ncbi / ngs-tools

ngs-tools

Quick instructions for building and installing ngs-tools from source.

1. Create an ncbi source directory if needed. While this is not strictly required, our configuration scripts will benefit by being able to locate related projects without asking for explicit paths:

$ mkdir ncbi

2. Check out the sources:

$ cd ncbi

$ git clone https://github.com/ncbi/ngs-tools.git

3. If you have not yet installed ncbi-vdb, please do so now:

$ git clone https://github.com/ncbi/ncbi-vdb.git

and follow directions at [https://github.com/ncbi/ncbi-vdb/wiki/Building-and-Installing-from-Source] (https://github.com/ncbi/ncbi-vdb/wiki/Building-and-Installing-from-Source) .

4. Configure the build:

$ cd ngs-tools

$ ./configure

By default, configure will select a build-output directory under your $HOME and will install under /usr/local/ncbi/ngs-tools on Linux. The default settings can be changed, of course. For all options, you can run:

$ ./configure --help

5. Make the tools:

$ make

6. Install the tools as admin (you may be asked for a password):

$ sudo make install

At this point, the installation should be complete, although you will probably have to login again before all changes take place. If the installation is successful, you should find executables installed and an update to shell variables (only AFTER logging in again). To verify update of your environment:

$ echo $PATH # should now have the path to your installed ngs-tools, and

$ which sra-search # should return the location of this utility.

ngs-tools's Issues

configure finds ncbi-vdb libraries, but not includes

I'm installing ngs-tools 3.0.0 on a shared cluster environment where applications live on a network-mounted directory. I have compiled and installed ncbi-vdb 3.0.0 successfully and specified the location to configure using the --with-ncbi-vdb-build option:

$ ./configure --with-ncbi-vdb-build=/export/apps/ncbi-vdb/3.0.0 --prefix=/export/apps/ngs-tools/3.0.0 --debug
...
checking for ncbi-vdb package...        libraries... 
                checking /export/apps/ncbi-vdb/3.0.0/linux/gcc/x86_64/rel/lib/libncbi-vdb.a
                checking /export/apps/ncbi-vdb/3.0.0/lib64/libncbi-vdb.a
        /export/apps/ncbi-vdb/3.0.0/lib64
                not found ../ncbi-vdb
                not found /usr/local/ncbi/ncbi-vdb
                not found /home/aorth/ncbi/ncbi-vdb
no
                ncbi-vdb: includes: ; libs: /export/apps/ncbi-vdb/3.0.0/lib64; ilibs: not needed
configure: error: required ncbi-vdb package not found.

Why does the configure script look for the ncbi-vdb includes in a different location than the libs? The libs and includes were installed in the same place by ncbi-vdb's own install script:

$ ls -l /export/apps/ncbi-vdb/3.0.0/
total 8
drwxrwxr-x. 34 aorth aorth 4096 Mar 17 15:26 include/
drwxrwxr-x.  3 aorth aorth 4096 Mar 17 15:25 lib64/

I can edit setup/package.prl to look for the includes in the correct location for this system... but I'm wondering why?

Taxonomy analysis on SRA submission inconsistent

Case Information:
Case #: CAS-1078261-J6B3G5
Customer Name: Bergsagel, Leif, M.D.
Customer Email: [email protected]
Case Created: 3/12/2023, 3:33:05 AM

Summary: PRJNA938752

Details:
I have had a problem with Taxonomy analysis of murine samples I have submitted to SRA. I submitted multiple RNAseq, wxs and low pass mate-pair WGS aligned to GRCm39, which were all correctly identified as mus musculus. However, all of the regular WGS files were not identified as mus musculus, with no predominant organisms Identified. Independently I discovered that one of the samples (SRR23619415) contained a sequence from human chrY, and in fact the taxonomy analysis correctly identified 0.32% homo sapiens in that sample, but did not identify the predominant mus musculus sequences. Can you help correct this?

