wgd ksd error : AttributeError: type object 'object' has no attribute 'dtype'

[dongseok123]

When I run the command "wgd ksd wgd_blast/augustus.codingseq.blast.tsv.mcl augustus.codingseq" The error message comes out like upper figure...

I don't know what is the problem. Could you help me?

[arzwa]

I think you might need to update your pandas version (e.g. as here), but not entirely sure. Try pip install --upgrade pandas.

[dongseok123]

Oh, thank you for your fast reply. I will try it ᐧ

2021년 6월 23일 (수) 오후 3:12, Arthur Zwaenepoel @.***>님이 작성:

I think you might need to update your pandas version (e.g. as here https://github.com/pandas-dev/pandas/issues/39520), but not entirely sure. Try pip install --upgrade pandas.

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[dongseok123]

unfortunately, it doesn't work..

[arzwa]

could you do a pip freeze and report the output here then?

[dongseok123]

This is the result of pip freeze.

--------------------------------------
alabaster @ file:///home/ktietz/src/ci/alabaster_1611921544520/work
anaconda-client==1.7.2
anaconda-navigator==2.0.3
anaconda-project @ file:///tmp/build/80754af9/anaconda-project_1610472525955/work
anyio @ file:///opt/concourse/worker/volumes/live/64740ac7-3a9c-4fbb-6685-a51c4ff8b4ca/volume/anyio_1617783319350/work/dist
appdirs==1.4.4
applaunchservices==0.2.1
appnope @ file:///opt/concourse/worker/volumes/live/5f13e5b3-5355-4541-5fc3-f08850c73cf9/volume/appnope_1606859448618/work
appscript @ file:///opt/concourse/worker/volumes/live/82e8b4c7-2416-4d10-509e-144ca79d9b1d/volume/appscript_1611426996703/work
argh==0.26.2
argon2-cffi @ file:///opt/concourse/worker/volumes/live/d733ceb5-7f19-407b-7da7-a386540ab855/volume/argon2-cffi_1613037492998/work
asn1crypto @ file:///tmp/build/80754af9/asn1crypto_1596577642040/work
astroid @ file:///opt/concourse/worker/volumes/live/343a8902-287c-47fb-6db8-923a63364302/volume/astroid_1613500849157/work
astropy @ file:///opt/concourse/worker/volumes/live/0a514e04-301a-48f9-530f-90365df6420e/volume/astropy_1617745469121/work
async-generator @ file:///home/ktietz/src/ci/async_generator_1611927993394/work
atomicwrites==1.4.0
attrs @ file:///tmp/build/80754af9/attrs_1604765588209/work
autopep8 @ file:///tmp/build/80754af9/autopep8_1615918855173/work
Babel @ file:///tmp/build/80754af9/babel_1607110387436/work
backcall @ file:///home/ktietz/src/ci/backcall_1611930011877/work
backports.functools-lru-cache @ file:///tmp/build/80754af9/backports.functools_lru_cache_1618170165463/work
backports.shutil-get-terminal-size @ file:///tmp/build/80754af9/backports.shutil_get_terminal_size_1608222128777/work
backports.tempfile @ file:///home/linux1/recipes/ci/backports.tempfile_1610991236607/work
backports.weakref==1.0.post1
beautifulsoup4 @ file:///home/linux1/recipes/ci/beautifulsoup4_1610988766420/work
bitarray @ file:///opt/concourse/worker/volumes/live/21dd8f41-3cae-47b4-5fab-684b9b2db14f/volume/bitarray_1618434866960/work
bkcharts==0.2
black==19.10b0
bleach @ file:///tmp/build/80754af9/bleach_1612211392645/work
bokeh @ file:///opt/concourse/worker/volumes/live/65ce9588-f765-4deb-5b52-1c552a693654/volume/bokeh_1620783891289/work
