ImportError: No module named pandas

[laibinhuang]

Dear Mike,

I get some error like this:

I have pandas installed in my base Envs actually, I don't know why this happens. Thank you!

code bit-update-ncbi-taxonomy

cd /home/lbhuang/Moore/results/K2/k2_outputs/ for f1 in *_k-output.txt do filename=$(basename "$f1")
sample="${filename%_k-output.txt}"
bit-kraken2-to-taxon-summaries -i ${sample}_k-output.txt -o ${sample}-k-tax.tsv done

bit-combine-kraken2-taxon-summaries -i *-k-tax.tsv -o combined-k-tax.tsv

Errors: Traceback (most recent call last): File "/home/lbhuang/mambaforge/envs/bit/bin/bit-kraken2-to-taxon-summaries", line 26, in import pandas as pd ImportError: No module named pandas Traceback (most recent call last): File "/home/lbhuang/mambaforge/envs/bit/bin/bit-kraken2-to-taxon-summaries", line 26, in import pandas as pd ImportError: No module named pandas Traceback (most recent call last): File "/home/lbhuang/mambaforge/envs/bit/bin/bit-combine-kraken2-taxon-summaries", line 9, in import pandas as pd ImportError: No module named pandas

[AstrobioMike]

hi there, @laibinhuang :)

Weird, pandas should have been installed with the conda install of the bit environment

Did you do the bit environment creation/installation like this?

mamba create -n bit -c conda-forge -c bioconda -c defaults -c astrobiomike bit

Also, can you send the output of the following 2 things:

bit-version

conda list

(or maybe mamba list if there is no conda program from the mambaforge install)

That's the one definitely new thing, i haven't done any testing using mambaforge instead of conda and then installing mamba. I did recently hear from a friend that they've had trouble installing other things after trying mamba forge. So that might be causing a problem (i know mamba forge is the recommended way to use mamba, but i've still be using a conda install and then installing mamba)

Get back to me with the above info if/when you can, and i'll try setting up a system with mamba forge to try to see if i hit the same issue when i can, and then maybe i can help trouble shoot.

One attempted fix you could try is installing pandas in the bit environment, e.g., when the bit environment is active:

mamba install -c conda-forge pandas=1.4.2

But even if that works, if that was missing, other things might be too, so i'd be wary

[laibinhuang]

Yes, sure: thank you

*(bit) @.**:~$ bit-version

            Bioinformatics Tools v1.8.57
            github.com/AstrobioMike/bit

If you happen to find this toolset useful in your work, please be sure

to cite it :)

Lee M. bit: a multipurpose collection of bioinformatics tools. F1000Research 2022, 11:122 https://doi.org/10.12688/f1000research.79530.1