Wgs https://dataview.ncbi.nlm.nih.gov/object/SRR23619373 0.08% mus caroli
wgs https://dataview.ncbi.nlm.nih.gov/object/SRR23619415 0.32% homo sapiens

mate-pair https://dataview.ncbi.nlm.nih.gov/object/SRR23619250 70.62% mus musculus
wxs https://dataview.ncbi.nlm.nih.gov/object/SRR23619426 71.95% mus musculus
RNAseq https://dataview.ncbi.nlm.nih.gov/object/SRR23619404 55.01% mus musculus

Response from NLM
From: NLM Support [email protected]
Date: Tuesday, March 14, 2023 at 9:46 AM
To: Bergsagel, Leif, M.D. [email protected]
Subject: [EXTERNAL] Re: case #CAS-1078261-J6B3G5: PRJNA938752 TRACKING:000414000018578
We cannot fix taxonomy analysis produced by software.
Perhaps you sample was contaminated?

How does "merge_kingdoms" mentioned in the "build_db_and_run.sh" script work?

Hello,

I'm trying to use the STAT tools to build a database from fasta sequences, and then using it to do metagenomics/taxonomic analyses.
So I'm following the tutorial in the build_db_and_run.sh script.
It says that we can do the identify_tax_ids part in multiple instances, but if we do, we have to use the tool called merge_kingdoms to combine results into a single file.
My problem is that there is no informations about the use of this tool.
The help of the tool is : need <tax.parents>
I don't understand what I should put in each argument (except for tax.parents).

Also, I'm using the default parameters :
KMER_LEN=32
DENSE_WINDOW=4 # 1 kmer of 4 for dense db (just for example)
SPARSE_WINDOW=128 # 1 kmer of 128 for sparse db (just for example)
But I don't know if I really should ?

Same question for MAX_KMER_DICTIONARY_SIZE=5000000 # This number should be roughly as max kmers expected * 2.
I don't really know how I could know the maximum number of kmers expected.

Thank you in advance !

genes.jar not found

Hi, I followed the installation from the closed issue, and I was able to configure ngs/ ngs-tools/ and ncbi-vdb/ and sra-tools/. However, in the README for spark_genes it says I should have a genes.jar file along with other installations. If I can't find genes.jar does that mean I compiled wrong last time and is there installation instructions for the 3 dependencies listed? Thanks!

CMake Error: The source directory "/home/shutovo/test/ngs-tools" does not exist.

While trying to install STAT using the instructions here, I run across a problem running make in these steps:

cd ngs-tools
./configure
make -C tools/tax

The error looks like this:

/usr/bin/cmake -H/home/shutovo/test/ngs-tools -B/home/shutovo/test/ngs-tools/tools/tax --check-build-system
CMakeFiles/Makefile.cmake 0
CMake Error: The source directory "/home/shutovo/test/ngs-tools" does not exist.
Specify --help for usage, or press the help button on the CMake GUI.
make: *** [cmake_check_build_system] Error 1
make: Leaving directory `/home/ec2-user/src/ngs-tools/tools/tax' 

It is true; /home/shutovo/test/ngs-tools does not exist. Should it? Can anyone help me figure out how to fix this?

Here's some system info:
NAME="Amazon Linux" VERSION="2"
and kernel info:
Linux 4.14.232-177.418.amzn2.x86_64 #1 SMP Tue Jun 15 20:57:50 UTC 2021

cmake version 2.8.12.2
gcc (GCC) 7.3.1 20180712 (Red Hat 7.3.1-13)
Apache Ant(TM) version 1.9.2 compiled on November 13 2017

Thanks!

Way to access NCBI STAT data in bulk

Hi,
I'm wondering is there any way to access the taxonomic data that STAT is automatically generating on each NCBI run? Every metagenomic upload on the SRA has this analysis generated and displayed as a Krona, but is there a route by which we could download this data in simple text form for playing around with association rule mining?

Also, is there a roadmap or website besides github anywhere dedicated to this project? Is there anywhere people can find more information about STAT like who works on it or what your future goals for it might be?

Thanks!
-Pete

Make this work with NCBI .gff3 files

Hi! We are going to be using this a lot in the NCBI-assisted Boston Genomics Hackathon at Brandeis on April 25-27. Could we make this work with NCBI gff3 files before that?

Cheers!