boto==2.49.0
Bottleneck==1.3.2
brotlipy==0.7.0
certifi==2020.12.5
cffi @ file:///opt/concourse/worker/volumes/live/0ef369cc-6ba0-47e7-75da-208c6400381d/volume/cffi_1613246948181/work
chardet @ file:///opt/concourse/worker/volumes/live/c798b2ee-88b1-4341-6830-161a92c2399e/volume/chardet_1607706832595/work
click @ file:///home/linux1/recipes/ci/click_1610990599742/work
cloudpickle @ file:///tmp/build/80754af9/cloudpickle_1598884132938/work
clyent==1.2.2
colorama @ file:///tmp/build/80754af9/colorama_1607707115595/work
conda==4.10.1
conda-build==3.21.4
conda-content-trust @ file:///tmp/build/80754af9/conda-content-trust_1617045594566/work
conda-package-handling @ file:///opt/concourse/worker/volumes/live/73497069-9b43-4ad9-50ec-1abb340e14eb/volume/conda-package-handling_1618262140058/work
conda-repo-cli @ file:///tmp/build/80754af9/conda-repo-cli_1620168426516/work
conda-token @ file:///tmp/build/80754af9/conda-token_1620076980546/work
conda-verify==3.4.2
contextlib2==0.6.0.post1
cryptography @ file:///opt/concourse/worker/volumes/live/c515855a-effc-46df-74dc-542901b701da/volume/cryptography_1616769282442/work
cycler==0.10.0
Cython @ file:///opt/concourse/worker/volumes/live/da4db94a-3449-4978-4400-64181f888dab/volume/cython_1618435143829/work
cytoolz==0.11.0
dask @ file:///tmp/build/80754af9/dask-core_1617390489108/work
decorator @ file:///tmp/build/80754af9/decorator_1617916966915/work
defusedxml @ file:///tmp/build/80754af9/defusedxml_1615228127516/work
diff-match-patch @ file:///tmp/build/80754af9/diff-match-patch_1594828741838/work
distributed @ file:///opt/concourse/worker/volumes/live/061a375f-fbe4-45b4-4d80-0ba96d3ee7cb/volume/distributed_1617384077473/work
docutils @ file:///opt/concourse/worker/volumes/live/c75adaac-4aab-4f8b-53ac-e2f0ae899bdf/volume/docutils_1617481416178/work
entrypoints==0.3
et-xmlfile==1.0.1
fastcache==1.1.0
filelock @ file:///home/linux1/recipes/ci/filelock_1610993975404/work
flake8 @ file:///tmp/build/80754af9/flake8_1615834841867/work
Flask @ file:///home/ktietz/src/ci/flask_1611932660458/work
fsspec @ file:///tmp/build/80754af9/fsspec_1617959894824/work
future==0.18.2
gevent @ file:///opt/concourse/worker/volumes/live/123efac8-0706-463e-4084-078386897222/volume/gevent_1616772940436/work
glob2 @ file:///home/linux1/recipes/ci/glob2_1610991677669/work
gmpy2==2.0.8
greenlet @ file:///opt/concourse/worker/volumes/live/de3154a2-fbbd-4797-71f5-5fe8ea617adf/volume/greenlet_1611958369459/work
h5py==2.10.0
HeapDict==1.0.1
html5lib @ file:///tmp/build/80754af9/html5lib_1593446221756/work
idna @ file:///home/linux1/recipes/ci/idna_1610986105248/work
imageio @ file:///tmp/build/80754af9/imageio_1617700267927/work
imagesize @ file:///home/ktietz/src/ci/imagesize_1611921604382/work
importlib-metadata @ file:///opt/concourse/worker/volumes/live/a634a87c-b5e5-41bd-628d-cd0413666c93/volume/importlib-metadata_1617877368300/work
iniconfig @ file:///home/linux1/recipes/ci/iniconfig_1610983019677/work
intervaltree @ file:///tmp/build/80754af9/intervaltree_1598376443606/work
ipykernel @ file:///opt/concourse/worker/volumes/live/88f541d3-5a27-498f-7391-f2e50ca36560/volume/ipykernel_1596206680118/work/dist/ipykernel-5.3.4-py3-none-any.whl
