Downloading Qiime2 2024.10 on Hoffman2

User Support
1

Hello everyone this is my first post here! I am in a remote bioinformatics lab and am would very much appreciate assistance on downloading qiime2 2024.10 onto Hoffman2. I am still fairly new to all this so please bear with me. From what I understand only qiime2-2021.8 is available on Hoffman2. However, I need to run the following code as a batch job:

qiime dada2 denoise-ccs \

--i-demultiplexed-seqs pacbio-demux.qza \

--p-front *** \

--p-adapter *** \

--p-min-len 1000 \

--p-max-len 1600 \

--p-n-threads 1 \

--p-pooling-method independent \

--p-chimera-method consensus \

--o-representative-sequences rep-seqs.qza \

--o-table table.qza \

--o-denoising-stats denoising-stats.qza

The problem with this is that qiime2-2021.8 does not have denoise-ccs but I know that qiime2 2024.10 does since I have it on my local computer which prompted me to try to download qiime2 2024.10 onto Hoffman2 but this is where I am having trouble. So I logged into Hoffman2, ran the following code to get an interactive session, qrsh -l h_data=50G,h_rt=24:00:00, and then ran the following:

module load anaconda3/2022.05

source /u/local/Modules/default/init/bash

conda create -n qiime2-2024.10 -c qiime2 -c conda-forge -c bioconda qiime2=2024.10

After that last command I received the following:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 25.9.1

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /u/home/e/coin125/.conda/envs/qiime2-2024.10

added / updated specs:

  • qiime2=2024.10

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
appdirs-1.4.4              |     pyhd8ed1ab_1          14 KB  conda-forge
atpublic-6.0.2             |     pyhd8ed1ab_0          12 KB  conda-forge
bcrypt-5.0.0               |  py310hd8f68c5_0         284 KB  conda-forge
bibtexparser-1.4.3         |     pyhd8ed1ab_0          41 KB  conda-forge
brotli-python-1.2.0        |  py310h8cfb67f_0         359 KB  conda-forge
bzip2-1.0.8                |       hda65f42_8         254 KB  conda-forge
ca-certificates-2025.10.5  |       hbd8a1cb_0         152 KB  conda-forge
certifi-2025.10.5          |     pyhd8ed1ab_0         156 KB  conda-forge
cffi-2.0.0                 |  py310he7384ee_1         239 KB  conda-forge
charset-normalizer-3.4.4   |     pyhd8ed1ab_0          50 KB  conda-forge
cryptography-46.0.3        |  py310hed992bd_0         1.6 MB  conda-forge
dill-0.4.0                 |     pyhd8ed1ab_0          89 KB  conda-forge
filelock-3.20.0            |     pyhd8ed1ab_0          18 KB  conda-forge
flufl.lock-8.2.0           |     pyhd8ed1ab_0          17 KB  conda-forge
globus-sdk-4.1.0           |     pyhd8ed1ab_0         236 KB  conda-forge
h2-4.3.0                   |     pyhcf101f3_0          94 KB  conda-forge
hpack-4.1.0                |     pyhd8ed1ab_0          30 KB  conda-forge
hyperframe-6.1.0           |     pyhd8ed1ab_0          17 KB  conda-forge
idna-3.11                  |     pyhd8ed1ab_0          50 KB  conda-forge
importlib-metadata-8.7.0   |     pyhe01879c_1          34 KB  conda-forge
invoke-2.2.1               |     pyhd8ed1ab_0         130 KB  conda-forge
keyutils-1.6.3             |       hb9d3cd8_0         131 KB  conda-forge
krb5-1.21.3                |       h659f571_0         1.3 MB  conda-forge
ld_impl_linux-64-2.44      |       h1aa0949_4         725 KB  conda-forge
libblas-3.9.0              |38_h4a7cf45_openblas          17 KB  conda-forge
libcblas-3.9.0             |38_h0358290_openblas          17 KB  conda-forge
libedit-3.1.20250104       | pl5321h7949ede_0         132 KB  conda-forge
libexpat-2.7.1             |       hecca717_0          73 KB  conda-forge
libffi-3.5.2               |       h9ec8514_0          56 KB  conda-forge
libgcc-15.2.0              |       h767d61c_7         803 KB  conda-forge
libgcc-ng-15.2.0           |       h69a702a_7          29 KB  conda-forge
libgfortran-15.2.0         |       h69a702a_7          29 KB  conda-forge
libgfortran5-15.2.0        |       hcd61629_7         1.5 MB  conda-forge
libgomp-15.2.0             |       h767d61c_7         437 KB  conda-forge
libiconv-1.18              |       h3b78370_2         772 KB  conda-forge
liblapack-3.9.0            |38_h47877c9_openblas          17 KB  conda-forge
liblzma-5.8.1              |       hb9d3cd8_2         110 KB  conda-forge
libnsl-2.0.1               |       hb9d3cd8_1          33 KB  conda-forge
libopenblas-0.3.30         |pthreads_h94d23a6_3         5.6 MB  conda-forge
libsodium-1.0.20           |       h4ab18f5_0         201 KB  conda-forge
libsqlite-3.50.4           |       h0c1763c_0         911 KB  conda-forge
libstdcxx-15.2.0           |       h8f9b012_7         3.7 MB  conda-forge
libstdcxx-ng-15.2.0        |       h4852527_7          29 KB  conda-forge
libuuid-2.41.2             |       he9a06e4_0          36 KB  conda-forge
libxcrypt-4.4.36           |       hd590300_1          98 KB  conda-forge
libxml2-2.15.1             |       h031cc0b_0          44 KB  conda-forge
libxml2-16-2.15.1          |       hf2a90c1_0         542 KB  conda-forge
libxslt-1.1.43             |       h711ed8c_1         240 KB  conda-forge
libzlib-1.3.1              |       hb9d3cd8_2          60 KB  conda-forge
lxml-6.0.2                 |  py310he6d4be0_1         1.5 MB  conda-forge
ncurses-6.5                |       h2d0b736_3         871 KB  conda-forge
networkx-3.1               |     pyhd8ed1ab_0         1.4 MB  conda-forge
numpy-2.2.6                |  py310hefbff90_0         7.5 MB  conda-forge
openssl-3.5.4              |       h26f9b46_0         3.0 MB  conda-forge
pandas-2.2.2               |  py310hf9f9076_1        12.4 MB  conda-forge
paramiko-4.0.0             |     pyhd8ed1ab_0         156 KB  conda-forge
parsl-2024.4.15            |     pyhd8ed1ab_0         307 KB  conda-forge
pip-25.2                   |     pyh8b19718_0         1.1 MB  conda-forge
psutil-7.1.2               |  py310h139afa4_1         365 KB  conda-forge
pycparser-2.22             |     pyh29332c3_1         108 KB  conda-forge
pyjwt-2.10.1               |     pyhd8ed1ab_0          25 KB  conda-forge
pynacl-1.6.0               |  py310h7c4b9e2_0         1.1 MB  conda-forge
pyparsing-3.2.5            |     pyhcf101f3_0         102 KB  conda-forge
pysocks-1.7.1              |     pyha55dd90_7          21 KB  conda-forge
python-3.10.19             |h3c07f61_2_cpython        24.1 MB  conda-forge
python-dateutil-2.9.0.post0|     pyhe01879c_2         228 KB  conda-forge
python-tzdata-2025.2       |     pyhd8ed1ab_0         141 KB  conda-forge
python_abi-3.10            |          8_cp310           7 KB  conda-forge
pytz-2025.2                |     pyhd8ed1ab_0         185 KB  conda-forge
pyyaml-6.0.3               |  py310h3406613_0         177 KB  conda-forge
pyzmq-27.1.0               |  py310h4f33d48_0         319 KB  conda-forge
qiime2-2024.10.1           |  py310h0fb5ea9_0         687 KB  qiime2
readline-8.2               |       h8c095d6_2         276 KB  conda-forge
requests-2.32.5            |     pyhd8ed1ab_0          58 KB  conda-forge
setproctitle-1.3.6         |  py310h7c4b9e2_1          20 KB  conda-forge
setuptools-80.9.0          |     pyhff2d567_0         731 KB  conda-forge
six-1.17.0                 |     pyhe01879c_1          18 KB  conda-forge
tblib-3.1.0                |     pyhd8ed1ab_0          17 KB  conda-forge
tk-8.6.13                  |noxft_hd72426e_102         3.1 MB  conda-forge
tomlkit-0.13.3             |     pyha770c72_0          38 KB  conda-forge
typeguard-4.4.4            |     pyhd8ed1ab_0          34 KB  conda-forge
typing-extensions-4.15.0   |       h396c80c_0          89 KB  conda-forge
typing_extensions-4.15.0   |     pyhcf101f3_0          50 KB  conda-forge
tzdata-2025b               |       h78e105d_0         120 KB  conda-forge
urllib3-2.5.0              |     pyhd8ed1ab_0          99 KB  conda-forge
wheel-0.45.1               |     pyhd8ed1ab_1          61 KB  conda-forge
yaml-0.2.5                 |       h280c20c_3          83 KB  conda-forge
zeromq-4.3.5               |       h387f397_9         303 KB  conda-forge
zipp-3.23.0                |     pyhd8ed1ab_0          22 KB  conda-forge
zstandard-0.25.0           |  py310h139afa4_0         445 KB  conda-forge
zstd-1.5.7                 |       hb8e6e7a_2         554 KB  conda-forge
------------------------------------------------------------
                                       Total:        83.2 MB