Ben

Any recomendation for the two WINDOW parameters? for tools/tax (STAT)

I did download parts of the RefSeq DB (e.g. refseq/fungi) and now I want to build the STAT DB (tools/tax) as described in "examples/".
I am a bit lost when specifying the hyperparameters DENSE_ and SPARSE_WINDOW. From the paper, I think a KMER_LEN=32 should be optimal but the WINDOW parameters are not described (or I missed it).

KMER_LEN=32;
DENSE_WINDOW=4;
SPARSE_WINDOW=128; 

The examples files are all virus genomes, so these values probably are not correct for invertebrates or fungi.
How do I find out what to use, do you have any hints?
I know that SRA (within the run-browser) offers this service and parses any dataset but I don't know what parameters are used.

vdb-search.cpp:(.text+0x21d7): undefined reference

attempting to build ngs-tools. I use the following configure command from a clone of the ngs-tools repo.

$ ./configure --prefix /dev/shm/packages/ngs-tools-2.8.2 --build-prefix=/dev/shm/ncbi/build --with-ngs-sdk-prefix=/usr/local/packages/ngs-sdk-1.3.0 --with-ncbi-vdb-build=/usr/local/src/ncbi-vdb/ncbi-vdb-2.8.2/rhel6x86_64/ncbi-vdb-master/builddir/ncbi-vdb --with-ncbi-vdb-sources=/usr/local/src/ncbi-vdb/ncbi-vdb-2.8.2/rhel6x86_64/ncbi-vdb-master
Configuring NGS-TOOLS package
checking system type... Linux
checking OS distributor... CentOS
checking machine architecture... x86_64
checking for supported architecture... x86_64 (64 bits) is supported
checking for supported OS... Linux (linux) is supported
checking for supported tool chain... gcc tool chain is supported
checking for g++... yes
checking whether gcc accepts -Wno-array-bounds... yes
checking whether g++ accepts -static-libstdc++... yes
checking for ngs-sdk package...
        includes... /usr/local/packages/ngs-sdk-1.3.0
        libraries... /usr/local/packages/ngs-sdk-1.3.0/lib64
includes: /usr/local/packages/ngs-sdk-1.3.0/include
libraries: /usr/local/packages/ngs-sdk-1.3.0/lib64
checking for ncbi-vdb package source files and build results...
        includes... /usr/local/src/ncbi-vdb/ncbi-vdb-2.8.2/rhel6x86_64/ncbi-vdb-master
        libraries... /usr/local/src/ncbi-vdb/ncbi-vdb-2.8.2/rhel6x86_64/ncbi-vdb-master/builddir/ncbi-vdb/linux/gcc/x86_64/rel/ilib
includes: /usr/local/src/ncbi-vdb/ncbi-vdb-2.8.2/rhel6x86_64/ncbi-vdb-master/interfaces
libraries: /usr/local/src/ncbi-vdb/ncbi-vdb-2.8.2/rhel6x86_64/ncbi-vdb-master/builddir/ncbi-vdb/linux/gcc/x86_64/rel/lib
ilibraries: /usr/local/src/ncbi-vdb/ncbi-vdb-2.8.2/rhel6x86_64/ncbi-vdb-master/builddir/ncbi-vdb/linux/gcc/x86_64/rel/ilib

configure: creating 'build/ld.linux.exe_cmd.sh'
configure: creating 'build/Makefile.config.linux.x86_64'
configure: creating 'Makefile.config'
configure: creating 'reconfigure'
build type: release
build prefix: /dev/shm/ncbi/build/ngs-tools
build output path: /dev/shm/ncbi/build/ngs-tools/linux/gcc/x86_64/rel
includedir: /dev/shm/packages/ngs-tools-2.8.2/include
bindir: /dev/shm/packages/ngs-tools-2.8.2/bin
libdir: /dev/shm/packages/ngs-tools-2.8.2/lib
CC = gcc -c
CPP = g++
configured with: "'--prefix' '/dev/shm/packages/ngs-tools-2.8.2' '--build-prefix=/dev/shm/ncbi/build' '--with-ngs-sdk-prefix=/usr/local/packages/ngs-sdk-1.3.0' '--with-ncbi-vdb-build=/usr/local/src/ncbi-vdb/ncbi-vdb-2.8.2/rhel6x86_64/ncbi-vdb-master/builddir/ncbi-vdb' '--with-ncbi-vdb-sources=/usr/local/src/ncbi-vdb/ncbi-vdb-2.8.2/rhel6x86_64/ncbi-vdb-master'"

Make errors out with the following...