ipython @ file:///opt/concourse/worker/volumes/live/c432d8a7-d8f3-4e24-590f-f03d7e5f35e1/volume/ipython_1617120884257/work
ipython-genutils @ file:///tmp/build/80754af9/ipython_genutils_1606773439826/work
ipywidgets @ file:///tmp/build/80754af9/ipywidgets_1610481889018/work
isort @ file:///tmp/build/80754af9/isort_1616355431277/work
itsdangerous @ file:///home/ktietz/src/ci/itsdangerous_1611932585308/work
jdcal==1.4.1
jedi @ file:///opt/concourse/worker/volumes/live/12a2c347-a8e4-4b62-5b19-dcc92a2254f6/volume/jedi_1606932552286/work
Jinja2 @ file:///tmp/build/80754af9/jinja2_1612213139570/work
joblib @ file:///tmp/build/80754af9/joblib_1613502643832/work
json5==0.9.5
jsonschema @ file:///tmp/build/80754af9/jsonschema_1602607155483/work
jupyter==1.0.0
jupyter-client @ file:///tmp/build/80754af9/jupyter_client_1616770841739/work
jupyter-console @ file:///tmp/build/80754af9/jupyter_console_1616615302928/work
jupyter-core @ file:///opt/concourse/worker/volumes/live/c8df8dce-dbb3-46e7-649c-adf4ed2dd00a/volume/jupyter_core_1612213293829/work
jupyter-packaging @ file:///tmp/build/80754af9/jupyter-packaging_1613502826984/work
jupyter-server @ file:///opt/concourse/worker/volumes/live/4f2e970c-4cba-4227-75ae-10ebe3b5f9c3/volume/jupyter_server_1616084051538/work
jupyterlab @ file:///tmp/build/80754af9/jupyterlab_1619133235951/work
jupyterlab-pygments @ file:///tmp/build/80754af9/jupyterlab_pygments_1601490720602/work
jupyterlab-server @ file:///tmp/build/80754af9/jupyterlab_server_1617134334258/work
jupyterlab-widgets @ file:///tmp/build/80754af9/jupyterlab_widgets_1609884341231/work
keyring @ file:///opt/concourse/worker/volumes/live/107edf16-ab8b-49bb-692b-65f944af2b43/volume/keyring_1614616747185/work
kiwisolver @ file:///opt/concourse/worker/volumes/live/0b2f3e77-eaa3-4995-7dd0-c994762fcbde/volume/kiwisolver_1612282417472/work
lazy-object-proxy @ file:///opt/concourse/worker/volumes/live/e4bc3ba3-f365-4387-5772-cbb667714c62/volume/lazy-object-proxy_1616529072711/work
libarchive-c @ file:///tmp/build/80754af9/python-libarchive-c_1617780486945/work
llvmlite==0.36.0
locket==0.2.1
lxml @ file:///opt/concourse/worker/volumes/live/42fc56a4-88b4-4605-6037-9605f4e5eeeb/volume/lxml_1616443240194/work
MarkupSafe @ file:///opt/concourse/worker/volumes/live/cb778296-98db-45ad-411e-6f726e102dc3/volume/markupsafe_1594371638608/work
matplotlib @ file:///opt/concourse/worker/volumes/live/41e8cd50-031f-4dda-5787-dd3c4f4e0f08/volume/matplotlib-suite_1613407855571/work
mccabe==0.6.1
mistune @ file:///opt/concourse/worker/volumes/live/95802d64-d39c-491b-74ce-b9326880ca54/volume/mistune_1594373201816/work
mkl-fft==1.3.0
mkl-random @ file:///opt/concourse/worker/volumes/live/54b31a45-1da5-4512-5c3a-93c9ff2af8bc/volume/mkl_random_1618853970587/work
mkl-service==2.3.0
mock @ file:///tmp/build/80754af9/mock_1607622725907/work
more-itertools @ file:///tmp/build/80754af9/more-itertools_1613676688952/work
mpmath==1.2.1
msgpack @ file:///opt/concourse/worker/volumes/live/d7400f3a-e5de-4e85-5d4c-0c984c648401/volume/msgpack-python_1612287157185/work
multipledispatch==0.6.0
mypy-extensions==0.4.3
navigator-updater==0.2.1
