text: user1008: Now jupyter installed on the server and I am using below code to plot the rarefaction plot but I am still getting some error. could you please suggest how I can get rid of it?
      #Run it in jupyter lab or notebook
  
  
  import seaborn as sns
  import matplotlib.pyplot as plt
  import pandas as pd
  import numpy as np
  import os
  
  #%matplotlib inline 
  
  qza = 'alpha-rarefaction-20000.qzv' # path to rarefaction file from qiime2
  os.system("unzip qza")
  
  digest = a[1].split('/')[0].replace('  inflating: ','')
  inf = digest + '/data/observed_otus.csv'
  otus = pd.read_csv(inf,index_col=0, sep=',')
  os.system('rm -r $digest')
  
  cols = [col for col in otus.columns if 'iter' not in col]
  mean,data = otus[cols],pd.DataFrame(columns=cols)
  depths = [col.split('_')[0] for col in otus.columns if 'depth' in col]
  otus = otus.drop(cols,axis=1)
  otus.columns = depths
  for depth in depths:
      mean['ASV'] = otus[depth].mean(axis=1)
      mean['depth']= depth.split('-')[-1]
      data = pd.concat([data,mean])
  # here provide colors for each item that will be plotted
  pal={'Irrigated':'brown','Rainfed':'red'} 
  fig,ax = plt.subplots(figsize=(2.5,2),dpi=600,tight_layout=True)
  sns.set(style='ticks',rc={"lines.linewidth":0.7,"axes.linewidth":0.5})
  # use your column name to plot here
  sns.lineplot(x='depth',y='ASV',data=data,palette=pal,hue='Season',sort=False,err_style='bars',\
               dashes=True,style='Season',ci=67)
  ax.set_xlabel('Sequencing depth',fontsize=8)
  ax.set_ylabel('Observed ASVs',fontsize=8)
  ax.tick_params(axis='x', labelrotation=90)
  ax.tick_params(axis='both',which='major',length=2,pad=0.5,labelsize=6)
  handles, labels = ax.get_legend_handles_labels()
  ax.legend(handles=handles[1:],labels=labels[1:],fontsize=5,frameon=False,numpoints=4,borderaxespad=0,handletextpad=0.2,loc=2,)
  plt.savefig('Infected_observed_ASVs.png', bbox_inches='tight')
  
  Error;
   $ python3 myscript.rarefaction.py
  Traceback (most recent call last):
    File "myscript.rarefaction.py", line 4, in <module>
      import seaborn as sns
    File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/__init__.py", line 2, in <module>
      from .rcmod import *  # noqa: F401,F403
    File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/rcmod.py", line 7, in <module>
      from . import palettes
    File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/palettes.py", line 9, in <module>
      from .utils import desaturate, get_color_cycle
    File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/utils.py", line 11, in <module>
      import pandas as pd
    File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/pandas/__init__.py", line 11, in <module>
      __import__(dependency)
    File "<frozen importlib._bootstrap>", line 983, in _find_and_load
    File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 668, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 638, in _load_backward_compatible
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py", line 1101, in <module>
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/lazy.py", line 101, in _lazy
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py", line 1098, in <genexpr>
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py", line 114, in resource_exists
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py", line 102, in open_resource
    File "<frozen importlib._bootstrap>", line 983, in _find_and_load
    File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
    File "<frozen importlib._bootstrap>", line 668, in _load_unlocked
    File "<frozen importlib._bootstrap>", line 638, in _load_backward_compatible
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2927, in <module>
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2913, in _call_aside
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2952, in _initialize_master_working_set
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 956, in subscribe
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2952, in <lambda>
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2515, in activate
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2097, in declare_namespace
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2047, in _handle_ns
    File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2066, in _rebuild_mod_path
  AttributeError: '_NamespacePath' object has no attribute 'sort'
  
           
       
      
      metadata file ;
      #SampleID       Villages        Region  Treatment       Batch   Season
      PN0086D.1.S1    Kholabari       Mymensingh      T1      batch1  Irrigated
      PN0086D.2.S2    Bogajan Mymensingh      T1      batch1  Irrigated
      PN0086D.3.S3    Bonkua  Mymensingh      T1      batch1  Irrigated
  
  
  user9109: This is a bash script (#!/bin/bash) and you try to run python in it.
  You should save your python script (e.g. in "myscript.py") and call it within your bash script.
  Maybe first try to see if you are able to run it in your terminal and then run it on your server with SLURM.
  EDIT1: Also I don't think you need 3 nodes to run such script and this will probably not be even possible here. I think you need some specific modules to parallelize a python script with MPI (see https://stackoverflow.com/questions/25792357/how-to-distribute-a-python-script-across-multiple-nodes), but again I think this would be an overkill. Try first with #SBATCH -c 1 instead.
  Edit2: Finally it might be possible to run jupyter-notebook on a node allocated by SLRUM instead of putting this into a python script by using jupyter-notebook --no-browser --port=${port} --ip=${node} command in your bash slurm script. Maybe you'll find this doc interesting: https://docs.ycrc.yale.edu/clusters-at-yale/guides/jupyter/ .
  
original_text: 1008: <p>Now jupyter installed on the server and I am using below code to plot the rarefaction plot but I am still getting some error. could you please suggest how I can get rid of it?</p>
  <pre><code>    #Run it in jupyter lab or notebook
  
  
  import seaborn as sns
  import matplotlib.pyplot as plt
  import pandas as pd
  import numpy as np
  import os
  
  #%matplotlib inline 
  
  qza = 'alpha-rarefaction-20000.qzv' # path to rarefaction file from qiime2
  os.system(&quot;unzip qza&quot;)
  
  digest = a[1].split('/')[0].replace('  inflating: ','')
  inf = digest + '/data/observed_otus.csv'
  otus = pd.read_csv(inf,index_col=0, sep=',')
  os.system('rm -r $digest')
  
  cols = [col for col in otus.columns if 'iter' not in col]
  mean,data = otus[cols],pd.DataFrame(columns=cols)
  depths = [col.split('_')[0] for col in otus.columns if 'depth' in col]
  otus = otus.drop(cols,axis=1)
  otus.columns = depths
  for depth in depths:
      mean['ASV'] = otus[depth].mean(axis=1)
      mean['depth']= depth.split('-')[-1]
      data = pd.concat([data,mean])
  # here provide colors for each item that will be plotted
  pal={'Irrigated':'brown','Rainfed':'red'} 
  fig,ax = plt.subplots(figsize=(2.5,2),dpi=600,tight_layout=True)
  sns.set(style='ticks',rc={&quot;lines.linewidth&quot;:0.7,&quot;axes.linewidth&quot;:0.5})
  # use your column name to plot here
  sns.lineplot(x='depth',y='ASV',data=data,palette=pal,hue='Season',sort=False,err_style='bars',\
               dashes=True,style='Season',ci=67)
  ax.set_xlabel('Sequencing depth',fontsize=8)
  ax.set_ylabel('Observed ASVs',fontsize=8)
  ax.tick_params(axis='x', labelrotation=90)
  ax.tick_params(axis='both',which='major',length=2,pad=0.5,labelsize=6)
  handles, labels = ax.get_legend_handles_labels()
  ax.legend(handles=handles[1:],labels=labels[1:],fontsize=5,frameon=False,numpoints=4,borderaxespad=0,handletextpad=0.2,loc=2,)
  plt.savefig('Infected_observed_ASVs.png', bbox_inches='tight')
  </code></pre>
  <p>Error;</p>
  <pre><code> $ python3 myscript.rarefaction.py
  Traceback (most recent call last):
    File &quot;myscript.rarefaction.py&quot;, line 4, in &lt;module&gt;
      import seaborn as sns
    File &quot;/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/__init__.py&quot;, line 2, in &lt;module&gt;
      from .rcmod import *  # noqa: F401,F403
    File &quot;/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/rcmod.py&quot;, line 7, in &lt;module&gt;
      from . import palettes
    File &quot;/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/palettes.py&quot;, line 9, in &lt;module&gt;
      from .utils import desaturate, get_color_cycle
    File &quot;/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/utils.py&quot;, line 11, in &lt;module&gt;
      import pandas as pd
    File &quot;/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/pandas/__init__.py&quot;, line 11, in &lt;module&gt;
      __import__(dependency)
    File &quot;&lt;frozen importlib._bootstrap&gt;&quot;, line 983, in _find_and_load
    File &quot;&lt;frozen importlib._bootstrap&gt;&quot;, line 967, in _find_and_load_unlocked
    File &quot;&lt;frozen importlib._bootstrap&gt;&quot;, line 668, in _load_unlocked
    File &quot;&lt;frozen importlib._bootstrap&gt;&quot;, line 638, in _load_backward_compatible
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py&quot;, line 1101, in &lt;module&gt;
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/lazy.py&quot;, line 101, in _lazy
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py&quot;, line 1098, in &lt;genexpr&gt;
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py&quot;, line 114, in resource_exists
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py&quot;, line 102, in open_resource
    File &quot;&lt;frozen importlib._bootstrap&gt;&quot;, line 983, in _find_and_load
    File &quot;&lt;frozen importlib._bootstrap&gt;&quot;, line 967, in _find_and_load_unlocked
    File &quot;&lt;frozen importlib._bootstrap&gt;&quot;, line 668, in _load_unlocked
    File &quot;&lt;frozen importlib._bootstrap&gt;&quot;, line 638, in _load_backward_compatible
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py&quot;, line 2927, in &lt;module&gt;
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py&quot;, line 2913, in _call_aside
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py&quot;, line 2952, in _initialize_master_working_set
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py&quot;, line 956, in subscribe
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py&quot;, line 2952, in &lt;lambda&gt;
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py&quot;, line 2515, in activate
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py&quot;, line 2097, in declare_namespace
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py&quot;, line 2047, in _handle_ns
    File &quot;/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py&quot;, line 2066, in _rebuild_mod_path
  AttributeError: '_NamespacePath' object has no attribute 'sort'
  
           
       
      
      metadata file ;
      #SampleID       Villages        Region  Treatment       Batch   Season
      PN0086D.1.S1    Kholabari       Mymensingh      T1      batch1  Irrigated
      PN0086D.2.S2    Bogajan Mymensingh      T1      batch1  Irrigated
      PN0086D.3.S3    Bonkua  Mymensingh      T1      batch1  Irrigated
  </code></pre>
   9109: <p>This is a bash script (#!/bin/bash) and you try to run python in it.
  You should save your python script (e.g. in &quot;myscript.py&quot;) and call it within your bash script.
  Maybe first try to see if you are able to run it in your terminal and then run it on your server with SLURM.</p>
  <p>EDIT1: Also I don't think you need 3 nodes to run such script and this will probably not be even possible here. I think you need some specific modules to parallelize a python script with MPI (see <a href="https://stackoverflow.com/questions/25792357/how-to-distribute-a-python-script-across-multiple-nodes">https://stackoverflow.com/questions/25792357/how-to-distribute-a-python-script-across-multiple-nodes</a>), but again I think this would be an overkill. Try first with <code>#SBATCH -c 1</code> instead.</p>
  <p>Edit2: Finally it might be possible to run jupyter-notebook on a node allocated by SLRUM instead of putting this into a python script by using <code>jupyter-notebook --no-browser --port=${port} --ip=${node}</code> command in your bash slurm script. Maybe you'll find this doc interesting: <a href="https://docs.ycrc.yale.edu/clusters-at-yale/guides/jupyter/" rel="nofollow noreferrer">https://docs.ycrc.yale.edu/clusters-at-yale/guides/jupyter/</a> .</p>
  