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-4.5-2_gnu
appdirs conda-forge/noarch::appdirs-1.4.4-pyhd8ed1ab_1
atpublic conda-forge/noarch::atpublic-6.0.2-pyhd8ed1ab_0
bcrypt conda-forge/linux-64::bcrypt-5.0.0-py310hd8f68c5_0
bibtexparser conda-forge/noarch::bibtexparser-1.4.3-pyhd8ed1ab_0
brotli-python conda-forge/linux-64::brotli-python-1.2.0-py310h8cfb67f_0
bzip2 conda-forge/linux-64::bzip2-1.0.8-hda65f42_8
ca-certificates conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0
certifi conda-forge/noarch::certifi-2025.10.5-pyhd8ed1ab_0
cffi conda-forge/linux-64::cffi-2.0.0-py310he7384ee_1
charset-normalizer conda-forge/noarch::charset-normalizer-3.4.4-pyhd8ed1ab_0
cryptography conda-forge/linux-64::cryptography-46.0.3-py310hed992bd_0
decorator conda-forge/noarch::decorator-4.4.2-py_0
dill conda-forge/noarch::dill-0.4.0-pyhd8ed1ab_0
filelock conda-forge/noarch::filelock-3.20.0-pyhd8ed1ab_0
flufl.lock conda-forge/noarch::flufl.lock-8.2.0-pyhd8ed1ab_0
globus-sdk conda-forge/noarch::globus-sdk-4.1.0-pyhd8ed1ab_0
h2 conda-forge/noarch::h2-4.3.0-pyhcf101f3_0
hpack conda-forge/noarch::hpack-4.1.0-pyhd8ed1ab_0
hyperframe conda-forge/noarch::hyperframe-6.1.0-pyhd8ed1ab_0
idna conda-forge/noarch::idna-3.11-pyhd8ed1ab_0
importlib-metadata conda-forge/noarch::importlib-metadata-8.7.0-pyhe01879c_1
invoke conda-forge/noarch::invoke-2.2.1-pyhd8ed1ab_0
keyutils conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0
krb5 conda-forge/linux-64::krb5-1.21.3-h659f571_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.44-h1aa0949_4
libblas conda-forge/linux-64::libblas-3.9.0-38_h4a7cf45_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-38_h0358290_openblas
libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0
libexpat conda-forge/linux-64::libexpat-2.7.1-hecca717_0
libffi conda-forge/linux-64::libffi-3.5.2-h9ec8514_0
libgcc conda-forge/linux-64::libgcc-15.2.0-h767d61c_7
libgcc-ng conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7
libgfortran conda-forge/linux-64::libgfortran-15.2.0-h69a702a_7
libgfortran5 conda-forge/linux-64::libgfortran5-15.2.0-hcd61629_7
libgomp conda-forge/linux-64::libgomp-15.2.0-h767d61c_7
libiconv conda-forge/linux-64::libiconv-1.18-h3b78370_2
liblapack conda-forge/linux-64::liblapack-3.9.0-38_h47877c9_openblas
liblzma conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2
libnsl conda-forge/linux-64::libnsl-2.0.1-hb9d3cd8_1
libopenblas conda-forge/linux-64::libopenblas-0.3.30-pthreads_h94d23a6_3
libsodium conda-forge/linux-64::libsodium-1.0.20-h4ab18f5_0
libsqlite conda-forge/linux-64::libsqlite-3.50.4-h0c1763c_0
libstdcxx conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7
libuuid conda-forge/linux-64::libuuid-2.41.2-he9a06e4_0
libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
libxml2 conda-forge/linux-64::libxml2-2.15.1-h031cc0b_0
libxml2-16 conda-forge/linux-64::libxml2-16-2.15.1-hf2a90c1_0
libxslt conda-forge/linux-64::libxslt-1.1.43-h711ed8c_1
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
lxml conda-forge/linux-64::lxml-6.0.2-py310he6d4be0_1
ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3
networkx conda-forge/noarch::networkx-3.1-pyhd8ed1ab_0
numpy conda-forge/linux-64::numpy-2.2.6-py310hefbff90_0
openssl conda-forge/linux-64::openssl-3.5.4-h26f9b46_0
pandas conda-forge/linux-64::pandas-2.2.2-py310hf9f9076_1
paramiko conda-forge/noarch::paramiko-4.0.0-pyhd8ed1ab_0
parsl conda-forge/noarch::parsl-2024.4.15-pyhd8ed1ab_0
pip conda-forge/noarch::pip-25.2-pyh8b19718_0
psutil conda-forge/linux-64::psutil-7.1.2-py310h139afa4_1
pycparser conda-forge/noarch::pycparser-2.22-pyh29332c3_1
pyjwt conda-forge/noarch::pyjwt-2.10.1-pyhd8ed1ab_0
pynacl conda-forge/linux-64::pynacl-1.6.0-py310h7c4b9e2_0
pyparsing conda-forge/noarch::pyparsing-3.2.5-pyhcf101f3_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha55dd90_7
python conda-forge/linux-64::python-3.10.19-h3c07f61_2_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhe01879c_2
python-tzdata conda-forge/noarch::python-tzdata-2025.2-pyhd8ed1ab_0
python_abi conda-forge/noarch::python_abi-3.10-8_cp310
pytz conda-forge/noarch::pytz-2025.2-pyhd8ed1ab_0
pyyaml conda-forge/linux-64::pyyaml-6.0.3-py310h3406613_0
pyzmq conda-forge/linux-64::pyzmq-27.1.0-py310h4f33d48_0
qiime2 qiime2/linux-64::qiime2-2024.10.1-py310h0fb5ea9_0
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
requests conda-forge/noarch::requests-2.32.5-pyhd8ed1ab_0
setproctitle conda-forge/linux-64::setproctitle-1.3.6-py310h7c4b9e2_1
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
six conda-forge/noarch::six-1.17.0-pyhe01879c_1
tblib conda-forge/noarch::tblib-3.1.0-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_hd72426e_102
tomlkit conda-forge/noarch::tomlkit-0.13.3-pyha770c72_0
typeguard conda-forge/noarch::typeguard-4.4.4-pyhd8ed1ab_0
typing-extensions conda-forge/noarch::typing-extensions-4.15.0-h396c80c_0
typing_extensions conda-forge/noarch::typing_extensions-4.15.0-pyhcf101f3_0
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
tzlocal conda-forge/noarch::tzlocal-2.1-pyh9f0ad1d_0
urllib3 conda-forge/noarch::urllib3-2.5.0-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
yaml conda-forge/linux-64::yaml-0.2.5-h280c20c_3
zeromq conda-forge/linux-64::zeromq-4.3.5-h387f397_9
zipp conda-forge/noarch::zipp-3.23.0-pyhd8ed1ab_0
zstandard conda-forge/linux-64::zstandard-0.25.0-py310h139afa4_0
zstd conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2

