$PATH=/home/lx_sky6/software/miniconda3/envs/py_39/bin/
File "/home/lx_sky6/yt/soft/pcoc/src/profile_tools.py", line 33, in <module>
ModuleNotFoundError: No module named 'pandas'
pip install pandas
File "/home/lx_sky6/yt/soft/pcoc/src/bpp_lib.py", line 23, in <module>
ModuleNotFoundError: No module named 'commands'
##修改23行为import subprocess
ImportError: cannot import name 'TreeStyle' from 'ete3' (/home/lx_sky6/software/miniconda3/lib/python3.9/site-packages/ete3/__init__.py)
##pip3 install PyQt5==5.14.0
$python pcoc_num_tree.py -h
usage: pcoc_num_tree.py [-h] [--version] -t TREE -o OUTPUT [-m "x/y,z/..."] [-n] [-u OUTNWK]
File "/home/lx_sky6/yt/soft/pcoc/src/events_placing.py", line 26, in <module>
ModuleNotFoundError: No module named 'ete3'
##pip install ete3
File "/home/lx_sky6/yt/soft/pcoc/src/estim_data.py", line 27, in <module>
ModuleNotFoundError: No module named 'scipy'
##pip3 install scipy
File "/home/lx_sky6/yt/soft/pcoc/src/estim_data.py", line 27, in <module>
from scipy.misc import logsumexp
ImportError: cannot import name 'logsumexp' from 'scipy.misc' (/home/lx_sky6/software/miniconda3/envs/py_39/lib/python3.9/site-packages/scipy/misc/__init__.py)
##将27行改为from scipy.special import logsumexp
File "/home/lx_sky6/yt/soft/pcoc/src/pcoc_det.py", line 387, in <module>
TypeError: 'map' object is not subscriptable
将286行的l_e = map(int,e.split(","))改为l_e = map(float,e.split(","))
File "/home/lx_sky6/yt/soft/pcoc/src/events_placing.py", line 511, in mk_tree_4_simu
if bl_new >= 0:
TypeError: '>=' not supported between instances of 'NoneType' and 'int'
##修改511行为if int(bl_new) >= 0:
sh: bppml: 未找到命令
conda install -c bioconda bpp-core bpp-phyl bpp-seq bpp-popgen
https://github.com/BioPP/bppsuite/releases/download/v2.3.2/bppsuite-x86_64-bin-static-2.3.2.tar.gz
$python pcoc_det.py -h
usage: pcoc_det.py [-h] [--version] [-cpu CPU] -t TREE -aa ALI -m "x/y,z/..." -o OUTPUT_DIR [-f FILTER_T] [-f_pcoc FILTER_T_PCOC] [-f_pc FILTER_T_PC] [-f_oc FILTER_T_OC]
[-ph PH] [--plot] [--plot_complete_ali] [-plot_title PLOT_TITLE] [--reorder] [--svg] [--no_cleanup_fasta] [--auto_trim_tree]
[-est_profiles [C10,C60,filename]] [--gamma] [--inv_gamma] [--max_gap_allowed MAX_GAP_ALLOWED]
[--max_gap_allowed_in_conv_leaves MAX_GAP_ALLOWED_IN_CONV_LEAVES] [--no_cleanup] [-LD_LIB LD_LIBRARY_PATH] [--debug]
File "/home/lx_sky6/yt/soft/pcoc/src/plot_data.py", line 27, in <module>
ModuleNotFoundError: No module named 'PyQt4'
##这个软件也太老了，依赖的都是快淘汰的软件
修改/home/lx_sky6/yt/soft/pcoc/src/plot_data.py滴27行PyQt4.QtGui改为PyQt5.QtWidgets
File "/home/lx_sky6/yt/soft/pcoc/src/plot_data.py", line 27, in <module>
ImportError: cannot import name 'QPen' from 'PyQt5.QtWidgets'
##发现有的改名字了
修改/home/lx_sky6/yt/soft/pcoc/src/plot_data.py", line 27为from PyQt5.QtWidgets import * 即可
python pcoc_sim.py -h
usage: pcoc_sim.py [-h] [--version] [-cpu CPU] -td TREE_DIR -o OUTPUT_DIR [-n_sc INT] [-m "x/y,z/..."] [-c_max INT] [-c_min INT] [-c INT] [-cr FLOAT] [-flg FLOAT]
[-bl_new FLOAT] [--ali_noise] [--bl_noise] [--ev_noise {+1,-1,=1}] [--root_noise {ll,lr,rr,rl}] [-nb_sampled_couple INT] [-n_sites INT]
[-sim_profiles [C10,C60,filename]] [-min_dist_CAT FLOAT] [--plot_ali] [--get_likelihood_summaries] [--no_clean_seqs] [--pcoc] [--ident] [--topo]
[-est_profiles [C10,C60,filename]] [-p_conv FLOAT [0,1]] [--plot_event_repartition] [--no_cleanup] [-LD_LIB LD_LIBRARY_PATH]
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