Closed emmannaemeka closed 9 months ago
Hi @emmannaemeka! Thanks for your interest in parsnp. It looks like you are missing the automake package.
That being said, I'd highly suggest using Bioconda to install parsnp. The instructions are here. FWIW, nearly all major bioinformatics software is primarily installed via bioconda, so this will make installing parsnp easier as well as all future softwares (:
Happy to answer any questions you have about setting up bioconda and installing parsnp. Thanks!
-Bryce
Thanks Bryce, I have installed it using bioconda
However, I tried running
parsnp -r /Users/emmannaemeka/Documents/fastq.gz/T1:44_reference/genome_assemblies_genome_fasta/ncbi-genomes-2021-11-18/genome_assemblies_genome_gb/ncbi-genomes-2021-11-18/GCF_001564435.1_ASM156443v1_genomic.gbff -d /Users/emmannaemeka/Documents/fastq.gz/genomes -p 4 |--Parsnp v1.2--| For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
SETTINGS: |-refgenome: /Users/emmannaemeka/Documents/fastq.gz/T1:44_reference/genome_assemblies_genome_fasta/ncbi-genomes-2021-11-18/genome_assemblies_genome_gb/ncbi-genomes-2021-11-18/GCF_001564435.1_ASM156443v1_genomic.gbff |-aligner: libMUSCLE |-seqdir: /Users/emmannaemeka/Documents/fastq.gz/genomes |-outdir: /Users/emmannaemeka/Documents/fastq.gz/P_2021_11_18_234025028701 |-OS: Darwin |-threads: 4
<
-->Reading Genome (asm, fasta) files from /Users/emmannaemeka/Documents/fastq.gz/genomes.. |->[OK] -->Reading Genbank file(s) for reference (.gbk) .. |->[WARNING]: no genbank file provided for reference annotations, skipping.. Parsnp requires 2 or more genomes to run, exiting [] /Users/emmannaemeka/Documents/fastq.gz/P_2021_11_18_234025028701/GCF_001564435.1_ASM156443v1_genomic.gbff.ref
Please can you help?
It looks like parsnp v1.2 was installed and not v1.5. This often happens when the conda channels are not set up. Can you confirm that you set up the channels as described here?
This was how it was setup
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
sudo conda install parsnp
Nnaemeka Emmanuel Nnadi,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications:
https://orcid.org/0000-0002-8424-4859
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
On Fri, Nov 19, 2021 at 12:49 AM Bryce Kille @.***> wrote:
It looks like parsnp v1.2 was installed and not v1.5. This often happens when the conda channels are not set up. Can you confirm that you set up the channels as described here https://bioconda.github.io/user/install.html#set-up-channels?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/marbl/parsnp/issues/98#issuecomment-973471872, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ6WTNAWGVKZRKBJHLLUMWGKJANCNFSM5IKTD22A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
Hmmm you should not be using sudo with conda. Can you confirm that you're running Python 3.6 or higher?
which python
/Users/emmannaemeka/miniconda3/bin/python
Python 3.9.5 (default, May 18 2021, 12:31:01)
[Clang 10.0.0 ] :: Anaconda, Inc. on darwin
Type "help", "copyright", "credits" or "license" for more information.
If i just run conda install it will not but ask me to use sudo
Nnaemeka Emmanuel Nnadi,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications:
https://orcid.org/0000-0002-8424-4859
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
On Fri, Nov 19, 2021 at 6:01 AM Emmanuel Nnadi @.***> wrote:
This was how it was setup
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
sudo conda install parsnp
Nnaemeka Emmanuel Nnadi,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications:
https://orcid.org/0000-0002-8424-4859
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
On Fri, Nov 19, 2021 at 12:49 AM Bryce Kille @.***> wrote:
It looks like parsnp v1.2 was installed and not v1.5. This often happens when the conda channels are not set up. Can you confirm that you set up the channels as described here https://bioconda.github.io/user/install.html#set-up-channels?