nbclassic @ file:///tmp/build/80754af9/nbclassic_1616085367084/work
nbclient @ file:///tmp/build/80754af9/nbclient_1614364831625/work
nbconvert @ file:///opt/concourse/worker/volumes/live/2b9c1d93-d0fd-432f-7d93-66c93d81b614/volume/nbconvert_1601914875037/work
nbformat @ file:///tmp/build/80754af9/nbformat_1617383369282/work
nest-asyncio @ file:///tmp/build/80754af9/nest-asyncio_1613680548246/work
networkx @ file:///tmp/build/80754af9/networkx_1598376031484/work
nltk @ file:///tmp/build/80754af9/nltk_1618327084230/work
nose @ file:///tmp/build/80754af9/nose_1606773131901/work
notebook @ file:///opt/concourse/worker/volumes/live/06e4d8fc-70ed-4cb0-554c-65c20061cb7f/volume/notebook_1616443453928/work
numba @ file:///opt/concourse/worker/volumes/live/263a950e-7ddc-4297-63df-0c284f0b6d22/volume/numba_1616774255536/work
numexpr @ file:///opt/concourse/worker/volumes/live/e845d683-bbb9-4fa2-79ce-743b84c61560/volume/numexpr_1618856522192/work
numpy @ file:///opt/concourse/worker/volumes/live/84716fc3-63c0-4ad6-5a23-37f5ad6b3bfa/volume/numpy_and_numpy_base_1618497240837/work
numpydoc @ file:///tmp/build/80754af9/numpydoc_1605117425582/work
olefile==0.46
openpyxl @ file:///tmp/build/80754af9/openpyxl_1615411699337/work
packaging @ file:///tmp/build/80754af9/packaging_1611952188834/work
pandas==1.2.5
pandocfilters @ file:///opt/concourse/worker/volumes/live/c330e404-216d-466b-5327-8ce8fe854d3a/volume/pandocfilters_1605120442288/work
parso==0.7.0
partd @ file:///tmp/build/80754af9/partd_1618000087440/work
path @ file:///opt/concourse/worker/volumes/live/6493576b-552d-426b-432c-5e0fafcd8a43/volume/path_1614022213143/work
pathlib2 @ file:///opt/concourse/worker/volumes/live/cca4007b-e85e-4f77-430e-d30b2149548d/volume/pathlib2_1607024978319/work
pathspec==0.7.0
patsy==0.5.1
pep8==1.7.1
pexpect @ file:///tmp/build/80754af9/pexpect_1605563209008/work
pickleshare @ file:///tmp/build/80754af9/pickleshare_1606932040724/work
Pillow @ file:///opt/concourse/worker/volumes/live/ca23594b-6e35-4c8c-5637-50ac0b550473/volume/pillow_1617386168018/work
pkginfo==1.7.0
pluggy @ file:///opt/concourse/worker/volumes/live/2d655872-b6f5-4225-538c-dd87e481f5c8/volume/pluggy_1615976700299/work
ply==3.11
prometheus-client @ file:///tmp/build/80754af9/prometheus_client_1618088486455/work
prompt-toolkit @ file:///tmp/build/80754af9/prompt-toolkit_1616415428029/work
psutil @ file:///opt/concourse/worker/volumes/live/0673cd4b-30c1-4470-7490-d8955610f5d5/volume/psutil_1612298002202/work
ptyprocess @ file:///tmp/build/80754af9/ptyprocess_1609355006118/work/dist/ptyprocess-0.7.0-py2.py3-none-any.whl
py @ file:///tmp/build/80754af9/py_1607971587848/work
pycodestyle @ file:///home/ktietz/src/ci_mi/pycodestyle_1612807597675/work
pycosat==0.6.3
pycparser @ file:///tmp/build/80754af9/pycparser_1594388511720/work
pycurl==7.43.0.6
pydocstyle @ file:///tmp/build/80754af9/pydocstyle_1616182067796/work
pyerfa @ file:///opt/concourse/worker/volumes/live/499ad55d-d083-454d-5032-b5d62181519d/volume/pyerfa_1619390898734/work
pyflakes @ file:///home/ktietz/src/ci_ipy2/pyflakes_1612551159640/work
Pygments @ file:///tmp/build/80754af9/pygments_1615143339740/work