*(base) @.**:~$ conda list

packages in environment at /home/lbhuang/mambaforge:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge aioeasywebdav 2.4.0 pyha770c72_0 conda-forge aiohttp 3.7.4.post0 py310h6acc77f_1 conda-forge amply 0.1.5 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge async-timeout 3.0.1 py_1000 conda-forge attmap 0.13.2 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge bcrypt 3.2.2 py310h5764c6d_1 conda-forge binutils_impl_linux-64 2.40 hf600244_0 conda-forge boltons 23.0.0 pyhd8ed1ab_0 conda-forge boto3 1.26.135 pyhd8ed1ab_0 conda-forge botocore 1.29.135 pyhd8ed1ab_0 conda-forge brotlipy 0.7.0 py310h5764c6d_1005 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2023.5.7 hbcca054_0 conda-forge cachetools 5.3.0 pyhd8ed1ab_0 conda-forge cairo 1.16.0 hbbf8b49_1016 conda-forge certifi 2023.5.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_3 conda-forge chardet 4.0.0 py310hff52083_3 conda-forge charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge coin-or-cbc 2.10.10 h9002f0b_0 conda-forge coin-or-cgl 0.60.7 h516709c_0 conda-forge coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge coin-or-osi 0.108.8 ha2443b9_0 conda-forge coin-or-utils 2.11.9 hee58242_0 conda-forge coincbc 2.10.10 0_metapackage conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge conda 23.3.1 py310hff52083_0 conda-forge conda-package-handling 2.0.2 pyh38be061_0 conda-forge conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge configargparse 1.5.3 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge cryptography 40.0.1 py310h34c0648_0 conda-forge curl 8.1.2 h409715c_0 conda-forge datrie 0.8.2 py310h5764c6d_6 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge docutils 0.20.1 py310hff52083_0 conda-forge dpath 2.1.5 pyha770c72_1 conda-forge dropbox 11.36.0 pyhd8ed1ab_0 conda-forge exceptiongroup 1.1.1 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge filechunkio 1.8 py_2 conda-forge filelock 3.12.0 pyhd8ed1ab_0 conda-forge fmt 9.1.0 h924138e_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge ftputil 5.0.4 pyhd8ed1ab_0 conda-forge gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gfortran_impl_linux-64 12.2.0 h55be85b_19 conda-forge gitdb 4.0.10 pyhd8ed1ab_0 conda-forge gitpython 3.1.31 pyhd8ed1ab_0 conda-forge google-api-core 2.11.0 pyhd8ed1ab_0 conda-forge google-api-python-client 2.86.0 pyhd8ed1ab_0 conda-forge google-auth 2.18.0 pyh1a96a4e_0 conda-forge google-auth-httplib2 0.1.0 pyhd8ed1ab_1 conda-forge google-cloud-core 2.3.2 pyhd8ed1ab_0 conda-forge google-cloud-storage 2.9.0 pyh1a96a4e_0 conda-forge google-crc32c 1.1.2 py310he8fe98e_4 conda-forge google-resumable-media 2.5.0 pyhd8ed1ab_0 conda-forge googleapis-common-protos 1.57.1 pyhd8ed1ab_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge grpcio 1.54.2 py310heca2aa9_2 conda-forge gsl 2.7 he838d99_0 conda-forge gxx_impl_linux-64 12.2.0 hcc96c02_19 conda-forge harfbuzz 7.3.0 hdb3a94d_0 conda-forge httplib2 0.22.0 pyhd8ed1ab_0 conda-forge humanfriendly 10.0 py310hff52083_4 conda-forge icu 72.1 hcb278e6_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib-metadata 6.6.0 pyha770c72_0 conda-forge importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge jsonpatch 1.32 pyhd8ed1ab_0 conda-forge jsonpointer 2.0 py_0 conda-forge jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge jupyter_core 5.3.0 py310hff52083_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.20.1 h81ceb04_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20230125.2 cxx17_h59595ed_2 conda-forge libarchive 3.6.2 h039dbb9_1 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcurl 8.1.2 h409715c_0 conda-forge libdeflate 1.18 h0b41bf4_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libglib 2.76.3 hebfc3b9_0 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libgrpc 1.54.2 hb20ce57_2 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge liblapacke 3.9.0 16_linux64_openblas conda-forge libmamba 1.4.1 hcea66bb_0 conda-forge libmambapy 1.4.1 py310h1428755_0 conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libpng 1.6.39 h753d276_0 conda-forge libprotobuf 3.21.12 h3eb15da_0 conda-forge libsanitizer 12.2.0 h46fd767_19 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsolv 0.7.23 h3eb15da_0 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 hf14f497_3 conda-forge libstdcxx-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libtiff 4.5.1 h8b53f26_0 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.0 h0b41bf4_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxml2 2.11.4 h0d562d8_0 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge logmuse 0.2.6 pyh8c360ce_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge make 4.3 hd18ef5c_1 conda-forge mamba 1.4.1 py310h51d5547_0 conda-forge markdown-it-py 2.2.