Maximum likelihood demultiplexing
License: GNU General Public License v3.0
I am Gabriel. I am an associate professor in the Department of Health Technology at the Technical University of Denmark 🇩🇰. I am mostly interested in Bayesian/maximum-likelihood methods applied to modern and ancient DNA and sequencing in general.
You will find different repositories for various software I have coded with various collaborators. If you have any trouble (bug, installation, weird results), feel free to create an issue. I accept/welcome pull requests 😉.
Hey @grenaud ,
I am getting this error wheneven I use the "--error" option:
utils.h getCWD failed on d
Not sure if I need this error file but just wanted to report it
Thanks.
The article states the code is freely available under GPL but I could not find any information in the github repo. Could you please add a license file here?
Hello,
are there plans to support demultiplexing of single ended reads?
Hi,
I met the error in make. May I have your help? Thanks!
rm -rf SimpleJSON/
git clone --recursive https://github.com/MJPA/SimpleJSON.git
Cloning into 'SimpleJSON'...
remote: Enumerating objects: 325, done.
remote: Total 325 (delta 0), reused 0 (delta 0), pack-reused 325
Receiving objects: 100% (325/325), 77.23 KiB | 0 bytes/s, done.
Resolving deltas: 100% (162/162), done.
make -C SimpleJSON
make[1]: Entering directory `/home/zzhang78/illumina/deML/SimpleJSON'
g++ -c -Wall src/JSON.cpp -o obj/JSON.o
g++ -c -Wall src/JSONValue.cpp -o obj/JSONValue.o
g++ -c -Wall src/demo/nix-main.cpp -o obj/demo/nix-main.o
g++ -c -Wall src/demo/example.cpp -o obj/demo/example.o
g++ -c -Wall src/demo/testcases.cpp -o obj/demo/testcases.o
g++ -lm obj/JSON.o obj/JSONValue.o obj/demo/nix-main.o obj/demo/example.o obj/demo/testcases.o -o JSONDemo
make[1]: Leaving directory `/home/zzhang78/illumina/deML/SimpleJSON'
rm -rf bamtools/
git clone --recursive https://github.com/pezmaster31/bamtools.git
Cloning into 'bamtools'...
remote: Enumerating objects: 4857, done.
remote: Total 4857 (delta 0), reused 0 (delta 0), pack-reused 4857
Receiving objects: 100% (4857/4857), 6.06 MiB | 8.49 MiB/s, done.
Resolving deltas: 100% (3373/3373), done.
cd bamtools/ && mkdir -p build/ && cd build/ && cmake .. && make && cd ../..
CMake Error at CMakeLists.txt:9 (cmake_minimum_required):
CMake 3.0 or higher is required. You are running version 2.8.12.2
-- Configuring incomplete, errors occurred!
make: *** [bamtools/build/src/api/libbamtools.a] Error 1
Hello,
I have a similar query as in this biostar question that hasn't been answered yet.
https://www.biostars.org/p/342946/
I don't get an error per say but just making sure that the tool is compatible with dual indexed adapters where the combination of the indexes in unique but they might not be unique by themselves.
Would really appreciate any feedback!
Thanks.
..
Would be possible to accept index with aNy base?
Thanks!
Hi again,
I have questions for a couple of scenarios that are similar:
I have an index file where the first 11 bases are the barcode, then there are the UMI reads. I only need to use the barcode to demultiplex. Is it better if I trim the index reads to only contain the first 11 bases or does it not matter? Does deML look across the whole index read for matches?
In another extreme scenario, I have an index read that has basically 11 bases barcode then the rest are read into the adapter for a total of 125bp index reads. How would you advise to proceed when the index reads contains more information than just the barcode?
Thanks!
Hi, is it possible to avoid the additional prefix when demultiplexing fastq files? I would like the output files to have as prefix the name assigned in the index file. When i put a folder name as output, all the files end up starting with underscore.
Would it be possible to tag a release? I would like to add deML to the Bioconda project.
