billzt
commented
1 year ago Hi, sorry for my late reply since there seems existing problems in the email notification.
I guess the problem might due to python libraries.
By default, the software will visualize a picture of the phylogenetic tree the same as the web version using PyQT5, where it might exist some tricky points. Using -s option will skip the phylogenetic analysis, so your job would be finished smoothly under -s.
After viewing your conda environment, it seems you installed these python libraries by using conda, not pip. We've tested this software on two of our servers, CentOS 7 and Ubuntu 20.04.3. Here is the env.
In Ubuntu 20.04.3
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
asttokens 2.2.1 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
biopython 1.79 pypi_0 pypi
ca-certificates 2022.10.11 h06a4308_0
cachecontrol 0.12.11 pypi_0 pypi
certifi 2022.12.7 py39h06a4308_0
charset-normalizer 3.0.1 pypi_0 pypi
contourpy 1.0.7 pypi_0 pypi
cutadapt 4.1 pypi_0 pypi
cycler 0.11.0 pypi_0 pypi
cython 0.29.33 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
dnaio 0.10.0 pypi_0 pypi
duckdb 0.6.1 pypi_0 pypi
ete3 3.1.2 pypi_0 pypi
executing 1.2.0 pypi_0 pypi
fonttools 4.38.0 pypi_0 pypi
hdmedians 0.14.2 pypi_0 pypi
idna 3.4 pypi_0 pypi
ipython 8.8.0 pypi_0 pypi
isal 1.1.0 pypi_0 pypi
jedi 0.18.2 pypi_0 pypi
joblib 1.2.0 pypi_0 pypi
kiwisolver 1.4.4 pypi_0 pypi
ld_impl_linux-64 2.38 h1181459_1
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libstdcxx-ng 11.2.0 h1234567_1
lockfile 0.12.2 pypi_0 pypi
matplotlib 3.6.3 pypi_0 pypi
matplotlib-inline 0.1.6 pypi_0 pypi
mifish 1.0 dev_0 <develop>
msgpack 1.0.4 pypi_0 pypi
natsort 8.2.0 pypi_0 pypi
ncurses 6.3 h5eee18b_3
numpy 1.23.1 pypi_0 pypi
openssl 1.1.1s h7f8727e_0
packaging 23.0 pypi_0 pypi
pandas 1.5.3 pypi_0 pypi
parso 0.8.3 pypi_0 pypi
pexpect 4.8.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 9.4.0 pypi_0 pypi
pip 22.3.1 py39h06a4308_0
prompt-toolkit 3.0.36 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.2 pypi_0 pypi
pygments 2.14.0 pypi_0 pypi
pyparsing 3.0.9 pypi_0 pypi
pyqt5 5.15.7 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.11.0 pypi_0 pypi
python 3.9.13 haa1d7c7_2
python-dateutil 2.8.2 pypi_0 pypi
pytz 2022.7.1 pypi_0 pypi
readline 8.2 h5eee18b_0
requests 2.28.2 pypi_0 pypi
scikit-bio 0.5.6 pypi_0 pypi
scikit-learn 1.2.0 pypi_0 pypi
scipy 1.10.0 pypi_0 pypi
setuptools 65.6.3 py39h06a4308_0
six 1.16.0 pypi_0 pypi
sqlite 3.40.1 h5082296_0
stack-data 0.6.2 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tk 8.6.12 h1ccaba5_0
traitlets 5.8.1 pypi_0 pypi
tzdata 2022g h04d1e81_0
urllib3 1.26.14 pypi_0 pypi
wcwidth 0.2.6 pypi_0 pypi
wheel 0.37.1 pyhd3eb1b0_0
xlsxwriter 3.0.3 pypi_0 pypi
xopen 1.7.0 pypi_0 pypi
xz 5.2.10 h5eee18b_1
zlib 1.2.13 h5eee18b_0 In CentOS 7
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
asttokens 2.2.1 pypi_0 pypi
backcall 0.2.0 pypi_0 pypi
biopython 1.79 pypi_0 pypi
bzip2 1.0.8 h7f98852_4 conda-forge
