Make error

[Shokusei]

Hi, @macmanes . I installed ORP and tried to build it by "make" command.
However, errors occured. Please check the following information. I would like you to tell me where is wrong.
We are sorry for any inconvenience this may cause you, but we appreciate your cooperation.

(orp_v2) [iceplant4561@at138 Oyster_River_Protocol]$ make
/bin/bash: /lustre7/home/iceplant4561/Oyster_River_Protocol/software/anaconda/install/bin/conda: No such file or directory
(
source /lustre7/home/iceplant4561/Oyster_River_Protocol/software/anaconda/install/etc/profile.d/conda.sh;
conda activate;
conda update -y -n base conda;
conda config --add channels conda-forge;
conda config --add channels bioconda;
conda install mamba -n base -yc conda-forge;
mamba create -yc bioconda --name orp_spades spades=3.15.2;
mamba create -yc bioconda --name orp_trinity trinity=2.9.1 bwa=0.7.17 bashplotlib seqtk=1.3;
mamba create -yc bioconda --name orp_busco busco=5.1.2;
mamba create -yc bioconda --name orp_transabyss transabyss=2.0.1;
mamba create -yc bioconda --name orp_rcorrector rcorrector=1.0.4;
mamba create -yc bioconda --name orp_trimmomatic trimmomatic=0.39;
mamba create -yc bioconda --name orp_sam samtools=1.12 bwa=0.7.17 seqtk=1.3;
mamba create -yc bioconda --name orp_salmon salmon=1.4.0;
mamba create -yc bioconda --name orp_cdhit cd-hit=4.6.8;
mamba create -yc bioconda --name orp_diamond diamond=2.0.8;
mamba env create -f /lustre7/home/iceplant4561/Oyster_River_Protocol/orp_env.yml python=3.8;
mamba clean -ya;
conda deactivate;
)
/bin/bash: line 1: /lustre7/home/iceplant4561/Oyster_River_Protocol/software/anaconda/install/etc/profile.d/conda.sh: No such file or directory

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

• bash
• fish
• tcsh
• xonsh
• zsh
• powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /opt/pkg/intel/oneapi/intelpython/latest

added / updated specs:
- conda

The following NEW packages will be INSTALLED:

_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
brotlipy conda-forge/linux-64::brotlipy-0.7.0-py37h5e8e339_1003
charset-normalizer conda-forge/noarch::charset-normalizer-2.0.10-pyhd8ed1ab_0
colorama conda-forge/noarch::colorama-0.4.4-pyh9f0ad1d_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2
libblas conda-forge/linux-64::libblas-3.9.0-12_linux64_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-12_linux64_openblas
libgfortran-ng conda-forge/linux-64::libgfortran-ng-11.2.0-h69a702a_11
libgfortran5 conda-forge/linux-64::libgfortran5-11.2.0-h5c6108e_11
libgomp conda-forge/linux-64::libgomp-11.2.0-h1d223b6_11
liblapack conda-forge/linux-64::liblapack-3.9.0-12_linux64_openblas
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libopenblas conda-forge/linux-64::libopenblas-0.3.18-pthreads_h8fe5266_0
libzlib conda-forge/linux-64::libzlib-1.2.11-h36c2ea0_1013
python_abi conda-forge/linux-64::python_abi-3.7-2_cp37m
readline conda-forge/linux-64::readline-8.1-h46c0cb4_0

