NGSpeciesID
NGSpeciesID copied to clipboard
ksahlin
Problems installing NGSpeciesID
Hi,
We really would like to test and use your program, but we encounter some problems with installing it. It seems like the same problem that 2tony2 mentioned. So we tried his suggestion and installed (with sudo apt) m4, autoconf, automake, libtool. Unfortunately it still doesn't work. We run it on ubuntu 20.05 (fully updated), with miniconda. Running on Win10-WSL.
Could you maybe help us out?
kind regards, Peter
The error message is copy-pasted below:
pip install NGSpeciesID
Collecting NGSpeciesID
Using cached NGSpeciesID-0.1.1.1-py2.py3-none-any.whl
Collecting parasail==1.1.11
Using cached parasail-1.1.11.tar.gz (46 kB)
Collecting edlib>=1.1.2
Using cached edlib-1.3.8.post2-cp36-cp36m-manylinux2010_x86_64.whl (304 kB)
Requirement already satisfied: numpy in ./miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages (from parasail==1.1.11->NGSpeciesID) (1.16.1)
Building wheels for collected packages: parasail
Building wheel for parasail (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /home/data/miniconda3/envs/NGSpeciesID/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-26r5hzgx
cwd: /tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/
Complete output (264 lines):
running bdist_wheel
parasail/libparasail.so not found, attempting to build
Downloading latest parasail master
Unzipping parasail master archive
fixing executable bits after unzipping
Unable to find parasail configure script
Prepending /usr/bin to PATH
PATH=/usr/bin:/home/data/miniconda3/envs/NGSpeciesID/bin:/home/data/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu20.04onWindows_2004.2021.222.0_x64__79rhkp1fndgsc:/mnt/c/Program Files (x86)/Common Files/Oracle/Java/javapath:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program Files (x86)/Pulse Secure/VC142.CRT/X64:/mnt/c/Program Files (x86)/Pulse Secure/VC142.CRT/X86:/mnt/c/Users/NanoPore Data2/AppData/Local/Microsoft/WindowsApps:/snap/bin
Running autoreconf -fi from ./parasail-master
b'This is perl 5, version 30, subversion 0 (v5.30.0) built for x86_64-linux-gnu-thread-multi'
b'm4 (GNU M4) 1.4.18'
b'autoconf (GNU Autoconf) 2.69'
b'automake (GNU automake) 1.16.1'
b'libtool (GNU libtool) 2.4.6'
b'autoreconf (GNU Autoconf) 2.69'
libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'build-aux'.
libtoolize: copying file 'build-aux/ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:115: installing 'build-aux/compile'
configure.ac:74: installing 'build-aux/config.guess'
configure.ac:74: installing 'build-aux/config.sub'
configure.ac:66: installing 'build-aux/install-sh'
configure.ac:66: installing 'build-aux/missing'
Makefile.am: installing 'build-aux/depcomp'
parallel-tests: installing 'build-aux/test-driver'
autoreconf -fi exited with return code 0
configuring parasail in directory ./parasail-master
checking whether make supports nested variables... no
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... no
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
configure:
configure: C compiler
configure:
checking whether make supports the include directive... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for gcc option to accept ISO C99... none needed
checking for C compiler vendor... gnu
checking for a sed that does not truncate output... /usr/bin/sed
checking for C compiler version... 9.3.0
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking poll.h usability... yes
checking poll.h presence... yes
checking for poll.h... yes
checking for unistd.h... (cached) yes
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking sys/mman.h usability... yes
checking sys/mman.h presence... yes
checking for sys/mman.h... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for C/C++ restrict keyword... __restrict
checking size of int... 4
checking for struct __stat64... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for int8_t... yes
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for uint8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for off_t... yes
checking for size_t... yes
checking for OpenMP flag of C compiler... -fopenmp
checking for SSE2 support... default
checking for SSE2 _mm_set1_epi64x... yes
checking for SSE2 _mm_set_epi64x... yes
checking for SSE4.1 support... -msse4.1
checking for SSE4.1 _mm_insert_epi64... yes
checking for SSE4.1 _mm_extract_epi64... yes
checking for AVX2 support... -mavx2
checking for AVX2 _mm256_set1_epi64x... yes
checking for AVX2 _mm256_set_epi64x... yes
checking for AVX2 _mm256_insert_epi64... yes
checking for AVX2 _mm256_insert_epi32... yes
checking for AVX2 _mm256_insert_epi16... yes
checking for AVX2 _mm256_insert_epi8... yes
checking for AVX2 _mm256_extract_epi64... yes
checking for AVX2 _mm256_extract_epi32... yes
checking for AVX2 _mm256_extract_epi16... yes
checking for AVX2 _mm256_extract_epi8... yes
checking for AVX512F support... -mavx512f
checking for AVX512BW support... -mavx512bw
checking for AVX512VBMI support... -mavx512vbmi
checking for xgetbv... yes
checking for AltiVec support... no
checking for ARM NEON support... no
checking whether C compiler accepts -fopenmp-simd... yes
checking for _aligned_malloc... no
checking for aligned_alloc... yes
checking for filelength... no
checking for memalign... yes
checking for memset... yes
checking for poll... yes
checking for posix_memalign... yes
checking for getopt... yes
checking for SetUnhandledExceptionFilter... no
checking for _fstat64... no
checking for _stat64... no
checking for int64_t literal suffix... LL
checking for GetSystemTimeAsFileTime... no
checking for clock_get_time... no
checking for library containing clock_gettime... none required
checking for clock_gettime CLOCK_MONOTONIC... yes
checking for clock_gettime CLOCK_REALTIME... yes
checking for library containing sqrt... -lm
checking zlib.h usability... no
checking zlib.h presence... no
checking for zlib.h... no
checking for library containing gzopen... no
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking whether C compiler supports visibility flag... -fvisibility=hidden
configure:
configure: C++ compiler
configure:
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking dependency style of g++... none
checking for C++ compiler vendor... unknown
checking for C++ compiler version...