Proceed ([y]/n)? y

Downloading and Extracting Packages
libffi-3.5.2 | 56 KB | ############################################################################# | 100%
pycparser-2.22 | 108 KB | ############################################################################# | 100%
tblib-3.1.0 | 17 KB | ############################################################################# | 100%
zstandard-0.25.0 | 445 KB | ############################################################################# | 100%
python-tzdata-2025.2 | 141 KB | ############################################################################# | 100%
h2-4.3.0 | 94 KB | ############################################################################# | 100%
charset-normalizer-3 | 50 KB | ############################################################################# | 100%
zeromq-4.3.5 | 303 KB | ############################################################################# | 100%
typeguard-4.4.4 | 34 KB | ############################################################################# | 100%
flufl.lock-8.2.0 | 17 KB | ############################################################################# | 100%
readline-8.2 | 276 KB | ############################################################################# | 100%
numpy-2.2.6 | 7.5 MB | ############################################################################# | 100%
libstdcxx-15.2.0 | 3.7 MB | ############################################################################# | 100%
libcblas-3.9.0 | 17 KB | ############################################################################# | 100%
zipp-3.23.0 | 22 KB | ############################################################################# | 100%
networkx-3.1 | 1.4 MB | ############################################################################# | 100%
hyperframe-6.1.0 | 17 KB | ############################################################################# | 100%
libblas-3.9.0 | 17 KB | ############################################################################# | 100%
libzlib-1.3.1 | 60 KB | ############################################################################# | 100%
pytz-2025.2 | 185 KB | ############################################################################# | 100%
libxcrypt-4.4.36 | 98 KB | ############################################################################# | 100%
brotli-python-1.2.0 | 359 KB | ############################################################################# | 100%
ca-certificates-2025 | 152 KB | ############################################################################# | 100%
libxml2-16-2.15.1 | 542 KB | ############################################################################# | 100%
setproctitle-1.3.6 | 20 KB | ############################################################################# | 100%
bzip2-1.0.8 | 254 KB | ############################################################################# | 100%
pyzmq-27.1.0 | 319 KB | ############################################################################# | 100%
tk-8.6.13 | 3.1 MB | ############################################################################# | 100%
psutil-7.1.2 | 365 KB | ############################################################################# | 100%
cryptography-46.0.3 | 1.6 MB | ############################################################################# | 100%
globus-sdk-4.1.0 | 236 KB | ############################################################################# | 100%
pysocks-1.7.1 | 21 KB | ############################################################################# | 100%
libgcc-15.2.0 | 803 KB | ############################################################################# | 100%
paramiko-4.0.0 | 156 KB | ############################################################################# | 100%
ncurses-6.5 | 871 KB | ############################################################################# | 100%
pyparsing-3.2.5 | 102 KB | ############################################################################# | 100%
liblapack-3.9.0 | 17 KB | ############################################################################# | 100%
libiconv-1.18 | 772 KB | ############################################################################# | 100%
libopenblas-0.3.30 | 5.6 MB | ############################################################################# | 100%
libgfortran-15.2.0 | 29 KB | ############################################################################# | 100%
keyutils-1.6.3 | 131 KB | ############################################################################# | 100%
liblzma-5.8.1 | 110 KB | ############################################################################# | 100%
libsqlite-3.50.4 | 911 KB | ############################################################################# | 100%
parsl-2024.4.15 | 307 KB | ############################################################################# | 100%
atpublic-6.0.2 | 12 KB | ############################################################################# | 100%
typing_extensions-4. | 50 KB | ############################################################################# | 100%
certifi-2025.10.5 | 156 KB | ############################################################################# | 100%
libgfortran5-15.2.0 | 1.5 MB | ############################################################################# | 100%
openssl-3.5.4 | 3.0 MB | ############################################################################# | 100%
bcrypt-5.0.0 | 284 KB | ############################################################################# | 100%
six-1.17.0 | 18 KB | ############################################################################# | 100%
invoke-2.2.1 | 130 KB | ############################################################################# | 100%
pyyaml-6.0.3 | 177 KB | ############################################################################# | 100%
hpack-4.1.0 | 30 KB | ############################################################################# | 100%
libedit-3.1.20250104 | 132 KB | ############################################################################# | 100%
libsodium-1.0.20 | 201 KB | ############################################################################# | 100%
krb5-1.21.3 | 1.3 MB | ############################################################################# | 100%
lxml-6.0.2 | 1.5 MB | ############################################################################# | 100%
yaml-0.2.5 | 83 KB | ############################################################################# | 100%
libxslt-1.1.43 | 240 KB | ############################################################################# | 100%
requests-2.32.5 | 58 KB | ############################################################################# | 100%
libstdcxx-ng-15.2.0 | 29 KB | ############################################################################# | 100%
filelock-3.20.0 | 18 KB | ############################################################################# | 100%
libexpat-2.7.1 | 73 KB | ############################################################################# | 100%
pynacl-1.6.0 | 1.1 MB | ############################################################################# | 100%
zstd-1.5.7 | 554 KB | ############################################################################# | 100%
idna-3.11 | 50 KB | ############################################################################# | 100%
libgcc-ng-15.2.0 | 29 KB | ############################################################################# | 100%
libnsl-2.0.1 | 33 KB | ############################################################################# | 100%
setuptools-80.9.0 | 731 KB | ############################################################################# | 100%
python_abi-3.10 | 7 KB | ############################################################################# | 100%
cffi-2.0.0 | 239 KB | ############################################################################# | 100%
python-3.10.19 | 24.1 MB | ############################################################################# | 100%
pandas-2.2.2 | 12.4 MB | ############################################################################# | 100%
ld_impl_linux-64-2.4 | 725 KB | ############################################################################# | 100%
pyjwt-2.10.1 | 25 KB | ############################################################################# | 100%
tomlkit-0.13.3 | 38 KB | ############################################################################# | 100%
tzdata-2025b | 120 KB | ############################################################################# | 100%
wheel-0.45.1 | 61 KB | ############################################################################# | 100%
dill-0.4.0 | 89 KB | ############################################################################# | 100%
appdirs-1.4.4 | 14 KB | ############################################################################# | 100%
pip-25.2 | 1.1 MB | ############################################################################# | 100%
libgomp-15.2.0 | 437 KB | ############################################################################# | 100%
urllib3-2.5.0 | 99 KB | ############################################################################# | 100%
python-dateutil-2.9. | 228 KB | ############################################################################# | 100%
libxml2-2.15.1 | 44 KB | ############################################################################# | 100%
qiime2-2024.10.1 | 687 KB | ############################################################################# | 100%
bibtexparser-1.4.3 | 41 KB | ############################################################################# | 100%
libuuid-2.41.2 | 36 KB | ############################################################################# | 100%
importlib-metadata-8 | 34 KB | ############################################################################# | 100%
typing-extensions-4. | 89 KB | ############################################################################# | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

$ conda activate qiime2-2024.10

To deactivate an active environment, use

$ conda deactivate

So it looks like qiime2 2024.10 is downloaded, I get excited but when I ran conda activate qiime2-2024.10 and then qiime --help I got:

bash: qiime: command not found

I run conda deactivate and then remove it using conda remove -p /u/home/e/coin/.conda/envs/qiime2-2024.10 --all

(not actually coin, just changed it from my username for privacy)

Then I reinstalled it:

(/u/home/e/coin/miniconda3) [coin125@n1149 ~]$ conda create -n qiime2-2024.10 -c qiime2 -c conda-forge -c bioconda qiime2=2024.10

here are the results of that line:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 25.9.1

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /u/home/e/coin125/.conda/envs/qiime2-2024.10

added / updated specs:

  • qiime2=2024.10

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-4.5-2_gnu
appdirs conda-forge/noarch::appdirs-1.4.4-pyhd8ed1ab_1
atpublic conda-forge/noarch::atpublic-6.0.2-pyhd8ed1ab_0
bcrypt conda-forge/linux-64::bcrypt-5.0.0-py310hd8f68c5_0
bibtexparser conda-forge/noarch::bibtexparser-1.4.3-pyhd8ed1ab_0
brotli-python conda-forge/linux-64::brotli-python-1.2.0-py310h8cfb67f_0
bzip2 conda-forge/linux-64::bzip2-1.0.8-hda65f42_8
ca-certificates conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0
certifi conda-forge/noarch::certifi-2025.10.5-pyhd8ed1ab_0
cffi conda-forge/linux-64::cffi-2.0.0-py310he7384ee_1
charset-normalizer conda-forge/noarch::charset-normalizer-3.4.4-pyhd8ed1ab_0
cryptography conda-forge/linux-64::cryptography-46.0.3-py310hed992bd_0
decorator conda-forge/noarch::decorator-4.4.2-py_0
dill conda-forge/noarch::dill-0.4.0-pyhd8ed1ab_0
filelock conda-forge/noarch::filelock-3.20.0-pyhd8ed1ab_0
flufl.lock conda-forge/noarch::flufl.lock-8.2.0-pyhd8ed1ab_0
globus-sdk conda-forge/noarch::globus-sdk-4.1.0-pyhd8ed1ab_0
h2 conda-forge/noarch::h2-4.3.0-pyhcf101f3_0
hpack conda-forge/noarch::hpack-4.1.0-pyhd8ed1ab_0
hyperframe conda-forge/noarch::hyperframe-6.1.0-pyhd8ed1ab_0
idna conda-forge/noarch::idna-3.11-pyhd8ed1ab_0
importlib-metadata conda-forge/noarch::importlib-metadata-8.7.0-pyhe01879c_1
invoke conda-forge/noarch::invoke-2.2.1-pyhd8ed1ab_0
keyutils conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0
krb5 conda-forge/linux-64::krb5-1.21.3-h659f571_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.44-h1aa0949_4
libblas conda-forge/linux-64::libblas-3.9.0-38_h4a7cf45_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-38_h0358290_openblas
libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0
libexpat conda-forge/linux-64::libexpat-2.7.1-hecca717_0
libffi conda-forge/linux-64::libffi-3.5.2-h9ec8514_0
libgcc conda-forge/linux-64::libgcc-15.2.0-h767d61c_7
libgcc-ng conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7
libgfortran conda-forge/linux-64::libgfortran-15.2.0-h69a702a_7
libgfortran5 conda-forge/linux-64::libgfortran5-15.2.0-hcd61629_7
libgomp conda-forge/linux-64::libgomp-15.2.0-h767d61c_7
libiconv conda-forge/linux-64::libiconv-1.18-h3b78370_2
liblapack conda-forge/linux-64::liblapack-3.9.0-38_h47877c9_openblas
liblzma conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2
libnsl conda-forge/linux-64::libnsl-2.0.1-hb9d3cd8_1
libopenblas conda-forge/linux-64::libopenblas-0.3.30-pthreads_h94d23a6_3
libsodium conda-forge/linux-64::libsodium-1.0.20-h4ab18f5_0
libsqlite conda-forge/linux-64::libsqlite-3.50.4-h0c1763c_0
libstdcxx conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7
libuuid conda-forge/linux-64::libuuid-2.41.2-he9a06e4_0
libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
libxml2 conda-forge/linux-64::libxml2-2.15.1-h031cc0b_0
libxml2-16 conda-forge/linux-64::libxml2-16-2.15.1-hf2a90c1_0
libxslt conda-forge/linux-64::libxslt-1.1.43-h711ed8c_1
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
lxml conda-forge/linux-64::lxml-6.0.2-py310he6d4be0_1
ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3
networkx conda-forge/noarch::networkx-3.1-pyhd8ed1ab_0
numpy conda-forge/linux-64::numpy-2.2.6-py310hefbff90_0
openssl conda-forge/linux-64::openssl-3.5.4-h26f9b46_0
pandas conda-forge/linux-64::pandas-2.2.2-py310hf9f9076_1
paramiko conda-forge/noarch::paramiko-4.0.0-pyhd8ed1ab_0
parsl conda-forge/noarch::parsl-2024.4.15-pyhd8ed1ab_0
pip conda-forge/noarch::pip-25.2-pyh8b19718_0
psutil conda-forge/linux-64::psutil-7.1.2-py310h139afa4_1
pycparser conda-forge/noarch::pycparser-2.22-pyh29332c3_1
pyjwt conda-forge/noarch::pyjwt-2.10.1-pyhd8ed1ab_0
pynacl conda-forge/linux-64::pynacl-1.6.0-py310h7c4b9e2_0
pyparsing conda-forge/noarch::pyparsing-3.2.5-pyhcf101f3_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha55dd90_7
python conda-forge/linux-64::python-3.10.19-h3c07f61_2_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhe01879c_2
python-tzdata conda-forge/noarch::python-tzdata-2025.2-pyhd8ed1ab_0
python_abi conda-forge/noarch::python_abi-3.10-8_cp310
pytz conda-forge/noarch::pytz-2025.2-pyhd8ed1ab_0
pyyaml conda-forge/linux-64::pyyaml-6.0.3-py310h3406613_0
pyzmq conda-forge/linux-64::pyzmq-27.1.0-py310h4f33d48_0
qiime2 qiime2/linux-64::qiime2-2024.10.1-py310h0fb5ea9_0
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
requests conda-forge/noarch::requests-2.32.5-pyhd8ed1ab_0
setproctitle conda-forge/linux-64::setproctitle-1.3.6-py310h7c4b9e2_1
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
six conda-forge/noarch::six-1.17.0-pyhe01879c_1
tblib conda-forge/noarch::tblib-3.1.0-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_hd72426e_102
tomlkit conda-forge/noarch::tomlkit-0.13.3-pyha770c72_0
typeguard conda-forge/noarch::typeguard-4.4.4-pyhd8ed1ab_0
typing-extensions conda-forge/noarch::typing-extensions-4.15.0-h396c80c_0
typing_extensions conda-forge/noarch::typing_extensions-4.15.0-pyhcf101f3_0
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
tzlocal conda-forge/noarch::tzlocal-2.1-pyh9f0ad1d_0
urllib3 conda-forge/noarch::urllib3-2.5.0-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
yaml conda-forge/linux-64::yaml-0.2.5-h280c20c_3
zeromq conda-forge/linux-64::zeromq-4.3.5-h387f397_9
zipp conda-forge/noarch::zipp-3.23.0-pyhd8ed1ab_0
zstandard conda-forge/linux-64::zstandard-0.25.0-py310h139afa4_0
zstd conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

$ conda activate qiime2-2024.10

To deactivate an active environment, use

$ conda deactivate

So I run conda activate qiime2-2024.10 and qiime –help but still get

-bash: qiime: command not found

I deactivate and remove again using conda deactivate and conda env remove -p /u/home/e/coin125/.conda/envs/qiime2-2024.10

At this time I noticed the line about a newer version of conda existing so I ran this

