autoreconf: error: aclocal failed with exit status: 2

[emmannaemeka]

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

[bkille]

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

[emmannaemeka]

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?

[bkille]

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?

[emmannaemeka]

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.

[bkille]

Hmmm you should not be using sudo with conda. Can you confirm that you're running Python 3.6 or higher?

[emmannaemeka]

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.

[bkille]

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

[emmannaemeka]

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.

[emmannaemeka]

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.

[bkille]

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

[bkille]

I believe for genbank you need to use -g and not -r

Let me know if that helps.

[emmannaemeka]

Thanks for your help

Running conda install parsnp=1.5.6

Returns

PackagesNotFoundError: The following packages are not available from current channels:

• parsnp=1.5.6

Current channels:

• https://conda.anaconda.org/conda-forge/osx-64

• https://conda.anaconda.org/conda-forge/noarch

• https://conda.anaconda.org/bioconda/osx-64

• https://conda.anaconda.org/bioconda/noarch

• https://repo.anaconda.com/pkgs/main/osx-64

• https://repo.anaconda.com/pkgs/main/noarch

• https://repo.anaconda.com/pkgs/r/osx-64

• https://repo.anaconda.com/pkgs/r/noarch

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.

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[bkille]

Ahhh, I see. There is no OSX build for 1.5.6, but there are more recent builds which support OSX.