$ make
...
vdb-search.cpp:(.text+0x21d7): undefined reference to `ReferenceMatchIterator::ReferenceMatchIterator(SearchBlock::Factory&, std::string const&, std::vector<ReferenceSpec, std::allocator<ReferenceSpec> > const&, bool)'
collect2: error: ld returned 1 exit status
make[2]: *** [/dev/shm/ncbi/build/ngs-tools/linux/gcc/x86_64/rel/bin/sra-search] Error 1
make[2]: Leaving directory `/dev/shm/ncbi/ngs-tools/tools/sra-search'
make[1]: *** [std] Error 2
make[1]: Leaving directory `/dev/shm/ncbi/ngs-tools/tools/sra-search'
make: *** [tools/sra-search] Error 2

I'm running on CentOS6.7.

Relationship between the STAT analysis data available on the NCBI SRA Run Browser and that on the cloud platform

I am writing to seek your assistance with a question regarding the Cloud-based Taxonomy Analysis Information Table.

I noticed a discrepancy between the “identified_spot_count” available on the cloud platform and the "IDENTIFIED READS" displayed on the Sequence Read Archive Run Browser. For instance, in the case of ERR979125 on the Run Browser, 97.1% of the reads are listed as being of human origin (https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=ERR979125&display=analysis).

However, the data retrieved from the cloud shows the following:

• Identified Spot Count: 1945935
• Analyzed Spot Count: 12149592
• Total Spot Count: 789675109

Regardless of whether the denominator is the “analyzed_spot_count” or the “total_spot_count”, the percentages are significantly lower than those reported on the Run Browser (16.0% and 0.24%).

Could you kindly clarify the relationship between the data available on the Run Browser and that on the cloud platform?

I appreciate your assistance and look forward to your response.

Error at tax_analysis_parser

Hi there,

I have managed to run through most of the workflow and I created a sparse/dense databases and ran my samples through the 2 step analysis.

When I try to run hits-to-report.sh at the end, I get an error from the tax_analysis_parser.py as seen below:

I tried to manipulate the entrys (a.e. remove any colon (:) and so) but I still get error that hits are not sorted. But the sort commands proceeds all of this.

Traceback (most recent call last):
File "./bin/tax_analysis_parser.py", line 242, in
main()
File "./bin/tax_analysis_parser.py", line 237, in main
xml = parse(f, conn, args.wgs_mode, args.compact, args.include_tax_id or [])
File "./bin/tax_analysis_parser.py", line 196, in parse
for hits in iterate_merged_spots(f):
File "./bin/tax_analysis_parser.py", line 128, in iterate_merged_spots
assert last_spot <= spot, 'input is not sorted'
AssertionError: input is not sorted

Please let me know if you have any insight to why this may happen.

Thanks,

tax tool cannot compile

I know this is not released yet, but it would be nice to try it out and the online instuctions to install do not work:

git clone https://github.com/ncbi/ngs-tools.git --branch tax
cd ./ngs-tools/tools/tax
make Makefile
and in ./examples folder you can find helper *.sh scripts

$make Makefile
/bin/ngs-tools/build/Makefile.shell:27: *** "*** File '/bin/ngs-tools/build/Makefile.config' is missing. Please run /bin/ngs-tools/build/configure". Stop.

/bin/ngs-tools/build/configure: No such file or directory

Explain/Show general workflow for NCBI SRA Taxonomy Analysis Tool (STAT)

I was able to install this program.

However, It is hard to figure out which script/binary need to run first?
For example, do we need to download the list of taxonomy IDS in order to build an index?
What is tax.parents in the build_db_from_sequence_tree.sh?

It will be really helpful to add documentation about general flow of this program.

Thank you!

a couple of problems on CentOS 8

There are a couple of small issues when building ngs-sdk on CentOS 8.