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/marbl/parsnp/issues/98#issuecomment-973471872, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ6WTNAWGVKZRKBJHLLUMWGKJANCNFSM5IKTD22A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
There seems to be something wrong with your conda installation. You shouldn't need sudo permissions to install. Either way, could you show me the output of what happens when you run
conda create --name ptest python=3.7 parsnp=1.5
environment location: /Users/emmannaemeka/miniconda3/envs/ptest
added / updated specs:
- parsnp=1.5
- python=3.7
The following packages will be downloaded:
package | build
---------------------------|-----------------
boost-1.70.0 | py37hbf1eeb5_1 333 KB
conda-forge
boost-cpp-1.70.0 | hef959ae_3 18.9 MB
conda-forge
fastani-1.32 | he69ab0f_0 151 KB bioconda
fasttree-2.1.10 | hb4d813b_5 147 KB bioconda
harvesttools-1.2 | h1b062d3_1 684 KB bioconda
icu-67.1 | hb1e8313_0 12.6 MB
conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB
conda-forge
libgcc-4.8.5 | 1 785 KB
conda-forge
llvm-openmp-8.0.1 | h770b8ee_0 253 KB
conda-forge
mash-1.1 | 0 250 KB bioconda
mkl-service-2.4.0 | py37hbfd6c52_0 43 KB
conda-forge
mkl_fft-1.3.1 | py37h6365bc4_1 176 KB
conda-forge
mkl_random-1.2.2 | py37hb23ed4d_0 288 KB
conda-forge
numpy-1.21.2 | py37h4b4dc7a_0 23 KB
numpy-base-1.21.2 | py37he0bd621_0 4.6 MB
openmp-8.0.1 | 0 8 KB
conda-forge
openssl-3.0.0 | h0d85af4_2 2.5 MB
conda-forge
parsnp-1.5.4 | h7475705_0 1.1 MB bioconda
phipack-1.1 | hb4d813b_1 73 KB bioconda
pip-21.3.1 | pyhd8ed1ab_0 1.2 MB
conda-forge
python-3.7.12 |hf3644f1_100_cpython 24.3 MB
conda-forge
python_abi-3.7 | 2_cp37m 4 KB
conda-forge
raxml-8.2.12 | hb4d813b_3 2.6 MB bioconda
setuptools-59.1.1 | py37hf985489_0 1.0 MB
conda-forge
zstd-1.4.9 | h582d3a0_0 460 KB
conda-forge
------------------------------------------------------------
Total: 72.4 MB
The following NEW packages will be INSTALLED:
blas pkgs/main/osx-64::blas-1.0-mkl
boost conda-forge/osx-64::boost-1.70.0-py37hbf1eeb5_1
boost-cpp conda-forge/osx-64::boost-cpp-1.70.0-hef959ae_3
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
ca-certificates conda-forge/osx-64::ca-certificates-2021.10.8-h033912b_0
fastani bioconda/osx-64::fastani-1.32-he69ab0f_0
fasttree bioconda/osx-64::fasttree-2.1.10-hb4d813b_5
harvesttools bioconda/osx-64::harvesttools-1.2-h1b062d3_1
icu conda-forge/osx-64::icu-67.1-hb1e8313_0
intel-openmp pkgs/main/osx-64::intel-openmp-2021.4.0-hecd8cb5_3538
libcxx conda-forge/osx-64::libcxx-12.0.1-habf9029_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libgcc conda-forge/osx-64::libgcc-4.8.5-1
libzlib conda-forge/osx-64::libzlib-1.2.11-h9173be1_1013
llvm-openmp conda-forge/osx-64::llvm-openmp-8.0.1-h770b8ee_0
lz4-c conda-forge/osx-64::lz4-c-1.9.3-he49afe7_1
mash bioconda/osx-64::mash-1.1-0
mkl pkgs/main/osx-64::mkl-2021.4.0-hecd8cb5_637
mkl-service conda-forge/osx-64::mkl-service-2.4.0-py37hbfd6c52_0
mkl_fft conda-forge/osx-64::mkl_fft-1.3.1-py37h6365bc4_1
mkl_random conda-forge/osx-64::mkl_random-1.2.2-py37hb23ed4d_0
ncurses conda-forge/osx-64::ncurses-6.2-h2e338ed_4