(/u/home/e/coin125/miniconda3) [eimar125@n1149 ~]$ conda update -n base -c defaults conda

and got the following:

Collecting package metadata (current_repodata.json): - WARNING conda.models.version:get_matcher(535): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1., but conda is ignoring the . and treating it as 1.7.1
done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 25.9.1

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /u/local/apps/anaconda3/2022.05

added / updated specs:

  • conda

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
conda-pack-0.8.1           |   py39h06a4308_0          55 KB
pyjwt-2.10.1               |   py39h06a4308_0          75 KB
------------------------------------------------------------
                                       Total:         130 KB

The following packages will be UPDATED:

conda-pack pkgs/main/noarch::conda-pack-0.6.0-py~ --> pkgs/main/linux-64::conda-pack-0.8.1-py39h06a4308_0
pyjwt 2.1.0-py39h06a4308_0 --> 2.10.1-py39h06a4308_0

Proceed ([y]/n)? y

Downloading and Extracting Packages
conda-pack-0.8.1 | 55 KB | ############################################################################# | 100%
pyjwt-2.10.1 | 75 KB | ############################################################################# | 100%
Preparing transaction: done
Verifying transaction: failed

EnvironmentNotWritableError: The current user does not have write permissions to the target environment.
environment location: /u/local/apps/anaconda3/2022.05
uid: 22887
gid: 8627

which I think means that my conda did not update.

I don’t know why I thought this time might be different but I once again tried to download qiime2 2024.10. Here is the code:

(/u/home/e/coin125/miniconda3) [coin125@n1149 ~]$ conda create -p /u/home/e/coin125/miniconda3/envs/qiime2-2024.10 -c qiime2 -c conda-forge -c bioconda qiime2=2024.10

Here are the results:

WARNING: A conda environment already exists at '/u/home/e/coin125/miniconda3/envs/qiime2-2024.10'
Remove existing environment (y/[n])? y

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
current version: 4.12.0
latest version: 25.9.1

Please update conda by running

$ conda update -n base -c defaults conda

Package Plan

environment location: /u/home/e/coin125/miniconda3/envs/qiime2-2024.10

added / updated specs:

  • qiime2=2024.10

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-4.5-2_gnu
appdirs conda-forge/noarch::appdirs-1.4.4-pyhd8ed1ab_1
atpublic conda-forge/noarch::atpublic-6.0.2-pyhd8ed1ab_0
bcrypt conda-forge/linux-64::bcrypt-5.0.0-py310hd8f68c5_0
bibtexparser conda-forge/noarch::bibtexparser-1.4.3-pyhd8ed1ab_0
brotli-python conda-forge/linux-64::brotli-python-1.2.0-py310h8cfb67f_0
bzip2 conda-forge/linux-64::bzip2-1.0.8-hda65f42_8
ca-certificates conda-forge/noarch::ca-certificates-2025.10.5-hbd8a1cb_0
certifi conda-forge/noarch::certifi-2025.10.5-pyhd8ed1ab_0
cffi conda-forge/linux-64::cffi-2.0.0-py310he7384ee_1
charset-normalizer conda-forge/noarch::charset-normalizer-3.4.4-pyhd8ed1ab_0
cryptography conda-forge/linux-64::cryptography-46.0.3-py310hed992bd_0
decorator conda-forge/noarch::decorator-4.4.2-py_0
dill conda-forge/noarch::dill-0.4.0-pyhd8ed1ab_0
filelock conda-forge/noarch::filelock-3.20.0-pyhd8ed1ab_0
flufl.lock conda-forge/noarch::flufl.lock-8.2.0-pyhd8ed1ab_0
globus-sdk conda-forge/noarch::globus-sdk-4.1.0-pyhd8ed1ab_0
h2 conda-forge/noarch::h2-4.3.0-pyhcf101f3_0
hpack conda-forge/noarch::hpack-4.1.0-pyhd8ed1ab_0
hyperframe conda-forge/noarch::hyperframe-6.1.0-pyhd8ed1ab_0
idna conda-forge/noarch::idna-3.11-pyhd8ed1ab_0
importlib-metadata conda-forge/noarch::importlib-metadata-8.7.0-pyhe01879c_1
invoke conda-forge/noarch::invoke-2.2.1-pyhd8ed1ab_0
keyutils conda-forge/linux-64::keyutils-1.6.3-hb9d3cd8_0
krb5 conda-forge/linux-64::krb5-1.21.3-h659f571_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.44-h1aa0949_4
libblas conda-forge/linux-64::libblas-3.9.0-38_h4a7cf45_openblas