(1) In $TOPDIR/share/examples-java/Makefile NGS_CLASS_PATH is defined but the javac line is:

javac $(DEBUGGING) $^ -d .
when it needs to be:

javac -classpath $(NGS_CLASS_PATH) $(DEBUGGING) $^ -d .
This may be related to (5), below, as there was no CLASSPATH defined in the environment.

(2) In the source directories ngs-python/Makefile.python refers to "python", but there is no such beast on RH derivatives, only python2 or python3. The file was modified to use "python3".

(3) On the system in question the python packages are installed into /usr/common/lib/python3.6/site-packages (which is NFS shared with other machines) by setting PYTHONPATH to that value. The supplied Makefile in that directory ignored PYTHONPATH, so installation was done manually by:

cd /usr/common/src/ncbi/ngs/ngs-python
python3 setup.py  install --prefix=/usr/common 2>&1 \
      | tee ../install_python_2020_05_11.log

The default installation of the ngs python pieces goes into "~/.local".

(4) The build leaves a large directory ~/ncbi-outdir even after installation.
This directory is not discussed at all in the installation instructions:

https://github.com/ncbi/ngs/wiki/Building-and-Installing-from-Source

This should be documented, especially a comment about when it is safe to remove it.

(5) The installation instructions end with:

At this point, the installation should be complete, although you will probably have to login again before all changes take place. If the installation is successful, you should find library code installed and an update to shell variables (only AFTER logging in again). To verify update of your environment:
$ echo $LD_LIBRARY_PATH # should now have the path to your installed ngs libraries
$ echo $CLASSPATH # should now have the path to your installed ngs jar

I do not see any modifications to login configuration files (nor would I want the installation to do that automatically.) In a newly logged in session, after installation, neither LD_LIBRARY_PATH nor CLASSPATH were set as indicated. If this was supposed to happen with one of the "make install" steps, that must have failed.

Linking error during sra-search build

Hi,

I'm getting linking error trying to build ngs-tools.

> make

make[1]: Entering directory `/home/zilek2/ngs/ngs-tools/ngs-vdb/src'
make /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib/ngs-vdb
make[2]: Entering directory `/home/zilek2/ngs/ngs-tools/ngs-vdb/src'
ar rc /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib/libngs-vdb.a /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ngs-vdb/src/FragmentBlob.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ngs-vdb/src/FragmentBlobIterator.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ngs-vdb/src/NGS-VDB.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ngs-vdb/src/VdbReadCollection.o
make[2]: Leaving directory `/home/zilek2/ngs/ngs-tools/ngs-vdb/src'
make[1]: Leaving directory `/home/zilek2/ngs/ngs-tools/ngs-vdb/src'
make[1]: Entering directory `/home/zilek2/ngs/ngs-tools/tools/sra-search'
make /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/bin/sra-search
make[2]: Entering directory `/home/zilek2/ngs/ngs-tools/tools/sra-search'
g++ -o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/bin/sra-search.2.8.2 /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/tools/sra-search/searchblock.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/tools/sra-search/vdb-search.o /home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/tools/sra-search/main.o -L/home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib -lngs-vdb -L/home/zilek2/ncbi-outdir/ngs-sdk/linux/gcc/x86_64/rel/lib -L/home/zilek2/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -lncbi-ngs-c++ -lncbi-vdb-static -lngs-c++ -lpthread -ldl
/home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/tools/sra-search/vdb-search.o: In function `VdbSearch::VdbSearch(VdbSearch::Settings const&)':
vdb-search.cpp:(.text+0x16b7): undefined reference to `BlobMatchIterator::BlobMatchIterator(SearchBlock::Factory&, std::string const&)'
vdb-search.cpp:(.text+0x172a): undefined reference to `FragmentMatchIterator::FragmentMatchIterator(SearchBlock::Factory&, std::string const&, ngs::Read::ReadCategory)'
vdb-search.cpp:(.text+0x1807): undefined reference to `ReferenceMatchIterator::ReferenceMatchIterator(SearchBlock::Factory&, std::string const&, std::vector<ReferenceSpec, std::allocator<ReferenceSpec> > const&, bool)'
collect2: error: ld returned 1 exit status
make[2]: *** [/home/zilek2/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/bin/sra-search] Error 1
make[2]: Leaving directory `/home/zilek2/ngs/ngs-tools/tools/sra-search'
make[1]: *** [std] Error 2
make[1]: Leaving directory `/home/zilek2/ngs/ngs-tools/tools/sra-search'

It seems that sra-search needs to link to ./tools/sra-search/blobmatchiterator.cpp, which is not presented.

