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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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ModuleNotFoundError: No module named 'staramr' #142

Closed neelam19051 closed 2 years ago

neelam19051 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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_seriesfast 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 commented 2 years ago

Thanks. This looks an awful lot like this issue https://github.com/phac-nml/staramr/issues/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 commented 2 years ago

Fixed in #146