numpy pkgs/main/osx-64::numpy-1.21.2-py37h4b4dc7a_0
numpy-base pkgs/main/osx-64::numpy-base-1.21.2-py37he0bd621_0
openmp conda-forge/osx-64::openmp-8.0.1-0
openssl conda-forge/osx-64::openssl-3.0.0-h0d85af4_2
parsnp bioconda/osx-64::parsnp-1.5.4-h7475705_0
phipack bioconda/osx-64::phipack-1.1-hb4d813b_1
pip conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.7.12-hf3644f1_100_cpython
python_abi conda-forge/osx-64::python_abi-3.7-2_cp37m
raxml bioconda/osx-64::raxml-8.2.12-hb4d813b_3
readline conda-forge/osx-64::readline-8.1-h05e3726_0
setuptools conda-forge/osx-64::setuptools-59.1.1-py37hf985489_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
sqlite conda-forge/osx-64::sqlite-3.36.0-h23a322b_2
tk conda-forge/osx-64::tk-8.6.11-h5dbffcc_1
wheel conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1
xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
zlib conda-forge/osx-64::zlib-1.2.11-h9173be1_1013
zstd conda-forge/osx-64::zstd-1.4.9-h582d3a0_0
Proceed ([y]/n)? y Nnaemeka Emmanuel Nnadi,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications:
https://orcid.org/0000-0002-8424-4859
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
On Fri, Nov 19, 2021 at 7:00 AM Bryce Kille @.***> wrote:
There seems to be something wrong with your conda installation. You shouldn't need sudo permissions to install. Either way, could you show me the output of what happens when you run
conda create --name ptest python=3.7 parsnp=1.5
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/marbl/parsnp/issues/98#issuecomment-973778319, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ6RRBKL746EC3RKG2DUMXRXZANCNFSM5IKTD22A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
Running
parsnp -r /Users/emmannaemeka/Documents/fastq.gz/T1:44_reference/genome_assemblies_genome_fasta/ncbi-genomes-2021-11-18/genome_assemblies_genome_gb/ncbi-genomes-2021-11-18/GCF_001564435.1_ASM156443v1_genomic.gbff -d /Users/emmannaemeka/Documents/fastq.gz/genomes -p 4
|--Parsnp 1.5.3--|
For detailed documentation please see --> http://harvest.readthedocs.org/en/latest
07:17:50 - INFO -
SETTINGS:
|-refgenome: /Users/emmannaemeka/Documents/fastq.gz/T1:44_reference/genome_assemblies_genome_fasta/ncbi-genomes-2021-11-18/genome_assemblies_genome_gb/ncbi-genomes-2021-11-18/GCF_001564435.1_ASM156443v1_genomic.gbff
|-genomes:
/Users/emmannaemeka/Documents/fastq.gz/genomes/sample1.7.fasta
/Users/emmannaemeka/Documents/fastq.gz/genomes/sample_1.4.fasta
...4 more file(s)...
/Users/emmannaemeka/Documents/fastq.gz/genomes/sample1.8.fasta
/Users/emmannaemeka/Documents/fastq.gz/genomes/sample1.9.fasta
|-aligner: muscle
|-outdir: /Users/emmannaemeka/Documents/programs/parsnp/muscle/P_2021_11_19_071750673095
|-OS: Darwin
|-threads: 4
07:17:50 - INFO - <
07:17:50 - INFO - No genbank file provided for reference annotations, skipping..
07:17:50 - CRITICAL - Reference /Users/emmannaemeka/Documents/fastq.gz/T1:44_reference/genome_assemblies_genome_fasta/ncbi-genomes-2021-11-18/genome_assemblies_genome_gb/ncbi-genomes-2021-11-18/GCF_001564435.1_ASM156443v1_genomic.gbff has improperly formatted header.