> grep BlobMatchIterator -R .   

./tools/sra-search/blobmatchiterator.cpp:////////////////////////////////// BlobMatchIterator
./tools/sra-search/blobmatchiterator.cpp:BlobMatchIterator :: BlobMatchIterator ( SearchBlock :: Factory& p_factory, const std::string& p_accession )
./tools/sra-search/blobmatchiterator.cpp:BlobMatchIterator :: ~BlobMatchIterator ()
./tools/sra-search/blobmatchiterator.cpp:BlobMatchIterator :: NextBuffer ()
./tools/sra-search/blobmatchiterator.hpp:class BlobMatchIterator : public MatchIterator
./tools/sra-search/blobmatchiterator.hpp:    BlobMatchIterator ( SearchBlock :: Factory& p_factory, const std::string& p_accession );
./tools/sra-search/blobmatchiterator.hpp:    virtual ~BlobMatchIterator ();
./tools/sra-search/vdb-search.cpp:            m_searches . push ( new BlobMatchIterator ( m_sbFactory, *i ) );

Install instructions

Once I clone the repo, how do I install from there?

Publication and comparison details

Can you please provide pre-print or document for the method.

Have you performed comparison with other methods including 16S RNA based, assembly based and specific gene based.

Thanks

no 'build' directory found on skesa branch in tools/skesa

Hello,
I'm trying to install skesa. I cloned the repo as per README.md. Then had to checkout the skesa branch (which is not in the readme). Now I cannot find the build directory in the tools/skesa folder. Am I missing something? Thank you Paul

Error in "ncbi-vdb/configure" and "make -C ncbi-vdb" steps

Hi,

Thanks a lot for helping!
I got error after run make -C ncbi-vdb.

make[1]: Entering directory '/home/bingyu/softwares2/ncbi-vdb/vdb3'
mkdir -p /home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3; cd /home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3; cmake -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY=/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/ilib -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/lib -DCMAKE_RUNTIME_OUTPUT_DIRECTORY=/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/bin -DCMAKE_TEST_OUTPUT_DIRECTORY=/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/test-bin -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local/ncbi/ncbi-vdb/bin/.. -DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/g++  /home/bingyu/softwares2/ncbi-vdb/vdb3
-- The CXX compiler identification is GNU 5.4.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - failed
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ - broken
CMake Error at /usr/local/share/cmake-3.21/Modules/CMakeTestCXXCompiler.cmake:62 (message):
  The C++ compiler

    "/usr/bin/g++"

  is not able to compile a simple test program.

  It fails with the following output:

    Change Dir: /home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3/CMakeFiles/CMakeTmp
    
    Run Build Command(s):/home/bingyu/anaconda2/bin/make -f Makefile cmTC_1491a/fast && make[2]: Entering directory '/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3/CMakeFiles/CMakeTmp'
    /home/bingyu/anaconda2/bin/make  -f CMakeFiles/cmTC_1491a.dir/build.make CMakeFiles/cmTC_1491a.dir/build
    make[3]: Entering directory '/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3/CMakeFiles/CMakeTmp'
    Building CXX object CMakeFiles/cmTC_1491a.dir/testCXXCompiler.cxx.o
    /usr/bin/g++   -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/bingyu/anaconda2/include  -o CMakeFiles/cmTC_1491a.dir/testCXXCompiler.cxx.o -c /home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
    g++: error: unrecognized command line option ‘-fno-plt’
    make[3]: *** [CMakeFiles/cmTC_1491a.dir/build.make:78: CMakeFiles/cmTC_1491a.dir/testCXXCompiler.cxx.o] Error 1
    make[3]: Leaving directory '/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3/CMakeFiles/CMakeTmp'
    make[2]: *** [Makefile:127: cmTC_1491a/fast] Error 2
    make[2]: Leaving directory '/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3/CMakeFiles/CMakeTmp'
    
    

  

  CMake will not be able to correctly generate this project.
Call Stack (most recent call first):
  CMakeLists.txt:2 (project)


-- Configuring incomplete, errors occurred!
See also "/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3/CMakeFiles/CMakeOutput.log".
See also "/home/bingyu/ncbi-outdir/ncbi-vdb/linux/gcc/x86_64/rel/vdb3/CMakeFiles/CMakeError.log".
Makefile:32: recipe for target 'cmake' failed
make[1]: *** [cmake] Error 1
make[1]: Leaving directory '/home/bingyu/softwares2/ncbi-vdb/vdb3'
Makefile:48: recipe for target 'vdb3' failed
make: *** [vdb3] Error 2
make: Leaving directory '/home/bingyu/softwares2/ncbi-vdb'

I updated my g++ in conda, but no help with it.
Can anyone help with this?

Problem building NGS-TOOLS from source

Hi, I tried cloning and building NGS-TOOLS from github. I encountered an error. Please find the error below.

make

cd /home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj; cmake -DCMAKE_ARCHIVE_OUTPUT_DIRECTORY=/home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/lib -DCMAKE_RUNTIME_OUTPUT_DIRECTORY=/home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/bin -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local/ncbi/ngs-tools/bin/.. -DCMAKE_C_COMPILER=/usr/bin/gcc -DCMAKE_CXX_COMPILER=/usr/bin/g++ -DVDB_INCDIR=/home/joanna/Documents/NCBI/ncbi-vdb/interfaces -DVDB_LIBDIR=/usr/local/ncbi/ncbi-vdb/lib64 -DVDB_ILIBDIR= -DSRATOOLS_SRCDIR= -DSRATOOLS_BINDIR= -DVERSION=3.0.8 -DMAJVERS=3 -DPLATFORM=x86_64 -DOUTDIR=/home/joanna/ncbi-outdir/ngs-tools/.. /home/joanna/Documents/NCBI/ngs-tools
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.

Update the VERSION argument value or use a ... suffix to tell
CMake that the project does not need compatibility with older versions.

CMAKE_VERSION=3.27.7
CMAKE_CXX_STANDARD=11
-- Could NOT find Java (missing: Java_JAR_EXECUTABLE Java_JAVAC_EXECUTABLE Java_JAVADOC_EXECUTABLE) (found version "11.0.20")
CMake Warning at build/env.cmake:213 (message):
NGS includes are not found in /ngs/ngs-sdk.
Call Stack (most recent call first):
CMakeLists.txt:31 (include)

-- Found NCBI-VDB includes in /home/joanna/Documents/NCBI/ncbi-vdb/interfaces. Looking for NCBI-VDB libraries...
-- Configuring done (0.1s)
-- Generating done (0.1s)
-- Build files have been written to: /home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj
make -C /home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/obj/ --no-print-directory
[ 4%] Building C object libs/tk-version/src/CMakeFiles/tk-version.dir/toolkit.vers.c.o
[ 4%] Linking C static library /home/joanna/ncbi-outdir/ngs-tools/linux/gcc/x86_64/rel/ilib/libtk-version.a
[ 4%] Built target tk-version
[ 4%] Building CXX object tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/DumpReferenceFASTA.cpp.o
/home/joanna/Documents/NCBI/ngs-tools/tools/dump_ref_fasta/DumpReferenceFASTA.cpp:27:10: fatal error: ngs/ncbi/NGS.hpp: No such file or directory
27 | #include <ngs/ncbi/NGS.hpp>
| ^~~~~~~~~~~~~~~~~~
compilation terminated.
make[3]: *** [tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/build.make:76: tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/DumpReferenceFASTA.cpp.o] Error 1
make[2]: *** [CMakeFiles/Makefile2:399: tools/dump_ref_fasta/CMakeFiles/dump-ref-fasta.dir/all] Error 2
make[1]: *** [Makefile:166: all] Error 2
make: *** [/home/joanna/Documents/NCBI/ngs-tools/build/Makefile.env:386: cmake] Error 2

Can you help me identify the problem? Thanks.