The following packages will be REMOVED:

arrow-cpp-4.0.1-py37h3fd0f77_4
asn1crypto-1.4.0-py37hcd5400e_2
aws-c-common-0.6.8-h14c3975_1
aws-c-event-stream-0.1.6-h9574fa7_1
aws-checksums-0.1.11-h657cfb5_2
aws-sdk-cpp-1.8.185-hadc6d9a_1
brotli-1.0.9-hf484d3e_2
bzip2-1.0.8-hb9a14ef_8
c-ares-1.17.1-hff3d592_1
chardet-4.0.0-py37h7a55b9c_0
cycler-0.10.0-py37h77b6139_8
cython-0.29.24-py37had034fe_0
double-conversion-3.1.5-h79a9dd4_0
dpctl-0.9.0-py37h75156f8_0
dpnp-0.7.1-py37h75156f8_35
freetype-2.10.4-h8e2d9d6_0
funcsigs-1.0.2-py37hef9829d_8
future-0.18.2-py37hfabd62d_0
gflags-2.2.2-h79a9dd4_0
glog-0.4.0-hf484d3e_1
grpc-cpp-1.26.0-hdb13a8a_2
intelpython-2021.4.0-0
kiwisolver-1.3.1-py37h9065164_0
libarchive-3.4.2-ha657d38_7
libcurl-7.78.0-h471713a_2
libedit-3.1.20210714-h8f6a7d7_0
libevent-2.1.10-h5969dba_0
libllvm11-11.0.0-ha451071_0
libpng-1.6.37-7
libprotobuf-3.14.0-h28fbd06_0
libssh2-1.9.0-h4b1ad09_1
libthrift-0.14.1-h36a55ba_0
libxml2-2.9.12-h6441c91_0
llvm-11.0.0-hbdd1d9c_0
llvm-spirv-11.0.0-h4616538_0
llvmlite-0.37.0-py37h188ca7a_0
lz4-c-1.9.3-h688b341_1
lzo-2.10-h309b0be_6
matplotlib-3.1.2-py37h8b3d3d0_10
mkl-service-2.4.0-py37h5c78031_1
mkl_fft-1.3.1-py37hbd9d9a5_0
mkl_random-1.2.2-py37hd708486_1
mkl_umath-0.1.1-py37h244f2d4_9
mpi4py-3.0.3-py37hf484d3e_9
numba-0.54.0-py37h9556e7c_1
numba-dppy-0.15.0-py37h62346ee_0
numexpr-2.7.3-py37hfdc8c6c_1
numpy-base-1.20.3-py37hf707ed8_2
orc-1.6.6-h94e0d16_0
packaging-21.0-py37h1546d3d_3
pandas-1.2.0-py37hef31ef9_2
pyarrow-4.0.1-py37h497cf44_1
pyeditline-2.0.1-py37_1
pyparsing-2.4.7-py37h0618fa2_2
python-dateutil-2.8.2-py37_0
python-libarchive-c-2.8-py37h0d5a7d4_14
pytz-2021.1-py37h854a350_0
pyyaml-5.3.1-py37hae09b62_2
re2-2021.04.01-hf7f620c_0
scikit-ipp-1.2.0-py37he7a3b9b_6
sdc-0.40.0-py37h6eb09a8_0
smp-0.1.4-py37hab8cbcd_1
snappy-1.1.8-hf484d3e_4
spirv-tools-2020.5-h6bb024c_1
sys_check-2021.4-0
tcl-8.6.10-1
thrift-0.14.1-py37h84f2617_0
thrift-compiler-0.14.1-h36a55ba_0
thrift-cpp-0.14.1-0
uriparser-0.9.3-hf484d3e_1
utf8proc-2.6.1-h918b7a9_0
xgboost-1.4.2-1589_g3f5c8bpy37_3
zstd-1.4.5-h3f200d0_0