Nnaemeka Emmanuel Nnadi,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications:
https://orcid.org/0000-0002-8424-4859
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
On Fri, Nov 19, 2021 at 7:12 AM Emmanuel Nnadi @.***> wrote:
Package Plan
environment location: /Users/emmannaemeka/miniconda3/envs/ptest
added / updated specs:
- parsnp=1.5 - python=3.7
The following packages will be downloaded:
package | build ---------------------------|----------------- boost-1.70.0 | py37hbf1eeb5_1 333 KB
conda-forge
boost-cpp-1.70.0 | hef959ae_3 18.9 MB
conda-forge
fastani-1.32 | he69ab0f_0 151 KB bioconda fasttree-2.1.10 | hb4d813b_5 147 KB bioconda harvesttools-1.2 | h1b062d3_1 684 KB bioconda icu-67.1 | hb1e8313_0 12.6 MB
conda-forge
libffi-3.4.2 | h0d85af4_5 50 KB
conda-forge
libgcc-4.8.5 | 1 785 KB
conda-forge
llvm-openmp-8.0.1 | h770b8ee_0 253 KB
conda-forge
mash-1.1 | 0 250 KB bioconda mkl-service-2.4.0 | py37hbfd6c52_0 43 KB
conda-forge
mkl_fft-1.3.1 | py37h6365bc4_1 176 KB
conda-forge
mkl_random-1.2.2 | py37hb23ed4d_0 288 KB
conda-forge
numpy-1.21.2 | py37h4b4dc7a_0 23 KB numpy-base-1.21.2 | py37he0bd621_0 4.6 MB openmp-8.0.1 | 0 8 KB
conda-forge
openssl-3.0.0 | h0d85af4_2 2.5 MB
conda-forge
parsnp-1.5.4 | h7475705_0 1.1 MB bioconda phipack-1.1 | hb4d813b_1 73 KB bioconda pip-21.3.1 | pyhd8ed1ab_0 1.2 MB
conda-forge
python-3.7.12 |hf3644f1_100_cpython 24.3 MB
conda-forge
python_abi-3.7 | 2_cp37m 4 KB
conda-forge
raxml-8.2.12 | hb4d813b_3 2.6 MB bioconda setuptools-59.1.1 | py37hf985489_0 1.0 MB
conda-forge
zstd-1.4.9 | h582d3a0_0 460 KB
conda-forge
------------------------------------------------------------ Total: 72.4 MB
The following NEW packages will be INSTALLED:
blas pkgs/main/osx-64::blas-1.0-mkl
boost conda-forge/osx-64::boost-1.70.0-py37hbf1eeb5_1
boost-cpp conda-forge/osx-64::boost-cpp-1.70.0-hef959ae_3
bzip2 conda-forge/osx-64::bzip2-1.0.8-h0d85af4_4
ca-certificates conda-forge/osx-64::ca-certificates-2021.10.8-h033912b_0
fastani bioconda/osx-64::fastani-1.32-he69ab0f_0
fasttree bioconda/osx-64::fasttree-2.1.10-hb4d813b_5
harvesttools bioconda/osx-64::harvesttools-1.2-h1b062d3_1
icu conda-forge/osx-64::icu-67.1-hb1e8313_0
intel-openmp pkgs/main/osx-64::intel-openmp-2021.4.0-hecd8cb5_3538
libcxx conda-forge/osx-64::libcxx-12.0.1-habf9029_0
libffi conda-forge/osx-64::libffi-3.4.2-h0d85af4_5
libgcc conda-forge/osx-64::libgcc-4.8.5-1
libzlib conda-forge/osx-64::libzlib-1.2.11-h9173be1_1013
llvm-openmp conda-forge/osx-64::llvm-openmp-8.0.1-h770b8ee_0
lz4-c conda-forge/osx-64::lz4-c-1.9.3-he49afe7_1
mash bioconda/osx-64::mash-1.1-0
mkl pkgs/main/osx-64::mkl-2021.4.0-hecd8cb5_637
mkl-service conda-forge/osx-64::mkl-service-2.4.0-py37hbfd6c52_0
mkl_fft conda-forge/osx-64::mkl_fft-1.3.1-py37h6365bc4_1
mkl_random conda-forge/osx-64::mkl_random-1.2.2-py37hb23ed4d_0
ncurses conda-forge/osx-64::ncurses-6.2-h2e338ed_4
numpy pkgs/main/osx-64::numpy-1.21.2-py37h4b4dc7a_0
numpy-base pkgs/main/osx-64::numpy-base-1.21.2-py37he0bd621_0
openmp conda-forge/osx-64::openmp-8.0.1-0
openssl conda-forge/osx-64::openssl-3.0.0-h0d85af4_2
parsnp bioconda/osx-64::parsnp-1.5.4-h7475705_0
phipack bioconda/osx-64::phipack-1.1-hb4d813b_1
pip conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
python conda-forge/osx-64::python-3.7.12-hf3644f1_100_cpython
