G	A/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	A/G	N/N	G/G	G/G	G/G	A/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	A/G	G/G	A/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	A/A	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	A/G	G/G	G/G	A/G	G/G	G/G	A/A	A/G	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	G/G	-	G/G	G/G	G/G	G/G	A/G	G/G	G/G	G/G	G/G	G/G	A/A	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G	G/G
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95	210	/	/	/	-	/	/	/	/	/	/	/	/	-	/	/	/	/	/	/	-	/	-	/	/	/	/	/	/	/	/	/	/	/	-	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	-	/	/	/	/	/	/	/	/	/	-	/	/	/	/	/	/	/	/	-	/	/	/	/	-	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	-	/	/	/	/	/	/	/	-	-	/	/	/	-	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	-	/	/	-	/	-	/	/	-	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	-	/	-	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	-	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	-	/	/	/	/	/	/	/	/	/	/	/	/	/	/	-	/	/	/
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156	232	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/
113	232	T/T	T/T	C/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	N/N	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	C/T	C/T	C/T	T/T	T/T	T/T	C/T	T/T	T/T	C/T	N/N	C/T	C/T	C/T	T/T	T/T	T/T	C/T	T/T	T/T	C/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	C/C	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	C/T	C/T	C/T	T/T	N/N	C/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	C/T	T/T	T/T	C/T	T/T	T/T	C/T	C/T	C/T	T/T	T/T	T/T	T/T	T/T	C/T	C/T	C/T	T/T	T/T	T/T	T/T	C/T	T/T	C/T	T/T	T/T	C/T	T/T	N/N	C/T	N/N	T/T	T/T	C/T	T/T	C/C	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	C/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	C/T	C/T	T/T	T/T	T/T	T/T	C/C	T/T	T/T	T/T	C/T	T/T	T/T	C/T	C/T	T/T	C/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	C/T	T/T	C/T	T/T	C/C	T/T	T/T	C/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	C/T	C/T	C/C	T/T	C/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	C/T	C/T	C/T	C/T	T/T	T/T	C/T	C/T	C/C	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	N/N	T/T	T/T	C/T	T/T	T/T	C/T	C/T	T/T	T/T	T/T	T/T	T/T
160	231	C/T	N/N	C/C	C/C	C/T	C/T	C/C	C/C	T/T	T/T	C/C	C/T	C/T	C/C	C/C	C/C	C/T	C/T	C/T	C/T	T/T	C/T	C/T	C/T	C/T	T/T	C/T	C/T	C/C	C/T	C/C	C/T	C/C	T/T	T/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	T/T	C/T	C/T	C/C	T/T	C/C	C/C	C/C	T/T	C/C	-	T/T	C/T	C/T	T/T	T/T	C/T	C/T	T/T	T/T	T/T	C/C	C/T	C/C	T/T	C/C	C/C	C/C	C/C	C/C	N/N	C/T	C/C	C/T	C/T	C/C	C/C	C/T	C/T	C/C	T/T	T/T	C/T	C/C	C/C	C/T	T/T	C/C	C/T	C/C	C/C	C/C	C/C	C/T	C/C	C/T	C/C	C/T	C/C	C/C	T/T	C/C	C/T	C/C	C/C	C/T	C/C	T/T	C/T	C/C	C/T	C/T	C/T	C/T	N/N	C/C	C/C	C/C	C/T	C/T	C/T	C/C	C/C	C/C	C/C	C/T	C/T	C/C	T/T	N/N	C/C	C/C	N/N	C/C	C/C	C/C	C/T	T/T	C/T	C/T	T/T	C/T	C/C	C/T	T/T	C/C	C/T	C/C	C/C	C/T	C/T	T/T	C/C	C/T	C/C	C/C	C/T	C/T	T/T	C/C	C/C	T/T	N/N	C/C	C/T	C/C	C/C	C/T	C/T	C/C	C/C	T/T	C/T	C/C	C/C	C/T	C/T	C/T	T/T	C/C	C/T	C/T	C/C	C/C	C/T	C/T	C/T	C/T	C/T	C/T	C/T	C/C	C/T	C/T	C/C	C/T	C/C	C/T	C/T	T/T	T/T	C/T	N/N	T/T	C/T	C/T	C/C	C/T	C/C	C/C	C/T	C/C	C/C	C/T	C/C	C/T	C/T	C/T	C/C	C/T	C/T	T/T	C/T	C/T	C/T	C/T	T/T	C/C	C/C
206	232	N/N	C/C	G/G	G/G	C/C	C/G	G/G	C/G	C/C	N/N	C/C	C/G	C/C	C/G	C/G	C/C	G/G	G/G	C/G	C/G	C/G	N/N	C/G	G/G	G/G	G/G	C/G	C/C	C/G	C/G	N/N	N/N	C/C	C/G	C/G	C/C	G/G	G/G	G/G	C/C	G/G	C/C	C/G	G/G	G/G	N/N	C/G	C/C	C/C	C/G	C/C	C/G	G/G	G/G	G/G	C/C	C/C	C/G	C/C	C/C	G/G	N/N	G/G	C/C	C/C	C/C	G/G	C/G	C/C	C/C	C/G	C/G	G/G	G/G	C/G	C/C	G/G	G/G	C/G	G/G	C/C	C/C	C/C	G/G	C/C	C/C	C/C	C/G	G/G	C/C	G/G	G/G	C/G	G/G	C/C	C/C	C/G	C/G	C/G	C/C	N/N	C/C	C/C	C/G	C/C	N/N	N/N	N/N	C/C	C/C	C/C	G/G	G/G	C/C	C/G	N/N	G/G	C/G	G/G	C/C	N/N	C/G	N/N	C/G	C/C	C/C	G/G	C/C	N/N	N/N	C/C	C/C	N/N	G/G	G/G	G/G	N/N	C/C	C/G	N/N	G/G	C/C	G/G	C/C	C/C	C/G	C/G	C/G	C/G	C/C	N/N	C/G	C/C	C/C	C/G	C/C	C/C	C/G	C/G	C/C	C/C	N/N	C/C	C/C	G/G	G/G	C/C	C/C	C/C	C/C	N/N	G/G	C/G	G/G	G/G	C/G	G/G	C/C	G/G	C/G	C/C	N/N	C/C	G/G	G/G	C/G	N/N	C/C	C/G	N/N	C/C	C/C	C/C	C/C	C/C	C/C	C/G	G/G	N/N	C/C	C/C	G/G	C/G	C/G	G/G	G/G	N/N	N/N	C/C	N/N	C/C	N/N	C/C	N/N	N/N	C/C	G/G	N/N	G/C	C/C	C/G	C/C	N/N	G/G	C/C	C/G	C/C	C/G	C/G	C/G	G/G	C/C