checking for OpenMP flag of C++ compiler... unknown
checking for variadic macros... no
configure:
configure: Libtool setup
configure:
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for fgrep... /usr/bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /usr/bin/dd
checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking our pkgconfig libname... parasail-1
checking our pkgconfig version... 2.4.3
checking our pkgconfig_libdir... ${libdir}/pkgconfig
expanded our pkgconfig_libdir... /usr/local/lib/pkgconfig
checking our pkgconfig_libfile... parasail-1.pc
checking our package / suffix... Pairwise Sequence Alignment Library /
checking our pkgconfig description... Pairwise Sequence Alignment Library
checking our pkgconfig requires...
checking our pkgconfig ext libs... -lparasail
checking our pkgconfig cppflags...
checking our pkgconfig ldflags...
noninstalled pkgconfig -L /tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/parasail-master/src/.libs
noninstalled pkgconfig -I /tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/parasail-master/.
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: error: in `/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/parasail-master':
config.status: error: Something went wrong bootstrapping makefile fragments
for automatic dependency tracking. Try re-running configure with the
'--disable-dependency-tracking' option to at least be able to build
the package (albeit without support for automatic dependency tracking).
See `config.log' for more details
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py", line 447, in <module>
install_requires=INSTALL_REQUIRES,
File "/home/data/miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages/setuptools/__init__.py", line 163, in setup
return distutils.core.setup(**attrs)
File "/home/data/miniconda3/envs/NGSpeciesID/lib/python3.6/distutils/core.py", line 148, in setup
dist.run_commands()
File "/home/data/miniconda3/envs/NGSpeciesID/lib/python3.6/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/home/data/miniconda3/envs/NGSpeciesID/lib/python3.6/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py", line 409, in run
prepare_shared_lib()
File "/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py", line 403, in prepare_shared_lib
build_parasail(libname)
File "/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py", line 308, in build_parasail
raise RuntimeError("configure failed")
RuntimeError: configure failed
----------------------------------------
ERROR: Failed building wheel for parasail
Running setup.py clean for parasail
Failed to build parasail
Installing collected packages: parasail, edlib, NGSpeciesID
Attempting uninstall: parasail
Found existing installation: parasail 1.2.4
Uninstalling parasail-1.2.4:
Successfully uninstalled parasail-1.2.4
Running setup.py install for parasail ... error
ERROR: Command errored out with exit status 1:
command: /home/data/miniconda3/envs/NGSpeciesID/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-j3wa47lc/install-record.txt --single-version-externally-managed --compile --install-headers /home/data/miniconda3/envs/NGSpeciesID/include/python3.6m/parasail
cwd: /tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/
Complete output (8 lines):
running install
parasail/libparasail.so not found, attempting to build
Archive 'parasail-master.zip' already downloaded
Archive 'parasail-master.zip' already unzipped to /tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e
parasail archive executable permissions ok
parasail already configured in directory ./parasail-master
making parasail
error: [Errno 2] No such file or directory: 'make': 'make'
----------------------------------------
Rolling back uninstall of parasail
Moving to /home/data/miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages/parasail-1.2.4.dist-info/
from /home/data/miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages/~arasail-1.2.4.dist-info
Moving to /home/data/miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages/parasail/
from /home/data/miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages/~arasail
ERROR: Command errored out with exit status 1: /home/data/miniconda3/envs/NGSpeciesID/bin/python3.6 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py'"'"'; __file__='"'"'/tmp/pip-install-cpvf0dwr/parasail_8994b80cbe3e4c9aade6bdf54850a90e/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-j3wa47lc/install-record.txt --single-version-externally-managed --compile --install-headers /home/data/miniconda3/envs/NGSpeciesID/include/python3.6m/parasail Check the logs for full command output.