The following packages will be UPDATED:

ca-certificates conda_channel::ca-certificates-2020.1~ --> conda-forge::ca-certificates-2021.10.8-ha878542_0
certifi conda_channel::certifi-2020.12.5-py37~ --> conda-forge::certifi-2021.10.8-py37h89c1867_1
cffi conda_channel::cffi-1.14.5-py37h30406~ --> conda-forge::cffi-1.15.0-py37h036bc23_0
conda conda_channel::conda-4.10.3-py37hb2eb~ --> conda-forge::conda-4.11.0-py37h89c1867_0
conda-package-han~ conda_channel::conda-package-handling~ --> conda-forge::conda-package-handling-1.7.3-py37h5e8e339_1
cryptography conda_channel::cryptography-3.3.2-py3~ --> pkgs/main::cryptography-36.0.0-py37h9ce1e76_0
joblib conda_channel/linux-64::joblib-1.0.1-~ --> conda-forge/noarch::joblib-1.1.0-pyhd8ed1ab_0
libffi conda_channel::libffi-3.3-13 --> conda-forge::libffi-3.4.2-h7f98852_5
libgcc-ng conda_channel::libgcc-ng-9.3.0-hdf63c~ --> conda-forge::libgcc-ng-11.2.0-h1d223b6_11
libstdcxx-ng conda_channel::libstdcxx-ng-9.3.0-hdf~ --> conda-forge::libstdcxx-ng-11.2.0-he4da1e4_11
ncurses conda_channel::ncurses-6.2-hf61fa16_1 --> conda-forge::ncurses-6.2-h58526e2_4
numpy conda_channel::numpy-1.20.3-py37h2742~ --> conda-forge::numpy-1.21.5-py37hf2998dd_0
openssl conda_channel::openssl-1.1.1k-h14c397~ --> conda-forge::openssl-3.0.0-h7f98852_2
pip conda_channel/linux-64::pip-21.1.1-py~ --> conda-forge/noarch::pip-21.3.1-pyhd8ed1ab_0
pycosat conda_channel::pycosat-0.6.3-py37hf49~ --> conda-forge::pycosat-0.6.3-py37h5e8e339_1009
pycparser conda_channel/linux-64::pycparser-2.2~ --> conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
pyopenssl conda_channel/linux-64::pyopenssl-20.~ --> conda-forge/noarch::pyopenssl-21.0.0-pyhd8ed1ab_0
pysocks conda_channel::pysocks-1.7.0-py37h0d5~ --> conda-forge::pysocks-1.7.1-py37h89c1867_4
python conda_channel::python-3.7.11-h5762be8~ --> conda-forge::python-3.7.12-hf930737_100_cpython
requests conda_channel/linux-64::requests-2.25~ --> conda-forge/noarch::requests-2.27.1-pyhd8ed1ab_0
scikit-learn conda_channel::scikit-learn-0.24.2-py~ --> conda-forge::scikit-learn-1.0.2-py37hf9e9bfc_0
scipy conda_channel::scipy-1.6.2-py37h3fee7~ --> conda-forge::scipy-1.7.3-py37hf2a6cf1_0
setuptools conda_channel::setuptools-52.0.0-py37~ --> conda-forge::setuptools-60.5.0-py37h89c1867_0
sqlite conda_channel::sqlite-3.36.0-hb9a14ef~ --> conda-forge::sqlite-3.37.0-h9cd32fc_0
threadpoolctl conda_channel/linux-64::threadpoolctl~ --> conda-forge/noarch::threadpoolctl-3.0.0-pyh8a188c0_0
tk conda_channel::tk-8.6.10-h8e2d9d6_3 --> conda-forge::tk-8.6.11-h27826a3_1
tqdm conda_channel/linux-64::tqdm-4.60.0-p~ --> conda-forge/noarch::tqdm-4.62.3-pyhd8ed1ab_0
urllib3 conda_channel/linux-64::urllib3-1.26.~ --> conda-forge/noarch::urllib3-1.26.8-pyhd8ed1ab_1
wheel conda_channel/linux-64::wheel-0.36.2-~ --> conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0
yaml conda_channel::yaml-0.1.7-7 --> conda-forge::yaml-0.2.5-h7f98852_2