184	231	T/T	T/T	T/T	-	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/C	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	C/T	C/T	C/T	T/T	C/T	T/T	T/T	T/T	T/T	C/T	T/T	C/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T	N/N	T/T	T/T	T/T	T/T	T/T	T/T	T/T	T/T
275	231	/	/	/	-	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/	/
211	231	N/N	C/C	N/N	C/C	C/C	C/C	C/T	C/C	C/T	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/T	C/C	C/C	C/T	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/C	C/C	-	C/C	C/C	C/T	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	N/N	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	N/N	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/T	C/T	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/C	C/C	C/T	C/T	C/T	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C
371	231	N/N	A/A	A/A	-	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	G/G	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/G	A/G	A/A	A/A	A/A	A/A	A/G	A/G	A/G	A/A	A/A	A/G	A/A	A/G	A/A	A/A	A/A	A/A	A/G	A/A	A/G	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/G	N/N	A/G	A/G	A/A	A/G	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/G	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/G	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/G	A/A	A/A	A/G	A/A	A/A	A/G	A/A	A/G	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/A	A/G	A/A	A/A	A/A
340	232	N/N	N/N	A/A	G/G	A/A	A/G	A/G	A/G	G/G	A/A	A/G	G/G	A/G	A/G	A/G	G/G	G/G	A/A	N/N	G/G	A/G	A/G	N/N	A/G	A/A	G/G	G/G	A/G	A/G	A/G	G/G	G/G	A/A	A/G	A/G	G/G	A/A	A/G	A/G	A/A	A/A	A/G	G/G	A/A	A/G	A/G	A/G	G/G	G/G	A/G	A/G	A/G	A/A	A/G	A/G	N/N	A/A	A/G	A/A	A/G	A/A	A/G	G/G	A/G	G/G	A/A	A/G	A/G	A/G	A/G	A/G	A/A	A/A	A/A	A/G	A/G	A/G	A/G	A/A	G/G	A/A	A/A	G/G	A/A	G/G	G/G	A/A	A/A	A/G	A/G	A/G	G/G	G/G	G/G	G/G	A/G	A/G	A/A	A/G	A/A	A/G	G/G	A/A	A/G	A/G	A/G	A/G	A/G	A/G	A/G	A/A	N/N	G/G	A/G	A/G	A/G	A/A	A/G	N/N	A/G	A/G	G/G	A/A	A/A	A/G	A/A	N/N	A/A	A/G	A/G	A/G	A/A	N/N	A/G	A/A	A/A	A/G	A/G	G/G	A/G	G/G	A/A	A/G	G/G	A/G	A/G	N/N	A/G	G/G	A/A	A/G	A/A	G/G	A/A	A/G	G/G	A/G	G/G	A/A	A/A	A/G	G/G	A/A	G/G	A/G	A/G	G/G	A/A	A/G	G/G	A/G	A/A	G/G	A/G	A/A	A/G	G/G	A/G	A/G	G/G	G/G	A/G	A/G	A/A	A/G	A/A	A/G	A/G	G/G	A/G	N/N	G/G	A/G	A/G	A/A	G/G	A/G	G/G	G/G	A/G	G/G	A/A	G/G	A/G	G/G	A/A	A/G	A/G	A/G	A/G	A/G	A/G	A/G	A/G	A/G	A/A	A/G	A/G	A/G	A/A	G/G	A/A	G/G	A/G	A/A	A/G	A/G	A/G	A/G	A/A	A/A	G/G
383	202	C/C	C/C	C/C	C/C	N/N	-	C/C	C/C	C/C	T/T	C/C	C/T	C/C	-	C/C	C/C	C/C	C/C	C/C	-	C/C	C/C	C/C	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	T/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/T	-	C/C	C/C	C/C	C/C	C/C	-	T/T	C/C	C/C	C/C	T/T	C/C	C/C	-	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/T	C/C	C/C	C/C	T/T	C/C	C/T	C/C	C/C	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	-	C/C	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	N/N	C/C	C/C	C/T	C/C	C/C	C/C	C/C	T/T	C/C	-	C/C	T/T	C/C	C/C	C/C	C/C	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/C	-	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/C	C/C	-	T/T	C/T	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	C/C	-	-	C/C	C/C	C/C	-	-	C/C	C/C	T/T	-	C/C	C/C	C/C	-	C/C	-	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	-	C/C	-	C/C	C/C	-	C/C	C/C	C/C	C/C	C/C	C/C	C/C	T/T	C/C	C/C	C/C	C/C	C/C