Hi @PKuperus,
Thanks for reporting! The key line in the error message seems to be
error: [Errno 2] No such file or directory: 'make': 'make'.
You can install make by apt-get -y install make or sudo apt-get install build-essential (I took this answer from here).
after installing make see if it works and let me know.
I will in the meantime have a look at what makes parasail cause this trouble.
Best, K
The build-essential builds other things as well which you might need for parasail, so if apt-get -y install make does not do it, maybe the heat weight build-essential will.
I was also looking at more recent issues on the parasail repository, and observed this one: https://github.com/jeffdaily/parasail/issues/87. Where it is suggested to run sudo apt update; sudo apt install autoconf automake libtool. Let me know how it goes.
thank you! I will try now.
...ill start with sudo apt-get install build-essential
great, I think "sudo apt-get install build-essential" worked...but still an error, as far as I understand the error...something with a incompatibl new version of pysam==0.15.2
pip install NGSpeciesID Collecting NGSpeciesID Using cached NGSpeciesID-0.1.1.1-py2.py3-none-any.whl Collecting parasail==1.1.11 Using cached parasail-1.1.11.tar.gz (46 kB) Collecting edlib>=1.1.2 Using cached edlib-1.3.8.post2-cp36-cp36m-manylinux2010_x86_64.whl (304 kB) Requirement already satisfied: numpy in ./miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages (from parasail==1.1.11->NGSpeciesID) (1.16.1) Building wheels for collected packages: parasail Building wheel for parasail (setup.py) ... done Created wheel for parasail: filename=parasail-1.1.11-py2.py3-none-linux_x86_64.whl size=13863996 sha256=e7b2077b7f532626a11eb40b6cf43f37a7484887357cb32041618a2ddc1a87ed Stored in directory: /home/data/.cache/pip/wheels/86/9f/57/e4b92eb9286a92d9e461327be0860a7d531bcadce88ec9871c Successfully built parasail Installing collected packages: parasail, edlib, NGSpeciesID Attempting uninstall: parasail Found existing installation: parasail 1.2.4 Uninstalling parasail-1.2.4: Successfully uninstalled parasail-1.2.4 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. medaka 0.11.5 requires pysam==0.15.2, but you have pysam 0.16.0.1 which is incompatible. Successfully installed NGSpeciesID-0.1.1.1 edlib-1.3.8.post2 parasail-1.1.11
Ok good. Could you try removing the conda environment you previously set up for NGSpeciesID completely (with the erroneous parasail) and then do a fresh install?
conda deactivate NGSpeciesID
conda env remove --name NGSpeciesID
// then install from scratch
The problem seems to be that you have some other program in your environment using a newer version of pysam. Creating a new environment in conda for NGSpeciesID and not installing any other software using pysam in this specific conda environment should hopefully fix this.
Okay: conda deactivate NGSpeciesID conda env remove --name NGSpeciesID
conda create -n NGSpeciesID python=3.6 pip conda activate NGSpeciesID conda install --yes -c conda-forge -c bioconda medaka=0.11.5 openblas==0.3.3 spoa racon minimap2 pip install NGSpeciesID
To bad! the pysam0.16.0.1 is still there
error: pip install NGSpeciesID Collecting NGSpeciesID Using cached NGSpeciesID-0.1.1.1-py2.py3-none-any.whl Collecting parasail==1.1.11 Using cached parasail-1.1.11-py2.py3-none-linux_x86_64.whl Collecting edlib>=1.1.2 Using cached edlib-1.3.8.post2-cp36-cp36m-manylinux2010_x86_64.whl (304 kB) Requirement already satisfied: numpy in ./miniconda3/envs/NGSpeciesID/lib/python3.6/site-packages (from parasail==1.1.11->NGSpeciesID) (1.16.1) Installing collected packages: parasail, edlib, NGSpeciesID Attempting uninstall: parasail Found existing installation: parasail 1.2.4 Uninstalling parasail-1.2.4: Successfully uninstalled parasail-1.2.4 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. medaka 0.11.5 requires pysam==0.15.2, but you have pysam 0.16.0.1 which is incompatible. Successfully installed NGSpeciesID-0.1.1.1 edlib-1.3.8.post2 parasail-1.1.11
Ok, I will look into this soon.
Reading from the log, it seems that you have NGSpeciesID installed now (just not the medaka module). In that case, NGSpeciesID can be run with racon instead of medaka for polishing. This is specified with:
NGSpeciesID --ont --consensus --racon --racon_iter 3 --fastq [reads.fastq] --outfolder [/path/to/output]
Thank you so much for your help!
...and about the pysam0.16.0.1 thingy... When I installed NGSpecieID on our second computer I noticed that pysam 0.16.0.1 gets installed during the execution of the "conda install --yes -c conda-forge -c bioconda medaka=0.11.5 openblas==0.3.3 spoa racon minimap2" command!
kind regards, Peter