The following packages will be SUPERSEDED by a higher-priority channel:

idna conda_channel/linux-64::idna-3.1-py37~ --> conda-forge/noarch::idna-3.1-pyhd3deb0d_0
ruamel_yaml conda_channel::ruamel_yaml-0.15.99-py~ --> conda-forge::ruamel_yaml-0.15.80-py37h5e8e339_1006
six conda_channel/linux-64::six-1.16.0-py~ --> conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
xz conda_channel::xz-5.2.5-h74280d8_2 --> conda-forge::xz-5.2.5-h516909a_1
zlib conda_channel::zlib-1.2.11.1-h1e99aa7~ --> conda-forge::zlib-1.2.11-h36c2ea0_1013

Preparing transaction: done
Verifying transaction: failed

EnvironmentNotWritableError: The current user does not have write permissions to the target environment.
environment location: /opt/pkg/intel/oneapi/intelpython/latest
uid: 5585
gid: 11294

Warning: 'conda-forge' already in 'channels' list, moving to the top
Warning: 'bioconda' already in 'channels' list, moving to the top
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /opt/pkg/intel/oneapi/intelpython/latest

added / updated specs:
- mamba

The following NEW packages will be INSTALLED:

_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
libgomp conda-forge/linux-64::libgomp-11.2.0-h1d223b6_11
libiconv conda-forge/linux-64::libiconv-1.16-h516909a_0
libsolv conda-forge/linux-64::libsolv-0.7.19-h780b84a_5
mamba conda-forge/linux-64::mamba-0.15.3-py37h7f483ca_0
python_abi conda-forge/linux-64::python_abi-3.7-2_cp37m
reproc conda-forge/linux-64::reproc-14.2.3-h7f98852_0
reproc-cpp conda-forge/linux-64::reproc-cpp-14.2.3-h9c3ff4c_0

The following packages will be UPDATED:

ca-certificates conda_channel::ca-certificates-2020.1~ --> conda-forge::ca-certificates-2021.10.8-ha878542_0
certifi conda_channel::certifi-2020.12.5-py37~ --> conda-forge::certifi-2021.10.8-py37h89c1867_1
conda conda_channel::conda-4.10.3-py37hb2eb~ --> conda-forge::conda-4.11.0-py37h89c1867_0
libarchive conda_channel::libarchive-3.4.2-ha657~ --> intel::libarchive-3.5.2-h27f34a6_0
libgcc-ng conda_channel::libgcc-ng-9.3.0-hdf63c~ --> conda-forge::libgcc-ng-11.2.0-h1d223b6_11
libstdcxx-ng conda_channel::libstdcxx-ng-9.3.0-hdf~ --> conda-forge::libstdcxx-ng-11.2.0-he4da1e4_11
openssl conda_channel::openssl-1.1.1k-h14c397~ --> conda-forge::openssl-1.1.1l-h7f98852_0

Preparing transaction: done
Verifying transaction: failed

EnvironmentNotWritableError: The current user does not have write permissions to the target environment.
environment location: /opt/pkg/intel/oneapi/intelpython/latest
uid: 5585
gid: 11294

/bin/bash: line 7: mamba: command not found
/bin/bash: line 8: mamba: command not found
/bin/bash: line 9: mamba: command not found
/bin/bash: line 10: mamba: command not found
/bin/bash: line 11: mamba: command not found
/bin/bash: line 12: mamba: command not found
/bin/bash: line 13: mamba: command not found
/bin/bash: line 14: mamba: command not found
/bin/bash: line 15: mamba: command not found
/bin/bash: line 16: mamba: command not found
/bin/bash: line 17: mamba: command not found
/bin/bash: line 18: mamba: command not found

CommandNotFoundError: Your shell has not been properly configured to use 'conda deactivate'.
To initialize your shell, run

$ conda init <SHELL_NAME>

Currently supported shells are:

• bash
• fish
• tcsh
• xonsh
• zsh
• powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

make: *** [Makefile:50: orp] Error 1

[claumer]

I'm getting a very similar error, 10 months later - is the ORP no longer being maintained?