python_abi conda-forge/osx-64::python_abi-3.7-2_cp37m
raxml bioconda/osx-64::raxml-8.2.12-hb4d813b_3
readline conda-forge/osx-64::readline-8.1-h05e3726_0
setuptools conda-forge/osx-64::setuptools-59.1.1-py37hf985489_0
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
sqlite conda-forge/osx-64::sqlite-3.36.0-h23a322b_2
tk conda-forge/osx-64::tk-8.6.11-h5dbffcc_1
wheel conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1
xz conda-forge/osx-64::xz-5.2.5-haf1e3a3_1
zlib conda-forge/osx-64::zlib-1.2.11-h9173be1_1013
zstd conda-forge/osx-64::zstd-1.4.9-h582d3a0_0
Proceed ([y]/n)? y Nnaemeka Emmanuel Nnadi,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications:
https://orcid.org/0000-0002-8424-4859
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
On Fri, Nov 19, 2021 at 7:00 AM Bryce Kille @.***> wrote:
There seems to be something wrong with your conda installation. You shouldn't need sudo permissions to install. Either way, could you show me the output of what happens when you run
conda create --name ptest python=3.7 parsnp=1.5
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/marbl/parsnp/issues/98#issuecomment-973778319, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZ6RRBKL746EC3RKG2DUMXRXZANCNFSM5IKTD22A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
Interesting. It seems to pick up parsnp 1.5 when you do that. I think that python 3.9 is likely too new to be supported. I'd suggest using a python 3.7 environment.
conda install python=3.7
conda install parsnp=1.5.6
and you should be good to go. If you run into issues w/ the second line, you can try 1.5 instead of 1.5.4
I believe for genbank you need to use -g and not -r
Let me know if that helps.
Thanks for your help
Running conda install parsnp=1.5.6
Returns
PackagesNotFoundError: The following packages are not available from current channels:
Current channels:
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
Nnaemeka Emmanuel Nnadi,Ph.D Department of Microbiology, Faculty of Natural and Applied Science, Plateau State University, Bokkos, Plateau State, Nigeria. +2348068124819 Publications:
https://orcid.org/0000-0002-8424-4859
https://www.researchgate.net/profile/Emmanuel_Nnadi/publications
On Fri, Nov 19, 2021 at 7:34 AM Bryce Kille @.***> wrote:
I believe for genbank you need to use -g and not -r
Let me know if that helps.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/marbl/parsnp/issues/98#issuecomment-973792490, or unsubscribe https://github.com/notifications/unsubscribe-auth/AHVLNZYAPZMG3GPG3NMMSXLUMXVV7ANCNFSM5IKTD22A . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
Ahhh, I see. There is no OSX build for 1.5.6, but there are more recent builds which support OSX.
Hello, Please am trying to install parsnp on my mac
./autogen.sh Can't exec "aclocal": No such file or directory at /usr/local/Cellar/autoconf/2.71/share/autoconf/Autom4te/FileUtils.pm line 274. autoreconf: error: aclocal failed with exit status: 2 Now run ./configure --prefix=/Users/emmannaemeka && make install Add --disable-shared to the configure line if building on Mac OS X
Also while running ./configure --prefix=$PWD CXXFLAGS='-fopenmp'
I get
configure: error: cannot find install-sh, install.sh, or shtool in config "."/config