Hi,
My colleagues got some error messages when he helped me to install deML on the cluster. He told me there were no functions returnOpenFileDescriptors and returnOpenFileDescriptorsMax declared when he tried to build the source code. Here are the error messages he attached to me:
deML.cpp: In function ‘void checkFD()’:
deML.cpp:587:43: error: ‘returnOpenFileDescriptors’ was not declared in this scope
int rofd = returnOpenFileDescriptors();
^
deML.cpp:588:46: error: ‘returnOpenFileDescriptorsMax’ was not declared in this scope
int rofdM = returnOpenFileDescriptorsMax();
We couldn't find information regarding this issue online. Could you please help me to take a look at it? Thanks a lot!
Hi,
Thanks so much for creating this software. Just now I tried to demultiplex my data very quickly. But the output makes me confusing. Since many outputs I did not expected, shown in figure below. I only have one index.fq
Some fail.fq, some unknow.fq. which make me confusing.
The code I am using is src/deML -i index.txt -f sample_S0_L001_R1_001.fastq -r sample_S0_L001_R2_001.fastq -if1 sample_S0_L001_I1_001.fastq -o demultiplexed.
The format of my fq input files are shown in the picture below. May I know are there anything wrong? Thanks so much.
And my index file
Hello,
I'm getting a compilation error
/home/jkimsis/install/deML/bamtools/src/api/internal/bam/BamMultiMerger_p.h:135:18: required from ?void BamTools::Internal::MultiMerger::Add(BamTools::Internal::MergeItem) [with Compare = BamTools::Algorithms::Sort::ByPosition]?
/home/jkimsis/install/deML/bamtools/src/api/internal/bam/BamMultiMerger_p.h:128:13: required from here
/usr/include/c++/12/bits/stl_tree.h:770:15: error: static assertion failed: comparison object must be invocable as const
/usr/include/c++/12/bits/stl_tree.h:770:15: note: ?std::is_invocable_v<const BamTools::Internal::MergeItemSorterBamTools::Algorithms::Sort::ByPosition&, const BamTools::Internal::MergeItem&, const BamTools::Internal::MergeItem&>? evaluates to false
make[3]: *** [src/api/CMakeFiles/BamTools.dir/build.make:244: src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o] Error 1
make[3]: Leaving directory '/home/jkimsis/install/deML/bamtools/build'
make[2]: *** [CMakeFiles/Makefile2:318: src/api/CMakeFiles/BamTools.dir/all] Error 2
make[2]: Leaving directory '/home/jkimsis/install/deML/bamtools/build'
make[1]: *** [Makefile:136: all] Error 2
make[1]: Leaving directory '/home/jkimsis/install/deML/bamtools/build'
make: *** [Makefile:32: bamtools/build/src/api/libbamtools.a] Error 2
I've already found a similar issue in an unrelated git, which was solved by using g++ 8 instead of of a newer one. Is there a way to fix this or should I just try to get the older g++ version?
Hi Gerard,
I was hoping to use deML to recover reads from the undetermined*.fastq.gz, after running bcl2fastq2.
On Ubuntu 22.04 (with git 2.34.1 & cmake 3.22.1), I get the following, when running make:
rm -rf SimpleJSON/
git clone --recursive https://github.com/MJPA/SimpleJSON.git
Cloning into 'SimpleJSON'...
remote: Enumerating objects: 325, done.
remote: Total 325 (delta 0), reused 0 (delta 0), pack-reused 325
Receiving objects: 100% (325/325), 77.22 KiB | 2.34 MiB/s, done.