libcblas conda-forge/linux-64::libcblas-3.9.0-38_h0358290_openblas
libedit conda-forge/linux-64::libedit-3.1.20250104-pl5321h7949ede_0
libexpat conda-forge/linux-64::libexpat-2.7.1-hecca717_0
libffi conda-forge/linux-64::libffi-3.5.2-h9ec8514_0
libgcc conda-forge/linux-64::libgcc-15.2.0-h767d61c_7
libgcc-ng conda-forge/linux-64::libgcc-ng-15.2.0-h69a702a_7
libgfortran conda-forge/linux-64::libgfortran-15.2.0-h69a702a_7
libgfortran5 conda-forge/linux-64::libgfortran5-15.2.0-hcd61629_7
libgomp conda-forge/linux-64::libgomp-15.2.0-h767d61c_7
libiconv conda-forge/linux-64::libiconv-1.18-h3b78370_2
liblapack conda-forge/linux-64::liblapack-3.9.0-38_h47877c9_openblas
liblzma conda-forge/linux-64::liblzma-5.8.1-hb9d3cd8_2
libnsl conda-forge/linux-64::libnsl-2.0.1-hb9d3cd8_1
libopenblas conda-forge/linux-64::libopenblas-0.3.30-pthreads_h94d23a6_3
libsodium conda-forge/linux-64::libsodium-1.0.20-h4ab18f5_0
libsqlite conda-forge/linux-64::libsqlite-3.50.4-h0c1763c_0
libstdcxx conda-forge/linux-64::libstdcxx-15.2.0-h8f9b012_7
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-15.2.0-h4852527_7
libuuid conda-forge/linux-64::libuuid-2.41.2-he9a06e4_0
libxcrypt conda-forge/linux-64::libxcrypt-4.4.36-hd590300_1
libxml2 conda-forge/linux-64::libxml2-2.15.1-h031cc0b_0
libxml2-16 conda-forge/linux-64::libxml2-16-2.15.1-hf2a90c1_0
libxslt conda-forge/linux-64::libxslt-1.1.43-h711ed8c_1
libzlib conda-forge/linux-64::libzlib-1.3.1-hb9d3cd8_2
lxml conda-forge/linux-64::lxml-6.0.2-py310he6d4be0_1
ncurses conda-forge/linux-64::ncurses-6.5-h2d0b736_3
networkx conda-forge/noarch::networkx-3.1-pyhd8ed1ab_0
numpy conda-forge/linux-64::numpy-2.2.6-py310hefbff90_0
openssl conda-forge/linux-64::openssl-3.5.4-h26f9b46_0
pandas conda-forge/linux-64::pandas-2.2.2-py310hf9f9076_1
paramiko conda-forge/noarch::paramiko-4.0.0-pyhd8ed1ab_0
parsl conda-forge/noarch::parsl-2024.4.15-pyhd8ed1ab_0
pip conda-forge/noarch::pip-25.2-pyh8b19718_0
psutil conda-forge/linux-64::psutil-7.1.2-py310h139afa4_1
pycparser conda-forge/noarch::pycparser-2.22-pyh29332c3_1
pyjwt conda-forge/noarch::pyjwt-2.10.1-pyhd8ed1ab_0
pynacl conda-forge/linux-64::pynacl-1.6.0-py310h7c4b9e2_0
pyparsing conda-forge/noarch::pyparsing-3.2.5-pyhcf101f3_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha55dd90_7
python conda-forge/linux-64::python-3.10.19-h3c07f61_2_cpython
python-dateutil conda-forge/noarch::python-dateutil-2.9.0.post0-pyhe01879c_2
python-tzdata conda-forge/noarch::python-tzdata-2025.2-pyhd8ed1ab_0
python_abi conda-forge/noarch::python_abi-3.10-8_cp310
pytz conda-forge/noarch::pytz-2025.2-pyhd8ed1ab_0
pyyaml conda-forge/linux-64::pyyaml-6.0.3-py310h3406613_0
pyzmq conda-forge/linux-64::pyzmq-27.1.0-py310h4f33d48_0
qiime2 qiime2/linux-64::qiime2-2024.10.1-py310h0fb5ea9_0
readline conda-forge/linux-64::readline-8.2-h8c095d6_2
requests conda-forge/noarch::requests-2.32.5-pyhd8ed1ab_0
setproctitle conda-forge/linux-64::setproctitle-1.3.6-py310h7c4b9e2_1
setuptools conda-forge/noarch::setuptools-80.9.0-pyhff2d567_0
six conda-forge/noarch::six-1.17.0-pyhe01879c_1
tblib conda-forge/noarch::tblib-3.1.0-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_hd72426e_102
tomlkit conda-forge/noarch::tomlkit-0.13.3-pyha770c72_0
typeguard conda-forge/noarch::typeguard-4.4.4-pyhd8ed1ab_0
typing-extensions conda-forge/noarch::typing-extensions-4.15.0-h396c80c_0
typing_extensions conda-forge/noarch::typing_extensions-4.15.0-pyhcf101f3_0
tzdata conda-forge/noarch::tzdata-2025b-h78e105d_0
tzlocal conda-forge/noarch::tzlocal-2.1-pyh9f0ad1d_0
urllib3 conda-forge/noarch::urllib3-2.5.0-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.45.1-pyhd8ed1ab_1
yaml conda-forge/linux-64::yaml-0.2.5-h280c20c_3
zeromq conda-forge/linux-64::zeromq-4.3.5-h387f397_9
zipp conda-forge/noarch::zipp-3.23.0-pyhd8ed1ab_0
zstandard conda-forge/linux-64::zstandard-0.25.0-py310h139afa4_0
zstd conda-forge/linux-64::zstd-1.5.7-hb8e6e7a_2

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

To activate this environment, use

$ conda activate /u/home/e/coin125/miniconda3/envs/qiime2-2024.10

To deactivate an active environment, use

$ conda deactivate

I once again get excited and run conda activate /u/home/e/coin125/miniconda3/envs/qiime2-2024.10 and qiime --help but still get

-bash: qiime: command not found

I am incredibly sad about this and just want to do my work and would really appreciate any help with this issue.

2

Hello @Coinenthusiast,

This looks like something you need to contact the sysadmin for your HPC about.

In particular, this makes it look like you don't have permission to create new conda environments.

EnvironmentNotWritableError: The current user does not have write permissions to the target environment.

Though it is very confusing that conda seems to be under the impression that something was created. If you run the commands

ls /u/home/e/coin125/miniconda3/envs/qiime2-2024.10

and

stat /u/home/e/coin125/miniconda3/envs/qiime2-2024.10

What is the output? That might help us, or your sysadmin, understand why this is happening. It is doubtful we can fix whatever is causing this on our end, though.

2 Likes
3

Hello! Thank you very much for your response! Here are the outputs for the commands you suggested.

First code and output:

(base) [coin125@n1821 ~]$ ls /u/home/e/coin125/miniconda3/envs/qiime2-2024.10 bin

compiler_compat conda-meta etc include lib man sbin share ssl x86_64-conda-linux-gnu

Second code and output:

(base) [coin125@n1821 ~]$ stat /u/home/e/coin125/miniconda3/envs/qiime2-2024.10

File: '/u/home/e/coin125/miniconda3/envs/qiime2-2024.10'
Size: 4096 Blocks: 0 IO Block: 32768 directory
Device: 38h/56d Inode: 13545432553334769519 Links: 2
Access: (0755/drwxr-xr-x) Uid: (22887/coin125) Gid: ( 8627/ pi)
Context: system_u:object_r:nfs_t:s0
Access: 2025-10-29 23:24:18.478882115 -0700
Modify: 2025-10-29 23:24:18.478882115 -0700
Change: 2025-10-29 23:24:18.478882115 -0700
Birth: -

In the line Gid: ( 8627/ pi) from this output I replaced my PI’s last name with just “pi” for anonymity

4

@Coinenthusiast conda definitely created something.

I'm looking up at the command you ran again:

conda create -p /u/home/e/coin125/miniconda3/envs/qiime2-2024.10 -c qiime2 -c conda-forge -c bioconda qiime2=2024.10

And on second inspection, it doesn't look quite right. I think the EnvironmentError was a red herring that threw me off, and the issue with your second command is something else entirely. I apologize.

Setting the prefix was a good idea, but I don't think you pointed it at the correct env file. Can you please remove the current conda environment and run the following command adapted from our docs here?

conda env create \
  -p /u/home/e/coin125/miniconda3/envs/qiime2-2024.10 \
  --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2024.10/amplicon/released/qiime2-amplicon-ubuntu-latest-conda.yml
5

Really appreciate your help once again! Before I try that I do want to mention that I did mention system admin for my HPC about this issue. I was recommended to use qiime2 from a container and was told that an earlier version of qiime2_amplicon_2024.5 already existed and to try the following code:

qrsh -l h_data=10G

module load apptainer

apptainer run $H2_CONTAINER_LOC/qiime2_amplicon_2024.5.sif

When I am in the apptainer the denoise ccs command works! I ran the following modified command as a batch job by opening up the nano text editor and submitting it with qsub qiime2_batch.sh after saving it in the text editor.

#!/bin/bash

#$ -N qiime2_denoise

#$ -pe shared 1

#$ -l h_vmem=70G

#$ -l h_rt=64:00:00

#$ -m bea

#$ -M coin125@gmail.com

#$ -cwd

source /u/local/Modules/default/init/bash

module load apptainer

WORKDIR=/u/scratch/e/coin125

echo "Using container location: $H2_CONTAINER_LOC"

apptainer exec -B ${WORKDIR}:/data $H2_CONTAINER_LOC/qiime2_amplicon_2024.5.sif \

qiime dada2 denoise-ccs \

--i-demultiplexed-seqs /data/pacbio-demux.qza \

--p-front AGRGTTYGATYMTGGCTCAG \

--p-adapter RGYTACCTTGTTACGACTT \

--p-min-len 1000 \

--p-max-len 1600 \

--p-n-threads 1 \

--p-pooling-method independent \

--p-chimera-method consensus \

--o-representative-sequences /data/rep-seqs.qza \

--o-table /data/table.qza \

--o-denoising-stats /data/denoising-stats.qza

My job status is currently in queue and I am a bit concerned since it has been in queue for over 12 hours but hopefully this helps someone figure out how to use a newer version of qiime2 on Hoffman2! And thank you once again for your help!

1 Like
6

Did your command finish running? These commands can take a VERY long time on large datasets.

7

Hello again!

Sorry for not replying back for a while but no my code did not work. Initially the problem with my code was the line # -l h_vmem=70G should have been replaced with # -l h_data=70G. You are correct that this command can take a VERY long time as my labmate mentioned that it took over 2 days for their denoising step to finish. I edited my code and reran it. Here is my edited code: #!/bin/bash

#$ -N qiime2_denoise

#$ -pe shared 1

#$ -l h_data=100G

#$ -l h_rt=96:00:00

#$ -m bea

#$ -M coin125@gmail.com

#$ -cwd

source /u/local/Modules/default/init/bash

module load apptainer

WORKDIR=/u/scratch/e/coin125

echo "Using container location: $H2_CONTAINER_LOC"

apptainer exec -B ${WORKDIR}:/data $H2_CONTAINER_LOC/qiime2_amplicon_2024.5.sif \

qiime dada2 denoise-ccs \

--i-demultiplexed-seqs /data/pacbio-demux.qza \

--p-front AGRGTTYGATYMTGGCTCAG \

--p-adapter RGYTACCTTGTTACGACTT \

--p-max-ee 30 \

--p-min-len 1000 \

--p-max-len 1600 \

--p-n-threads 1 \

--p-pooling-method independent \

--p-chimera-method consensus \

--o-representative-sequences /data/rep-seqs.qza \

--o-table /data/table.qza \

--o-denoising-stats /data/denoising-stats.qza

But then I received the following email today:

Job 11292093 (qiime2_denoise) Aborted
Exit Status = 137
Signal = KILL
User = coin125
Queue = pod_highmem.q@n7005
Host = n7005.hoffman2.idre.ucla.edu
Start Time = 11/05/2025 16:53:50.406
End Time = 11/09/2025 16:53:50.056
CPU = 2:13:17:59
Max vmem = 18.574G
Max rss = NA
failed execd enforced h_rt limit because:
job 11292093.1 died through signal KILL (9)

Which was incredibly disappointing as I felt that it would run this time after my edit but it took 4 days and was unsuccessful. I am unsure what else I can do other than add more runtime but am also confused since my labmate ran the same data in less time even with requesting only 1 CPU core. I am going to try to run the same code but request 2 CPU cores and more runtime and will update. However, I do want to say that I reached out to Hoffman support and was able to access a newer version of Qiime2 from a container! Here it what worked:

module load apptainer

apptainer run $H2_CONTAINER_LOC/qiime2_amplicon_2024.5.sif

So hopefully this helps someone too!

1 Like
9

Hi @Coinenthusiast,
Are you able to increase the number of threads and the number of CPUs that this job has access to? I usually run my denoise commands on at least 8 CPUs. Note that the amount of diversity and/or sequencing error can impact the runtime of these jobs, so it's unfortunately not just a function of the number of sequences (which is why your runtime might differ from your colleague's runtime). Requesting 16 or 32 CPUs and that same number of threads should decrease your runtime dramatically.

10

Hi! Thank you for responding! I tried to request 4 CPUs before but the job never got started. Then I tried 3 which also never got started so I then just ran it with 1 CPU. I’m trying 2 CPU and 2 threads this time but I submitted the job yesterday and have not yet gotten an email that the job started yet :frowning:

11

Based on a quick google of Hoffman2, it looks like it has various queues:

The idea here is to request from a different queue so you can actually run this job faster. I would try getting an interactive node so you can just run the Qiime2 commands directly.

12

Thanks for looking into that @colinbrislawn, and for the additional information @Coinenthusiast. I think the key here is going to be figuring out how to get this running in parallel, ideally on 8+ CPUs (16, 32, or 64 would probably work great). Are you able to reach out to a help email address for this server to see if you can get help running in parallel?

1 Like