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.2 py310h1fa729e_0 conda-forge mdurl 0.1.0 pyhd8ed1ab_0 conda-forge multidict 6.0.4 py310h1fa729e_0 conda-forge nbformat 5.8.0 pyhd8ed1ab_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge numpy 1.24.3 py310ha4c1d20_0 conda-forge oauth2client 4.1.3 py_0 conda-forge openssl 3.1.1 hd590300_1 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandas 2.0.2 pypi_0 pypi pango 1.50.14 heaa33ce_1 conda-forge paramiko 3.1.0 pyhd8ed1ab_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge peppy 0.35.5 pyhd8ed1ab_0 conda-forge perl 5.32.1 2_h7f98852_perl5 conda-forge pip 23.0.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge plac 1.3.5 pyhd8ed1ab_0 conda-forge platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge pluggy 1.0.0 pyhd8ed1ab_5 conda-forge ply 3.11 py_1 conda-forge prettytable 3.7.0 pyhd8ed1ab_0 conda-forge protobuf 4.21.12 py310heca2aa9_0 conda-forge psutil 5.9.5 py310h1fa729e_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pulp 2.7.0 py310hff52083_0 conda-forge pyasn1 0.4.8 py_0 conda-forge pyasn1-modules 0.2.7 py_0 conda-forge pybind11-abi 4 hd8ed1ab_3 conda-forge pycosat 0.6.4 py310h5764c6d_1 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.15.1 pyhd8ed1ab_0 conda-forge pynacl 1.5.0 py310h5764c6d_2 conda-forge pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pyrsistent 0.19.3 py310h1fa729e_0 conda-forge pysftp 0.2.9 py_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 7.3.1 pyhd8ed1ab_0 conda-forge python 3.10.10 he550d4f_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge python-irodsclient 1.1.6 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 3_cp310 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py310h5764c6d_5 conda-forge r-base 4.3.0 hfabd6f2_1 conda-forge re2 2023.03.02 h8c504da_0 conda-forge readline 8.2 h8228510_1 conda-forge rename 1.601 hdfd78af_1 bioconda reproc 14.2.4 h0b41bf4_0 conda-forge reproc-cpp 14.2.4 hcb278e6_0 conda-forge requests 2.28.2 pyhd8ed1ab_1 conda-forge reretry 0.11.8 pyhd8ed1ab_0 conda-forge rich 13.3.5 pyhd8ed1ab_0 conda-forge rsa 4.9 pyhd8ed1ab_0 conda-forge ruamel.yaml 0.17.21 py310h1fa729e_3 conda-forge ruamel.yaml.clib 0.2.7 py310h1fa729e_1 conda-forge s3transfer 0.6.1 pyhd8ed1ab_0 conda-forge sed 4.8 he412f7d_0 conda-forge setuptools 65.6.3 pyhd8ed1ab_0 conda-forge setuptools-scm 7.1.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge slacker 0.14.0 py_0 conda-forge smart_open 6.3.0 pyhd8ed1ab_1 conda-forge smmap 3.0.5 pyh44b312d_0 conda-forge snakemake 7.28.3 hdfd78af_0 bioconda snakemake-minimal 7.28.3 pyhdfd78af_0 bioconda stone 3.3.1 pyhd8ed1ab_0 conda-forge stopit 1.1.2 py_0 conda-forge sysroot_linux-64 2.12 he073ed8_15 conda-forge tabulate 0.9.0 pyhd8ed1ab_1 conda-forge throttler 1.2.1 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tktable 2.10 hb7b940f_3 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge toposort 1.10 pyhd8ed1ab_0 conda-forge tqdm 4.65.0 pyhd8ed1ab_1 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge typing-extensions 4.5.0 hd8ed1ab_0 conda-forge typing_extensions 4.5.0 pyha770c72_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge ubiquerg 0.6.2 pyhd8ed1ab_0 conda-forge uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge veracitools 0.1.3 py_0 conda-forge wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge wget 1.20.3 ha35d2d1_1 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge wrapt 1.15.0 py310h1fa729e_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.5 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.3.0 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yaml-cpp 0.7.0 h27087fc_2 conda-forge yarl 1.9.1 py310h2372a71_0 conda-forge yte 1.5.1 py310hff52083_1 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstandard 0.19.0 py310hdeb6495_1 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge

On Wed, Jun 21, 2023 at 7:08 PM Mike Lee @.***> wrote:

hi there, @laibinhuang https://github.com/laibinhuang :)

Weird, pandas should have been installed with the conda install of the bit environment

Did you do the bit environment creation/installation like this?

mamba create -n bit -c conda-forge -c bioconda -c defaults -c astrobiomike bit

Also, can you send the output of the following 2 things:

bit-version

conda list

(or maybe mamba list if there is no conda program from the mambaforge install)

That's the one definitely new thing, i haven't done any testing using mambaforge instead of conda and then installing mamba. I did recently hear from a friend that they've had trouble installing other things after trying mamba forge. So that might be causing a problem (i know mamba forge is the recommended way to use mamba, but i've still be using a conda install and then installing mamba)

Get back to me with the above info if/when you can, and i'll try setting up a system with mamba forge to try to see if i hit the same issue when i can, and then maybe i can help trouble shoot.

One attempted fix you could try is installing pandas in the bit environment, e.g., when the bit environment is active:

mamba install -c conda-forge pandas=1.4.2

But even if that works, if that was missing, other things might be too, so i'd be wary

— Reply to this email directly, view it on GitHub https://github.com/AstrobioMike/bit/issues/14#issuecomment-1601918446, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIQOU762JRML55DC23GUKTXMOSK5ANCNFSM6AAAAAAZPQUUNQ . You are receiving this because you were mentioned.Message ID: @.***>

-- ----------------------------------------------------------- Laibin Huang, Ph.D.

Assistant Professor of Microbiology Saint Louis University, St. Louis, MO Department of Biology Macelwane Hall 301 3507 Laclede Ave. St. Louis, MO 63103

---

[laibinhuang]

Hi Mike

I figure out the pandas thing: I just delete the python2 and leave python3 version in my all conda evans

however, this time I got an error from bit itself:

bit-update-ncbi-taxonomy bit-kraken2-to-taxon-summaries -i ${sample}_k-output.txt -o ${sample}-k-tax.tsv

Traceback (most recent call last): File "/home/lbhuang/mambaforge/envs/bit/bin/bit-kraken2-to-taxon-summaries", line 91, in taxid_counts_df = taxid_counts_df.astype({"taxid":'int64'}) File "/home/lbhuang/mambaforge/envs/bit/lib/python3.9/site-packages/pandas/core/generic.py", line 6305, in astype res_col = col.astype(dtype=cdt, copy=copy, errors=errors) File "/home/lbhuang/mambaforge/envs/bit/lib/python3.9/site-packages/pandas/core/generic.py", line 6324, in astype new_data = self._mgr.astype(dtype=dtype, copy=copy, errors=errors) File "/home/lbhuang/mambaforge/envs/bit/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 451, in astype return self.apply( File "/home/lbhuang/mambaforge/envs/bit/lib/python3.9/site-packages/pandas/core/internals/managers.py", line 352, in apply applied = getattr(b, f)(*kwargs) File "/home/lbhuang/mambaforge/envs/bit/lib/python3.9/site-packages/pandas/core/internals/blocks.py", line 511, in astype new_values = astype_array_safe(values, dtype, copy=copy, errors=errors) File "/home/lbhuang/mambaforge/envs/bit/lib/python3.9/site-packages/pandas/core/dtypes/astype.py", line 242, in astype_array_safe new_values = astype_array(values, dtype, copy=copy) File "/home/lbhuang/mambaforge/envs/bit/lib/python3.9/site-packages/pandas/core/dtypes/astype.py", line 187, in astype_array values = _astype_nansafe(values, dtype, copy=copy) File "/home/lbhuang/mambaforge/envs/bit/lib/python3.9/site-packages/pandas/core/dtypes/astype.py", line 138, in _astype_nansafe return arr.astype(dtype, copy=True) ValueError: invalid literal for int() with base 10: 'Nocardia asteroides (taxid 1824)': Error while type casting for column 'taxid'*