Resolving deltas: 100% (162/162), done.
make -C SimpleJSON
make[1]: Entering directory '/home/schimar/bio/deML/SimpleJSON'
g++ -c -Wall src/JSON.cpp -o obj/JSON.o
g++ -c -Wall src/JSONValue.cpp -o obj/JSONValue.o
g++ -c -Wall src/demo/nix-main.cpp -o obj/demo/nix-main.o
g++ -c -Wall src/demo/example.cpp -o obj/demo/example.o
g++ -c -Wall src/demo/testcases.cpp -o obj/demo/testcases.o
g++ -lm obj/JSON.o obj/JSONValue.o obj/demo/nix-main.o obj/demo/example.o obj/demo/testcases.o -o JSONDemo
make[1]: Leaving directory '/home/schimar/bio/deML/SimpleJSON'
cd bamtools/ && git reset --hard d24d850de17134fe4e7984b26493c5c0a1844b35 && mkdir -p build/ && cd build/ && if cmake ..; then echo ""; else if cmake3 ..; then echo ""; else echo "cmake failed, please install cmake v3"; fi fi && make && cd ../..
HEAD is now at d24d850 Cut 2.5.1 release
CMake Deprecation Warning at CMakeLists.txt:20 (cmake_policy):
The OLD behavior for policy CMP0042 will be removed from a future version
of CMake.
The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.
-- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE)
-- Checking for one of the modules 'jsoncpp>=1'
Did NOT find system JsonCpp, instead using bundled version
-- Configuring done
-- Generating done
-- Build files have been written to: /home/schimar/bio/deML/bamtools/build
make[1]: Entering directory '/home/schimar/bio/deML/bamtools/build'
make[2]: Entering directory '/home/schimar/bio/deML/bamtools/build'
make[3]: Entering directory '/home/schimar/bio/deML/bamtools/build'
make[3]: Leaving directory '/home/schimar/bio/deML/bamtools/build'
make[3]: Entering directory '/home/schimar/bio/deML/bamtools/build'
make[3]: Leaving directory '/home/schimar/bio/deML/bamtools/build'
[ 0%] Built target SharedHeaders
make[3]: Entering directory '/home/schimar/bio/deML/bamtools/build'
Consolidate compiler generated dependencies of target BamTools
make[3]: Leaving directory '/home/schimar/bio/deML/bamtools/build'
make[3]: Entering directory '/home/schimar/bio/deML/bamtools/build'
[ 1%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o
In file included from /usr/include/c++/11/map:60,
from /home/schimar/bio/deML/bamtools/src/api/BamMultiReader.h:13,
from /home/schimar/bio/deML/bamtools/src/api/internal/bam/BamMultiReader_p.h:25,
from /home/schimar/bio/deML/bamtools/src/api/internal/bam/BamMultiReader_p.cpp:10:
/usr/include/c++/11/bits/stl_tree.h: In instantiation of ‘static const _Key& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_S_key(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Const_Link_type) [with _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Const_Link_type = const std::_Rb_tree_node<BamTools::Internal::MergeItem>*]’:
/usr/include/c++/11/bits/stl_tree.h:2102:44: required from ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_equal_pos(const key_type&) [with _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::key_type = BamTools::Internal::MergeItem]’
/usr/include/c++/11/bits/stl_tree.h:2151:4: required from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_equal(_Arg&&) [with _Arg = const BamTools::Internal::MergeItem&; _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator = std::_Rb_tree<BamTools::Internal::MergeItem, BamTools::Internal::MergeItem, std::_Identity<BamTools::Internal::MergeItem>, BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>, std::allocator<BamTools::Internal::MergeItem> >::iterator]’
/usr/include/c++/11/bits/stl_multiset.h:503:36: required from ‘std::multiset<_Key, _Compare, _Alloc>::iterator std::multiset<_Key, _Compare, _Alloc>::insert(const value_type&) [with _Key = BamTools::Internal::MergeItem; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; std::multiset<_Key, _Compare, _Alloc>::iterator = std::_Rb_tree<BamTools::Internal::MergeItem, BamTools::Internal::MergeItem, std::_Identity<BamTools::Internal::MergeItem>, BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>, std::allocator<BamTools::Internal::MergeItem> >::const_iterator; std::multiset<_Key, _Compare, _Alloc>::value_type = BamTools::Internal::MergeItem]’