ca-certificates 2022.12.7 ha878542_0 conda-forge
cachecontrol 0.12.11 pypi_0 pypi
certifi 2022.12.7 pypi_0 pypi
charset-normalizer 3.0.1 pypi_0 pypi
contourpy 1.0.7 pypi_0 pypi
cutadapt 4.1 pypi_0 pypi
cycler 0.11.0 pypi_0 pypi
cython 0.29.33 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
dnaio 0.10.0 pypi_0 pypi
duckdb 0.6.1 pypi_0 pypi
ete3 3.1.2 pypi_0 pypi
executing 1.2.0 pypi_0 pypi
fonttools 4.38.0 pypi_0 pypi
hdmedians 0.14.2 pypi_0 pypi
idna 3.4 pypi_0 pypi
ipython 8.8.0 pypi_0 pypi
isal 1.1.0 pypi_0 pypi
jedi 0.18.2 pypi_0 pypi
joblib 1.2.0 pypi_0 pypi
kiwisolver 1.4.4 pypi_0 pypi
ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libsqlite 3.40.0 h753d276_0 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
lockfile 0.12.2 pypi_0 pypi
matplotlib 3.6.3 pypi_0 pypi
matplotlib-inline 0.1.6 pypi_0 pypi
mifish 1.0 dev_0 <develop>
msgpack 1.0.4 pypi_0 pypi
natsort 8.2.0 pypi_0 pypi
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.23.1 pypi_0 pypi
openssl 3.0.7 h0b41bf4_1 conda-forge
packaging 23.0 pypi_0 pypi
pandas 1.5.2 pypi_0 pypi
parso 0.8.3 pypi_0 pypi
pexpect 4.8.0 pypi_0 pypi
pickleshare 0.7.5 pypi_0 pypi
pillow 9.4.0 pypi_0 pypi
pip 22.3.1 pyhd8ed1ab_0 conda-forge
prompt-toolkit 3.0.36 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.2 pypi_0 pypi
pygments 2.14.0 pypi_0 pypi
pyparsing 3.0.9 pypi_0 pypi
pyqt5 5.15.7 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.11.0 pypi_0 pypi
python 3.9.13 h2660328_0_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
pytz 2022.7.1 pypi_0 pypi
readline 8.1.2 h0f457ee_0 conda-forge
requests 2.28.2 pypi_0 pypi
scikit-bio 0.5.6 pypi_0 pypi
scikit-learn 1.2.0 pypi_0 pypi
scipy 1.10.0 pypi_0 pypi
setuptools 66.0.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pypi_0 pypi
sqlite 3.40.0 h4ff8645_0 conda-forge
stack-data 0.6.2 pypi_0 pypi
threadpoolctl 3.1.0 pypi_0 pypi
tk 8.6.12 h27826a3_0 conda-forge
traitlets 5.8.1 pypi_0 pypi
tzdata 2022g h191b570_0 conda-forge
urllib3 1.26.14 pypi_0 pypi
wcwidth 0.2.6 pypi_0 pypi
wheel 0.38.4 pyhd8ed1ab_0 conda-forge
xlsxwriter 3.0.3 pypi_0 pypi
xopen 1.7.0 pypi_0 pypi
xz 5.2.6 h166bdaf_0 conda-forgeYou can see most of our libraries were coming from pypi, not from conda-forge. I'm afraid whether there exist some tiny differences between pypi and conda-forge?
So can you try to install python libraries in a new conda environment by following https://github.com/billzt/MiFish#install ? Perhaps you were surprised why there are so many python libs needed with specific version. Because we want to keep the result the same as the web version.
sr-c
Hi, thank you for the great tool. I installed MiFish in a new conda environment as recommended. While testing with
mifish seq mifishdbv3.83.fa -d seq2, I got an error duringStep 5: Phylogenetic Analysis.If
-swas added, the pipeline would finish smoothly. In my conda env,ete3==3.1.2, as recommended. How can I rule this out?For your reference, my conda env was as follows: