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View Code? Open in Web Editor NEWA package for population structure inference from RAD-seq data
Home Page: https://www.milan-malinsky.org/fineradstructure
License: Other
A package for population structure inference from RAD-seq data
Home Page: https://www.milan-malinsky.org/fineradstructure
License: Other
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,
ignore
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?
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
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
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
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:
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...
fineRADstructure/Stacks2fineRAD.py
Line 56 in 1720ff1
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
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!
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 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
43 232 / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
61 232 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/A A/A A/A A/A A/A A/A 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/A A/A A/A A/A A/G A/G G/G A/G A/A A/A A/A A/A A/A A/A G/A A/A A/G 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/A A/A A/A A/A A/A A/A A/A A/A A/A A/A 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/G 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/A A/A A/A A/A A/G A/G 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 N/N 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/A A/A A/A A/G G/A A/A A/A A/G A/G A/G 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/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/A G/G A/A A/G A/G A/A A/A A/G 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/G G/A A/A 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/G A/A A/G A/A
94 232 / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / / /
95 210 / / / - / / / / / / / / - / / / / / / - / - / / / / / / / / / / / - / / / / / / / / / / / / / / / / / / / / / / - / / / / / / / / / - / / / / / / / / - / / / / - / / / / / / / / / / / / / / / / / - / / / / / / / - - / / / - / / / / / / / / / / / / / / / / / / - / / - / - / / - / / / / / / / / / / / / / / / / / / / / / / / / / - / - / / / / / / / / / / / / / / / / / / / / / / / / / / / / - / / / / / / / / / / / / / / / / / - / / / / / / / / / / / / / / - / / /
153 231 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 C/C C/C C/C 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/T C/C C/C C/T C/C C/T 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/T 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/T 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/T C/C C/C C/T C/C C/C C/C C/C N/N C/T C/C C/C C/C C/C C/T C/T C/C C/C - C/C C/C C/C C/C C/C C/T C/C C/C C/C N/N 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/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/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/T C/C C/C C/C C/C C/T C/C T/T 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/T 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/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/T C/C C/C C/C
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
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 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
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.
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.
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!
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?
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!
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 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:
+ 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:
BTW my dataset has 150 samples and the input filtered VCF before processing by stacks had 400k SNPs.
Thanks for any help
Jan
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! 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!
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...
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 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
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