/home/schimar/bio/deML/bamtools/src/api/internal/bam/BamMultiMerger_p.h:135:18: required from ‘void BamTools::Internal::MultiMerger<Compare>::Add(BamTools::Internal::MergeItem) [with Compare = BamTools::Algorithms::Sort::ByName]’
/home/schimar/bio/deML/bamtools/src/api/internal/bam/BamMultiMerger_p.h:128:13: required from here
/usr/include/c++/11/bits/stl_tree.h:770:15: error: static assertion failed: comparison object must be invocable as const
770 | is_invocable_v<const _Compare&, const _Key&, const _Key&>,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_tree.h:770:15: note: ‘std::is_invocable_v<const BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByName>&, const BamTools::Internal::MergeItem&, const BamTools::Internal::MergeItem&>’ evaluates to false
/usr/include/c++/11/bits/stl_tree.h: In instantiation of ‘static const _Key& std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_S_key(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Const_Link_type) [with _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Const_Link_type = const std::_Rb_tree_node<BamTools::Internal::MergeItem>*]’:
/usr/include/c++/11/bits/stl_tree.h:2102:44: required from ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_equal_pos(const key_type&) [with _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::key_type = BamTools::Internal::MergeItem]’
/usr/include/c++/11/bits/stl_tree.h:2151:4: required from ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_equal(_Arg&&) [with _Arg = const BamTools::Internal::MergeItem&; _Key = BamTools::Internal::MergeItem; _Val = BamTools::Internal::MergeItem; _KeyOfValue = std::_Identity<BamTools::Internal::MergeItem>; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator = std::_Rb_tree<BamTools::Internal::MergeItem, BamTools::Internal::MergeItem, std::_Identity<BamTools::Internal::MergeItem>, BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>, std::allocator<BamTools::Internal::MergeItem> >::iterator]’
/usr/include/c++/11/bits/stl_multiset.h:503:36: required from ‘std::multiset<_Key, _Compare, _Alloc>::iterator std::multiset<_Key, _Compare, _Alloc>::insert(const value_type&) [with _Key = BamTools::Internal::MergeItem; _Compare = BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>; _Alloc = std::allocator<BamTools::Internal::MergeItem>; std::multiset<_Key, _Compare, _Alloc>::iterator = std::_Rb_tree<BamTools::Internal::MergeItem, BamTools::Internal::MergeItem, std::_Identity<BamTools::Internal::MergeItem>, BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>, std::allocator<BamTools::Internal::MergeItem> >::const_iterator; std::multiset<_Key, _Compare, _Alloc>::value_type = BamTools::Internal::MergeItem]’
/home/schimar/bio/deML/bamtools/src/api/internal/bam/BamMultiMerger_p.h:135:18: required from ‘void BamTools::Internal::MultiMerger<Compare>::Add(BamTools::Internal::MergeItem) [with Compare = BamTools::Algorithms::Sort::ByPosition]’
/home/schimar/bio/deML/bamtools/src/api/internal/bam/BamMultiMerger_p.h:128:13: required from here
/usr/include/c++/11/bits/stl_tree.h:770:15: error: static assertion failed: comparison object must be invocable as const
/usr/include/c++/11/bits/stl_tree.h:770:15: note: ‘std::is_invocable_v<const BamTools::Internal::MergeItemSorter<BamTools::Algorithms::Sort::ByPosition>&, const BamTools::Internal::MergeItem&, const BamTools::Internal::MergeItem&>’ evaluates to false
make[3]: *** [src/api/CMakeFiles/BamTools.dir/build.make:244: src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o] Error 1
make[3]: Leaving directory '/home/schimar/bio/deML/bamtools/build'
make[2]: *** [CMakeFiles/Makefile2:318: src/api/CMakeFiles/BamTools.dir/all] Error 2
make[2]: Leaving directory '/home/schimar/bio/deML/bamtools/build'
make[1]: *** [Makefile:136: all] Error 2
make[1]: Leaving directory '/home/schimar/bio/deML/bamtools/build'
make: *** [Makefile:32: bamtools/build/src/api/libbamtools.a] Error 2
Thanks for your help!
All the best,
Martin
While running make I get the following error:
g++ -Wall -lm -O3 -I. -Igzstream/ -I/home/users/xxx/deML-master/bamtools/build/src/api/include/ -I/home/users/xxx/deML-master/bamtools/build/src/include/ -c ReconsReferenceBAM.cpp -o ReconsReferenceBAM.o
In file included from ReconsReferenceBAM.cpp:8:0:
ReconsReferenceBAM.h:14:10: fatal error: api/BamMultiReader.h: No such file or directory
#include "api/BamMultiReader.h"
^~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
Makefile:45: recipe for target 'ReconsReferenceBAM.o' failed
make[1]: *** [ReconsReferenceBAM.o] Error 1
Hello,
do you have a preferred way to cite deML?
Hey,
The program runs great. However, when I test the quality of the output files with gzip -t I get the following error "unexpected end of file". When I look up the meaning of the error the googles tells me that it means my file is corrupt. However, when i check the input file, everything is fine. So, Im not sure how to proceed. Thanks for any advise you can give
On Mac, seems to have compiled correctly. But get error on the test data, I don't think it is permissions issue.
src/deML -i testData/index.txt -f testData/todemultiplex.fq1.gz -r testData/todemultiplex.fq2.gz -if1 testData/todemultiplex.i1.gz -if2 testData/todemultiplex.i2.gz -o testData/
Conflicts for index1:
AGTCAGA from RG9 causes a conflict with RG57
AACTAGA from RG10 causes a conflict with RG58
CTATGGC from RG11 causes a conflict with RG59
CGACGGT from RG12 causes a conflict with RG60
AACCAAG from RG13 causes a conflict with RG61
CGGCGTA from RG14 causes a conflict with RG62
GCAGTCC from RG15 causes a conflict with RG63
CTCGCGC from RG16 causes a conflict with RG64
CTGCGAC from RG17 causes a conflict with RG65
ACGTATG from RG18 causes a conflict with RG66
ATACTGA from RG19 causes a conflict with RG67
AGTCAGA from RG57 causes a conflict with RG9
AACTAGA from RG58 causes a conflict with RG10
CTATGGC from RG59 causes a conflict with RG11
CGACGGT from RG60 causes a conflict with RG12
AACCAAG from RG61 causes a conflict with RG13
CGGCGTA from RG62 causes a conflict with RG14
GCAGTCC from RG63 causes a conflict with RG15
CTCGCGC from RG64 causes a conflict with RG16
CTGCGAC from RG65 causes a conflict with RG17
ACGTATG from RG66 causes a conflict with RG18
ATACTGA from RG67 causes a conflict with RG19
Conflicts for index2:
AATTCAA from RG1 causes a conflict with RG57
CGCGCAG from RG2 causes a conflict with RG58
AAGGTCT from RG3 causes a conflict with RG59
ACTGGAC from RG4 causes a conflict with RG60
AGCAGGT from RG5 causes a conflict with RG61
GTACCGG from RG6 causes a conflict with RG62
GGTCAAG from RG7 causes a conflict with RG63
AATGATG from RG8 causes a conflict with RG64
AGTCAGA from RG9 causes a conflict with RG65
AACTAGA from RG10 causes a conflict with RG66
CTATGGC from RG11 causes a conflict with RG67
AGTCAGA from RG57 causes a conflict with RG1
AACTAGA from RG58 causes a conflict with RG2
CTATGGC from RG59 causes a conflict with RG3
CGACGGT from RG60 causes a conflict with RG4
AACCAAG from RG61 causes a conflict with RG5
CGGCGTA from RG62 causes a conflict with RG6
GCAGTCC from RG63 causes a conflict with RG7
CTCGCGC from RG64 causes a conflict with RG8
CTGCGAC from RG65 causes a conflict with RG9
ACGTATG from RG66 causes a conflict with RG10
ATACTGA from RG67 causes a conflict with RG11
Conflicts for pairs:
Cannot write to file testData/_RG49_r1.fail.fq.gz either you do not have permissions or you have too many read groups, in that case, convert your input data to a single BAM file and demultiplex it
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