I can successfully run radpainter to make a coancestry matrix and then fineradstructure to make an mcmc.xml file, but I cannot seem to get the tree model to work. Here is my command:

finestructure -m T -x 10000 abbrev.populations.haps_chunks.out fineRADstru4.mcmc.xml fineRADstruoutput4.tree.xml

A tree file is produced but with no data in it. The slurm message is:

0%^H^H^H^H# 2%^H^H^H^H# 4%^H^H^H^H# 6%^H^H^H^H# 8%^H^H^H^H# 10%^H^H^H^H# 12%^H^H^H^H# 14%^H^H^H^H# 16%^H^H^H^H# 18%^H^H^H^H# 20%^H^H^H^H# 22%^H^H^H^H# 24%^H^H^H^H# 26%^H^H^H^H# 28%^H^H^H^H#$

Lgamma error: z=-6.99672e+08
terminate called after throwing an instance of 'std::__cxx11::basic_string<char, std::char_traits, std::allocator >'
/var/spool/slurmd/job5454124/slurm_script: line 7: 6780 Aborted finestructure -m T -x 10000 abbrev.populations.haps...

Hi,
I'm running on Ubuntu 20.04 and I'm facing issues with installing fineRADstructure.

I did all the command mentioned on your page :
git clone https://github.com/millanek/fineRADstructure
cd fineRADstructure
./configure

And when i try to enter "make" function, I get this message :
cd . && automake-1.16 --gnu
Makefile.am: error: required file './README' not found
make: *** [Makefile:531 : Makefile.in] Erreur 1

Because this king of error was mentionned as frequent, I ran
aclocal
autoconf
automake -a
And for automake, I received :
*Makefile.am: error: required file './README' not found

I, desesperately, tried to creat a directory in fineRADstructre directory called "README", but obviously, it didn't work.

Do you have any clues for a way that may solve this error ?

Thanks in advance !

PS : I'm a bit new on Linux and in Bash programming...

Hi,
I plan to build a [bio]conda package for fineRADstructure
Can you create a tag release since it's more stable than commit hash?

Thanks