pylint @ file:///opt/concourse/worker/volumes/live/39bfc6db-5da7-4bc4-5240-e8a1167491ff/volume/pylint_1617135827184/work
pyls-black @ file:///tmp/build/80754af9/pyls-black_1607553132291/work
pyls-spyder @ file:///tmp/build/80754af9/pyls-spyder_1613849700860/work
pyodbc===4.0.0-unsupported
pyOpenSSL @ file:///tmp/build/80754af9/pyopenssl_1608057966937/work
pyparsing @ file:///home/linux1/recipes/ci/pyparsing_1610983426697/work
pyrsistent @ file:///opt/concourse/worker/volumes/live/ff11f3f0-615b-4508-471d-4d9f19fa6657/volume/pyrsistent_1600141727281/work
PySocks @ file:///opt/concourse/worker/volumes/live/85a5b906-0e08-41d9-6f59-084cee4e9492/volume/pysocks_1594394636991/work
pytest==6.2.3
python-dateutil @ file:///home/ktietz/src/ci/python-dateutil_1611928101742/work
python-jsonrpc-server @ file:///tmp/build/80754af9/python-jsonrpc-server_1600278539111/work
python-language-server @ file:///tmp/build/80754af9/python-language-server_1607972495879/work
pytz @ file:///tmp/build/80754af9/pytz_1612215392582/work
PyWavelets @ file:///opt/concourse/worker/volumes/live/ea36e10f-66e8-43ae-511e-c4092764493f/volume/pywavelets_1601658378672/work
PyYAML==5.4.1
pyzmq==20.0.0
QDarkStyle==2.8.1
QtAwesome @ file:///tmp/build/80754af9/qtawesome_1615991616277/work
qtconsole @ file:///tmp/build/80754af9/qtconsole_1616775094278/work
QtPy==1.9.0
regex @ file:///opt/concourse/worker/volumes/live/e81f6b8c-e3b5-481b-6b5d-4fa8d9bb9405/volume/regex_1617569701251/work
requests @ file:///tmp/build/80754af9/requests_1608241421344/work
rope @ file:///tmp/build/80754af9/rope_1602264064449/work
Rtree @ file:///opt/concourse/worker/volumes/live/7b97d6e1-aeee-4f6d-418c-32be5bbd5ed3/volume/rtree_1618420839839/work
ruamel-yaml-conda @ file:///opt/concourse/worker/volumes/live/53b096c9-f5b7-4029-7f1b-056927554e08/volume/ruamel_yaml_1616016691174/work
scikit-image==0.18.1
scikit-learn @ file:///opt/concourse/worker/volumes/live/0c77b068-a026-4996-6842-33e5544ec13b/volume/scikit-learn_1614446667823/work
scipy @ file:///opt/concourse/worker/volumes/live/7d10d993-3825-404e-6e5d-9947c19e8c6d/volume/scipy_1618855951189/work
seaborn @ file:///tmp/build/80754af9/seaborn_1608578541026/work
Send2Trash @ file:///tmp/build/80754af9/send2trash_1607525499227/work
simplegeneric==0.8.1
singledispatch @ file:///tmp/build/80754af9/singledispatch_1614366001199/work
six @ file:///opt/concourse/worker/volumes/live/5b31cb27-1e37-4ca5-6e9f-86246eb206d2/volume/six_1605205320872/work
sniffio @ file:///opt/concourse/worker/volumes/live/1faeb672-6d3f-4f1f-7861-294fcf282962/volume/sniffio_1614030462215/work
snowballstemmer @ file:///tmp/build/80754af9/snowballstemmer_1611258885636/work
sortedcollections @ file:///tmp/build/80754af9/sortedcollections_1611172717284/work
sortedcontainers @ file:///tmp/build/80754af9/sortedcontainers_1606865132123/work
soupsieve @ file:///tmp/build/80754af9/soupsieve_1616183228191/work
Sphinx @ file:///tmp/build/80754af9/sphinx_1620777493457/work
sphinxcontrib-applehelp @ file:///home/ktietz/src/ci/sphinxcontrib-applehelp_1611920841464/work
sphinxcontrib-devhelp @ file:///home/ktietz/src/ci/sphinxcontrib-devhelp_1611920923094/work
sphinxcontrib-htmlhelp @ file:///home/ktietz/src/ci/sphinxcontrib-htmlhelp_1611920974801/work