Thank you Laibin

On Wed, Jun 21, 2023 at 7:27 PM Laibin Huang @.***> wrote:

Yes, sure: thank you

*(bit) @.**:~$ bit-version

            Bioinformatics Tools v1.8.57
            github.com/AstrobioMike/bit

If you happen to find this toolset useful in your work, please be sure

to cite it :)

Lee M. bit: a multipurpose collection of bioinformatics tools. F1000Research 2022, 11:122 https://doi.org/10.12688/f1000research.79530.1

*(base) @.**:~$ conda list

packages in environment at /home/lbhuang/mambaforge:

#

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge aioeasywebdav 2.4.0 pyha770c72_0 conda-forge aiohttp 3.7.4.post0 py310h6acc77f_1 conda-forge amply 0.1.5 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge async-timeout 3.0.1 py_1000 conda-forge attmap 0.13.2 pyhd8ed1ab_0 conda-forge attrs 23.1.0 pyh71513ae_1 conda-forge backports 1.0 pyhd8ed1ab_3 conda-forge backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge bcrypt 3.2.2 py310h5764c6d_1 conda-forge binutils_impl_linux-64 2.40 hf600244_0 conda-forge boltons 23.0.0 pyhd8ed1ab_0 conda-forge boto3 1.26.135 pyhd8ed1ab_0 conda-forge botocore 1.29.135 pyhd8ed1ab_0 conda-forge brotlipy 0.7.0 py310h5764c6d_1005 conda-forge bwidget 1.9.14 ha770c72_1 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2023.5.7 hbcca054_0 conda-forge cachetools 5.3.0 pyhd8ed1ab_0 conda-forge cairo 1.16.0 hbbf8b49_1016 conda-forge certifi 2023.5.7 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_3 conda-forge chardet 4.0.0 py310hff52083_3 conda-forge charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge coin-or-cbc 2.10.10 h9002f0b_0 conda-forge coin-or-cgl 0.60.7 h516709c_0 conda-forge coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge coin-or-osi 0.108.8 ha2443b9_0 conda-forge coin-or-utils 2.11.9 hee58242_0 conda-forge coincbc 2.10.10 0_metapackage conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge conda 23.3.1 py310hff52083_0 conda-forge conda-package-handling 2.0.2 pyh38be061_0 conda-forge conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge configargparse 1.5.3 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge cryptography 40.0.1 py310h34c0648_0 conda-forge curl 8.1.2 h409715c_0 conda-forge datrie 0.8.2 py310h5764c6d_6 conda-forge defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge docutils 0.20.1 py310hff52083_0 conda-forge dpath 2.1.5 pyha770c72_1 conda-forge dropbox 11.36.0 pyhd8ed1ab_0 conda-forge exceptiongroup 1.1.1 pyhd8ed1ab_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge filechunkio 1.8 py_2 conda-forge filelock 3.12.0 pyhd8ed1ab_0 conda-forge fmt 9.1.0 h924138e_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 hab24e00_0 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge fribidi 1.0.10 h36c2ea0_0 conda-forge ftputil 5.0.4 pyhd8ed1ab_0 conda-forge gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gfortran_impl_linux-64 12.2.0 h55be85b_19 conda-forge gitdb 4.0.10 pyhd8ed1ab_0 conda-forge gitpython 3.1.31 pyhd8ed1ab_0 conda-forge google-api-core 2.11.0 pyhd8ed1ab_0 conda-forge google-api-python-client 2.86.0 pyhd8ed1ab_0 conda-forge google-auth 2.18.0 pyh1a96a4e_0 conda-forge google-auth-httplib2 0.1.0 pyhd8ed1ab_1 conda-forge google-cloud-core 2.3.2 pyhd8ed1ab_0 conda-forge google-cloud-storage 2.9.0 pyh1a96a4e_0 conda-forge google-crc32c 