ModuleNotFoundError: No module named 'staramr'

[neelam19051]

Hi, I am trying to install 'staramr' and i am getting this error-
Does anyone know how to solve it?

Traceback (most recent call last):
File "/home/bvs/neelam/staramr/bin/staramr", line 44, in
from staramr import version
ModuleNotFoundError: No module named 'staramr'

Thank you!

[apetkau]

Hello @neelam19051, how did you install staramr? Was it using conda? Pip? Did you clone from GitHub? Which version of Python are you using (python --version)?

[neelam19051]

Actually i installed it with git clone and after that i also installed with pip (Python 3.8) then it didn't show that error and help manual run perfectly fine but when i try run this commands *staramr search -o out .fna it show this following error -

[Errno 39] Directory not empty: '/tmp/tmpb4uhg5zk'
Traceback (most recent call last):
File "/tmp/home/bvs/neelam/lib/python3.8/site-packages/staramr/subcommand/Search.py", line 283, in _generate_results
amr_detection.run_amr_detection(files,pid_threshold, plength_threshold_resfinder,
File "/tmp/home/bvs/neelam/lib/python3.8/site-packages/staramr/detection/AMRDetection.py", line 177, in run_amr_detection
self._amr_detection_handler.run_blasts_mlst(files, mlst_scheme)
File "/tmp/home/bvs/neelam/lib/python3.8/site-packages/staramr/blast/JobHandler.py", line 113, in run_blasts_mlst
mlst_result = future_mlst.result()
File "/tmp/home/bvs/neelam/lib/python3.8/concurrent/futures/_base.py", line 432, in result
return self.__get_result()
File "/tmp/home/bvs/neelam/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
raise self._exception
File "/tmp/home/bvs/neelam/lib/python3.8/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/tmp/home/bvs/neelam/lib/python3.8/site-packages/staramr/blast/JobHandler.py", line 154, in _schedule_mlst
output = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True)
File "/tmp/home/bvs/neelam/lib/python3.8/subprocess.py", line 493, in run
with Popen(*popenargs, **kwargs) as process:
File "/tmp/home/bvs/neelam/lib/python3.8/subprocess.py", line 858, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/tmp/home/bvs/neelam/lib/python3.8/subprocess.py", line 1706, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'mlst'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/bvs/neelam/staramr/bin/staramr", line 68, in
args.run_command(args)
File "/tmp/home/bvs/neelam/lib/python3.8/site-packages/staramr/subcommand/Search.py", line 447, in run
results = self._generate_results(database_repos=database_repos,
File "/tmp/home/bvs/neelam/lib/python3.8/site-packages/staramr/subcommand/Search.py", line 319, in _generate_results
results['settings'] = settings
File "/tmp/home/bvs/neelam/lib/python3.8/tempfile.py", line 827, in exit
self.cleanup()
File "/tmp/home/bvs/neelam/lib/python3.8/tempfile.py", line 831, in cleanup
self._rmtree(self.name)
File "/tmp/home/bvs/neelam/lib/python3.8/tempfile.py", line 813, in _rmtree
_shutil.rmtree(name, onerror=onerror)
File "/tmp/home/bvs/neelam/lib/python3.8/shutil.py", line 722, in rmtree
onerror(os.rmdir, path, sys.exc_info())
File "/tmp/home/bvs/neelam/lib/python3.8/shutil.py", line 720, in rmtree
os.rmdir(path)
OSError: [Errno 39] Directory not empty: '/tmp/tmpb4uhg5zk'

Thank you

[apetkau]

If possible you will likely want to install staramr using the Bioconda instructions (https://github.com/phac-nml/staramr#bioconda). Conda/bioconda will install all the necessary non-Python dependencies (like the software mlst which is missing and causing the error above).

You can install outside of conda/bioconda too, but then you have to install the following dependencies in addition to pip install staramr: https://github.com/phac-nml/staramr#dependencies

[neelam19051]

Hi, again i encountered some error, even i installed it with the help of bioconda staramr and the script was same -

ERROR ##'NoneType' object has no attribute 'tolist'##

Traceback (most recent call last):
File "/home/bvs/anaconda3/envs/myenv/bin/staramr", line 68, in
args.run_command(args)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/staramr/subcommand/Search.py", line 468, in run
unacceptable_num_contigs= args.unacceptable_num_contigs)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/staramr/subcommand/Search.py", line 286, in _generate_results
report_all_blast, ignore_invalid_files, mlst_scheme)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/staramr/detection/AMRDetection.py", line 198, in run_amr_detection
self._pointfinder_dataframe, self._plasmidfinder_dataframe, self._mlst_dataframe)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/staramr/detection/AMRDetectionResistance.py", line 70, in _create_amr_summary
return amr_detection_summary.create_summary(self._include_negative_results)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/staramr/results/AMRDetectionSummary.py", line 134, in create_summary
resistance_frame = self._compile_results(resistance_frame)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/staramr/results/AMRDetectionSummaryResistance.py", line 43, in _compile_results
.aggregate(self._aggregate_gene_phenotype)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/groupby/generic.py", line 1010, in aggregate
result = gba.agg()
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/apply.py", line 164, in agg
return self.agg_list_like()
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/apply.py", line 355, in agg_list_like
new_res = colg.aggregate(arg)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/groupby/generic.py", line 249, in aggregate
ret = self._aggregate_multiple_funcs(func)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/groupby/generic.py", line 303, in _aggregate_multiple_funcs
results[key] = self.aggregate(func)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/groupby/generic.py", line 265, in aggregate
return self._python_agg_general(func, *args, **kwargs)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/groupby/groupby.py", line 1332, in _python_agg_general
result = self.grouper.agg_series(obj, f)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/groupby/ops.py", line 1060, in agg_series
result = self._aggregate_series_fast(obj, func)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/groupby/ops.py", line 1085, in _aggregate_series_fast
result, _ = sgrouper.get_result()
File "pandas/_libs/reduction.pyx", line 281, in pandas._libs.reduction.SeriesGrouper.get_result
File "pandas/_libs/reduction.pyx", line 88, in pandas._libs.reduction._BaseGrouper._apply_to_group
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/pandas/core/groupby/groupby.py", line 1318, in
f = lambda x: func(x, *args, **kwargs)
File "/home/bvs/anaconda3/envs/myenv/lib/python3.7/site-packages/staramr/results/AMRDetectionSummaryResistance.py", line 25, in _aggregate_gene_phenotype
flattened_phenotype_list = [y.strip() for x in dataframe.get('Predicted Phenotype').tolist() for y in
AttributeError: 'NoneType' object has no attribute 'tolist'

Thank you

[apetkau]

Thanks. This looks an awful lot like this issue #136. I believe the solution is to downgrade the pandas package:

# Or if this does'nt work you can try 'pip install' instead
conda install pandas==1.1.5

[apetkau]

Fixed in #146