sphinxcontrib-jsmath @ file:///home/ktietz/src/ci/sphinxcontrib-jsmath_1611920942228/work
sphinxcontrib-qthelp @ file:///home/ktietz/src/ci/sphinxcontrib-qthelp_1611921055322/work
sphinxcontrib-serializinghtml @ file:///home/ktietz/src/ci/sphinxcontrib-serializinghtml_1611920755253/work
sphinxcontrib-websupport @ file:///tmp/build/80754af9/sphinxcontrib-websupport_1597081412696/work
spyder @ file:///opt/concourse/worker/volumes/live/b2db1f66-1cfc-4529-6e21-61097ab49952/volume/spyder_1616775698806/work
spyder-kernels @ file:///opt/concourse/worker/volumes/live/12a19b85-7733-4e39-55a2-982abb6f0274/volume/spyder-kernels_1614030593315/work
SQLAlchemy @ file:///opt/concourse/worker/volumes/live/31df50e1-4e8b-40a3-6d21-5c6d01ae48e8/volume/sqlalchemy_1618089538006/work
statsmodels @ file:///opt/concourse/worker/volumes/live/f55add71-53cb-4510-4c08-7ae9e294a482/volume/statsmodels_1614023740731/work
sympy @ file:///opt/concourse/worker/volumes/live/0bf7d347-8399-4af8-5e6f-4267d4aabdd9/volume/sympy_1618255318469/work
tables==3.6.1
tblib @ file:///tmp/build/80754af9/tblib_1597928476713/work
terminado==0.9.4
testpath @ file:///home/ktietz/src/ci/testpath_1611930608132/work
textdistance @ file:///tmp/build/80754af9/textdistance_1612461398012/work
threadpoolctl @ file:///tmp/tmp9twdgx9k/threadpoolctl-2.1.0-py3-none-any.whl
three-merge @ file:///tmp/build/80754af9/three-merge_1607553261110/work
tifffile==2020.10.1
toml @ file:///tmp/build/80754af9/toml_1616166611790/work
toolz @ file:///home/linux1/recipes/ci/toolz_1610987900194/work
tornado @ file:///opt/concourse/worker/volumes/live/05341796-4198-4ded-4a9a-332fde3cdfd1/volume/tornado_1606942323372/work
tqdm @ file:///tmp/build/80754af9/tqdm_1615925068909/work
traitlets @ file:///home/ktietz/src/ci/traitlets_1611929699868/work
typed-ast @ file:///opt/concourse/worker/volumes/live/b635b0af-0037-435d-5a8b-38d096f36bbf/volume/typed-ast_1610484559102/work
typing-extensions @ file:///home/ktietz/src/ci_mi/typing_extensions_1612808209620/work
ujson @ file:///opt/concourse/worker/volumes/live/b4182deb-c6ce-4bc8-7783-61027c162049/volume/ujson_1611259506235/work
unicodecsv==0.14.1
urllib3 @ file:///tmp/build/80754af9/urllib3_1615837158687/work
watchdog @ file:///opt/concourse/worker/volumes/live/ba071b65-d6ec-4539-5875-0791be503584/volume/watchdog_1612471127391/work
wcwidth @ file:///tmp/build/80754af9/wcwidth_1593447189090/work
webencodings==0.5.1
Werkzeug @ file:///home/ktietz/src/ci/werkzeug_1611932622770/work
widgetsnbextension==3.5.1
wrapt @ file:///opt/concourse/worker/volumes/live/e3646d84-e961-4523-6bed-01532273c57e/volume/wrapt_1597851473852/work
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xlrd @ file:///tmp/build/80754af9/xlrd_1608072521494/work
XlsxWriter @ file:///tmp/build/80754af9/xlsxwriter_1617224712951/work
xlwings==0.23.0
xlwt==1.3.0
xmltodict==0.12.0
yapf @ file:///tmp/build/80754af9/yapf_1615749224965/work
zict==2.0.0
zipp @ file:///tmp/build/80754af9/zipp_1615904174917/work
zope.event==4.5.0
zope.interface @ file:///opt/concourse/worker/volumes/live/2b8309a3-732c-445e-5670-ab75beb9637c/volume/zope.interface_1616357204515/work

[arzwa]

OK, maybe try

pip install pandas==1.2.1
pip install numpy==1.19.0

those work for me

[dongseok123]

I tried pip install command as you show me, but It doesn't work.. Same result...

[arzwa]

OK, I would suggest you try working with a virtual environment instead of your main python installation, because I cannot help much sorting out what exactly the issue is. See for instance issue #4 for some guidelines on how to install wgd in a virtualenv. Then you shoudl not have problems with dependencies, or at least they should be easier to sort out.

[dongseok123]

Okay, Thank you for ur kindly help

[dongseok123]

I used virtualenv as you mentioned, but the result is same. But, anyway the message such as "analysis is done" is printed out, and in "ks_tmp.XXX" folder, I can see the result of each "GF_XXX.ks". So is it possible to execute "wgd syn" command by revising my ongoing results? If it is possible, could you show me the full format of "sample.fasta.ks.tsv" for me? By using the format of "sample.fasta.ks.tsv", I can make my ongoing result like this, and can be excuted "wgd syn"

[dongseok123]

I think, all the analysis is done correctly, but "Making results data frame" part is not executed. So maybe I can replace my ongoing "not correctly finished results" to "sample.fasta.ks.tsv".

[arzwa]

I believe you are somehow not executing the version installed in the virtualenv, since the path for the wgd executable I am seeing in the above traceback is not leading to the virtualenv but to your main python installation (check by using which wgd)... Perhaps removing wgd from your main environment would help or, after installing wgd in the virtualenv, try using the executable in the bin folder of the environment <path to your virtual env>/bin/wgd or alternatively python3 <path to wgd repo>/wgd_cli.py instead of plain wgd.

Other than that you are right, you can just concatenate all the GF_*.ks files if you want to and work with that, you will only need to remove the first line of each file and have that only once on top of the concatenated file.

[dongseok123]

Ok, I will try that. Thank you so much.

2021년 6월 23일 (수) 오후 8:07, Arthur Zwaenepoel @.***>님이 작성:

I believe you are somehow not executing the version installed in the virtualenv, since the path for the wgd executable I am seeing in the above traceback is not leading to the virtualenv but to your main python installation... After installing wgd in the virtualenv, try using the executable in the bin folder of the environment <path to your virtual env>/bin/wgd or alternatively python3 /wgd_cli.py instead of plain wgd.

Other than that you are right, you can just concatenate all the GF_*.ks files if you want to and work with that, you will only need to remove the first line of each file and have that only once on top of the concatenated file.

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[dongseok123]

Oh, now I can execute the kds step

python3.6 ./wgd_cli.py ksd wgd_blast/augustus.codingseq.blast.tsv.mcl Ppur/augustus.codingseq

python3.5 ./wgd_cli.py is worked!! thank you soooo much.