1.1.2 py310he8fe98e_4 conda-forge google-resumable-media 2.5.0 pyhd8ed1ab_0 conda-forge googleapis-common-protos 1.57.1 pyhd8ed1ab_0 conda-forge graphite2 1.3.13 h58526e2_1001 conda-forge grpcio 1.54.2 py310heca2aa9_2 conda-forge gsl 2.7 he838d99_0 conda-forge gxx_impl_linux-64 12.2.0 hcc96c02_19 conda-forge harfbuzz 7.3.0 hdb3a94d_0 conda-forge httplib2 0.22.0 pyhd8ed1ab_0 conda-forge humanfriendly 10.0 py310hff52083_4 conda-forge icu 72.1 hcb278e6_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge importlib-metadata 6.6.0 pyha770c72_0 conda-forge importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jmespath 1.0.1 pyhd8ed1ab_0 conda-forge jsonpatch 1.32 pyhd8ed1ab_0 conda-forge jsonpointer 2.0 py_0 conda-forge jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge jupyter_core 5.3.0 py310hff52083_0 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.20.1 h81ceb04_0 conda-forge ld_impl_linux-64 2.40 h41732ed_0 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libabseil 20230125.2 cxx17_h59595ed_2 conda-forge libarchive 3.6.2 h039dbb9_1 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcurl 8.1.2 h409715c_0 conda-forge libdeflate 1.18 h0b41bf4_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libglib 2.76.3 hebfc3b9_0 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libgrpc 1.54.2 hb20ce57_2 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libidn2 2.3.4 h166bdaf_0 conda-forge libjpeg-turbo 2.1.5.1 h0b41bf4_0 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge liblapacke 3.9.0 16_linux64_openblas conda-forge libmamba 1.4.1 hcea66bb_0 conda-forge libmambapy 1.4.1 py310h1428755_0 conda-forge libnghttp2 1.52.0 h61bc06f_0 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libpng 1.6.39 h753d276_0 conda-forge libprotobuf 3.21.12 h3eb15da_0 conda-forge libsanitizer 12.2.0 h46fd767_19 conda-forge libsodium 1.0.18 h36c2ea0_1 conda-forge libsolv 0.7.23 h3eb15da_0 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 hf14f497_3 conda-forge libstdcxx-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libtiff 4.5.1 h8b53f26_0 conda-forge libunistring 0.9.10 h7f98852_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.0 h0b41bf4_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxml2 2.11.4 h0d562d8_0 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge logmuse 0.2.6 pyh8c360ce_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge lzo 2.10 h516909a_1000 conda-forge make 4.3 hd18ef5c_1 conda-forge mamba 1.4.1 py310h51d5547_0 conda-forge markdown-it-py 2.2.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.2 py310h1fa729e_0 conda-forge mdurl 0.1.0 pyhd8ed1ab_0 conda-forge multidict 6.0.4 py310h1fa729e_0 conda-forge nbformat 5.8.0 pyhd8ed1ab_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge numpy 1.24.3 py310ha4c1d20_0 conda-forge oauth2client 4.1.3 py_0 conda-forge openssl 3.1.1 hd590300_1 conda-forge packaging 23.1 pyhd8ed1ab_0 conda-forge pandas 2.0.2 pypi_0 pypi pango 1.50.14 heaa33ce_1 conda-forge paramiko 3.1.0 pyhd8ed1ab_0 conda-forge pcre2 10.40 hc3806b6_0 conda-forge peppy 0.35.5 pyhd8ed1ab_0 conda-forge perl 5.32.1 2_h7f98852_perl5 conda-forge pip 23.0.1 pyhd8ed1ab_0 conda-forge pixman 0.40.0 h36c2ea0_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge plac 1.3.5 pyhd8ed1ab_0 conda-forge platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge pluggy 1.0.0 pyhd8ed1ab_5 conda-forge ply 3.11 py_1 conda-forge prettytable 3.7.0 pyhd8ed1ab_0 conda-forge protobuf 4.21.12 py310heca2aa9_0 conda-forge psutil 5.9.5 py310h1fa729e_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pulp 2.7.0 py310hff52083_0 conda-forge pyasn1 0.4.8 py_0 conda-forge pyasn1-modules 0.2.7 py_0 conda-forge pybind11-abi 4 hd8ed1ab_3 conda-forge pycosat 0.6.4 py310h5764c6d_1 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.15.1 pyhd8ed1ab_0 conda-forge pynacl 1.5.0 py310h5764c6d_2 conda-forge pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pyrsistent 0.19.3 py310h1fa729e_0 conda-forge pysftp 0.2.9 py_1 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge pytest 7.3.1 pyhd8ed1ab_0 conda-forge python 3.10.10 he550d4f_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge python-irodsclient 1.1.6 pyhd8ed1ab_0 conda-forge python-tzdata 2023.3 pyhd8ed1ab_0 conda-forge python_abi 3.10 3_cp310 conda-forge pytz 2023.3 pyhd8ed1ab_0 conda-forge pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py310h5764c6d_5 conda-forge r-base 4.3.0 hfabd6f2_1 conda-forge re2 2023.03.02 h8c504da_0 conda-forge readline 8.2 h8228510_1 conda-forge rename 1.601 hdfd78af_1 bioconda reproc 14.2.4 h0b41bf4_0 conda-forge reproc-cpp 14.2.4 hcb278e6_0 conda-forge requests 2.28.2 pyhd8ed1ab_1 conda-forge reretry 0.11.8 pyhd8ed1ab_0 conda-forge rich 13.3.5 pyhd8ed1ab_0 conda-forge rsa 4.9 pyhd8ed1ab_0 conda-forge ruamel.yaml 0.17.21 py310h1fa729e_3 conda-forge ruamel.yaml.clib 0.2.7 py310h1fa729e_1 conda-forge s3transfer 0.6.1 pyhd8ed1ab_0 conda-forge sed 4.8 he412f7d_0 conda-forge setuptools 65.6.3 pyhd8ed1ab_0 conda-forge setuptools-scm 7.1.0 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge slacker 0.14.0 py_0 conda-forge smart_open 6.3.0 pyhd8ed1ab_1 conda-forge smmap 3.0.5 pyh44b312d_0 conda-forge snakemake 7.28.3 hdfd78af_0 bioconda snakemake-minimal 7.28.3 pyhdfd78af_0 bioconda stone 3.3.1 pyhd8ed1ab_0 conda-forge stopit 1.1.2 py_0 conda-forge sysroot_linux-64 2.12 he073ed8_15 conda-forge tabulate 0.9.0 pyhd8ed1ab_1 conda-forge throttler 1.2.1 pyhd8ed1ab_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge tktable 2.10 hb7b940f_3 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge toposort 1.10 pyhd8ed1ab_0 conda-forge tqdm 4.65.0 pyhd8ed1ab_1 conda-forge traitlets 5.9.0 pyhd8ed1ab_0 conda-forge typing-extensions 4.5.0 hd8ed1ab_0 conda-forge typing_extensions 4.5.0 pyha770c72_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge ubiquerg 0.6.2 pyhd8ed1ab_0 conda-forge uritemplate 4.1.1 pyhd8ed1ab_0 conda-forge urllib3 1.26.15 pyhd8ed1ab_0 conda-forge veracitools 0.1.3 py_0 conda-forge wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge wget 1.20.3 ha35d2d1_1 conda-forge wheel 0.40.0 pyhd8ed1ab_0 conda-forge wrapt 1.15.0 py310h1fa729e_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.5 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.10 h7f98852_1003 conda-forge xorg-libxt 1.3.0 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge yaml-cpp 0.7.0 h27087fc_2 conda-forge yarl 1.9.1 py310h2372a71_0 conda-forge yte 1.5.1 py310hff52083_1 conda-forge zipp 3.15.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstandard 0.19.0 py310hdeb6495_1 conda-forge zstd 1.5.2 h3eb15da_6 conda-forge

On Wed, Jun 21, 2023 at 7:08 PM Mike Lee @.***> wrote:

hi there, @laibinhuang https://github.com/laibinhuang :)

Weird, pandas should have been installed with the conda install of the bit environment

Did you do the bit environment creation/installation like this?

mamba create -n bit -c conda-forge -c bioconda -c defaults -c astrobiomike bit

Also, can you send the output of the following 2 things:

bit-version

conda list

(or maybe mamba list if there is no conda program from the mambaforge install)

That's the one definitely new thing, i haven't done any testing using mambaforge instead of conda and then installing mamba. I did recently hear from a friend that they've had trouble installing other things after trying mamba forge. So that might be causing a problem (i know mamba forge is the recommended way to use mamba, but i've still be using a conda install and then installing mamba)

Get back to me with the above info if/when you can, and i'll try setting up a system with mamba forge to try to see if i hit the same issue when i can, and then maybe i can help trouble shoot.

One attempted fix you could try is installing pandas in the bit environment, e.g., when the bit environment is active:

mamba install -c conda-forge pandas=1.4.2

But even if that works, if that was missing, other things might be too, so i'd be wary

— Reply to this email directly, view it on GitHub https://github.com/AstrobioMike/bit/issues/14#issuecomment-1601918446, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADIQOU762JRML55DC23GUKTXMOSK5ANCNFSM6AAAAAAZPQUUNQ . You are receiving this because you were mentioned.Message ID: @.***>

-- ----------------------------------------------------------- Laibin Huang, Ph.D.

Assistant Professor of Microbiology Saint Louis University, St. Louis, MO Department of Biology Macelwane Hall 301 3507 Laclede Ave. St. Louis, MO 63103

---

-- ----------------------------------------------------------- Laibin Huang, Ph.D.

Assistant Professor of Microbiology Saint Louis University, St. Louis, MO Department of Biology Macelwane Hall 301 3507 Laclede Ave. St. Louis, MO 63103

---

[laibinhuang]

I get the old version bit 1.8; it works

bit-kraken2-to-taxon-summaries1.8, so I think your new version had something wrong there.

[AstrobioMike]

Hey there, @laibinhuang

Sorry for leaving you hanging on this, i've been traveling. I'm glad you were able to get things to work for you!

It's odd that a python2 was getting called ahead of the bit environment python (version 3). The active conda environment should take precedence over other things in your path, and no python version 2 should have been installed with bit. So i'm not sure what was going on there ¯\_(ツ)_/¯

But that aside, one thing that was also going on is i think you needed to add the --names-included flag to the bit-kraken2-to-taxon-summaries call. Meaning, instead of this as you noted above:

bit-kraken2-to-taxon-summaries -i ${sample}_k-output.txt -o ${sample}-k-tax.tsv

It would have needed to be something like this:

bit-kraken2-to-taxon-summaries -i ${sample}_k-output.txt -o ${sample}-k-tax.tsv --names-included

That flag tells the program the kraken2 output includes names (like "Nocardia asteroides" you were seeing in the error output) and not just taxids.

But you seemed to work around it anyway, so not sure about that either, ha

That aside, you did make me spot a pandas version issue, so thanks for writing in and helping to fix that even though i was no help to you at all on this!