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douglasyao / FR-Perturb

Factorize-Recover for Perturb-seq analysis (FR-Perturb)
GNU General Public License v3.0
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Guide pool #4

Open jr-ran opened 1 year ago

jr-ran commented 1 year ago

For the guide-pooled screen,article focused on the 8,448 cells with 3 or more guides. When I was follow ,there are some issue. effect size is NaN or 0.

/nis_home/FR-Perturb/bin/python /locald/FR-Perturb/run_FR_Perturb.py \ --input-h5ad /path/GSM6858450_KD_guide_pooled.h5ad \ --input-perturbation-matrix /path/GSM6858450_KD_guide_pooled_perturbations.txt \ --control-perturbation-name non-targeting,safe-targeting \ --covariates Total_RNA_count,Percent_mitochondrial_reads,Cell_cycle_phase \ --compute-pval --fit-zero-pval --multithreaded \ --guide-pooled \ --out GSM6858450_KD_guide_pooled

[Traceback (most recent call last): File "/path/FR-Perturb/run_FR_Perturb.py", line 350, in fitted_pvals = thread_map(lambda i: fit_skew_norm(B_flattened[i], B_perms[i,:]), zero_indices) File "/nis_home/user/crispr/lib/python3.8/site-packages/tqdm/contrib/concurrent.py", line 94, in thread_map return _executor_map(ThreadPoolExecutor, fn, *iterables, tqdm_kwargs) File "/nis_home/user/crispr/lib/python3.8/site-packages/tqdm/contrib/concurrent.py", line 76, in _executor_map return list(tqdm_class(ex.map(fn, iterables, map_args), kwargs)) File "/nis_home/user/crispr/lib/python3.8/site-packages/tqdm/std.py", line 1195, in iter for obj in iterable: File "/nis_home/user/crispr/lib/python3.8/concurrent/futures/_base.py", line 619, in result_iterator yield fs.pop().result() File "/nis_home/user/crispr/lib/python3.8/concurrent/futures/_base.py", line 437, in result return self.__get_result() File "/nis_home/user/crispr/lib/python3.8/concurrent/futures/_base.py", line 389, in __get_result raise self._exception File "/nis_home/user/crispr/lib/python3.8/concurrent/futures/thread.py", line 57, in run result = self.fn(self.args, self.kwargs) File "/path/FR-Perturb/run_FR_Perturb.py", line 350, in fitted_pvals = thread_map(lambda i: fit_skew_norm(B_flattened[i], B_perms[i,:]), zero_indices) File "/path/FR-Perturb/run_FR_Perturb.py", line 81, in fit_skew_norm fit = scipy.stats.skewnorm.fit(t_nulls) File "/nis_home/user/crispr/lib/python3.8/site-packages/scipy/stats/_distn_infrastructure.py", line 2473, in fit raise RuntimeError("The data contains non-finite values.") RuntimeError: The data contains non-finite values.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/path/FR-Perturb/run_FR_Perturb.py", line 383, in log.log(traceback.format_exc(ex)) File "/nis_home/user/crispr/lib/python3.8/traceback.py", line 167, in format_exc return "".join(format_exception(*sys.exc_info(), limit=limit, chain=chain)) File "/nis_home/user/crispr/lib/python3.8/traceback.py", line 120, in format_exception return list(TracebackException( File "/nis_home/user/crispr/lib/python3.8/traceback.py", line 508, in init self.stack = StackSummary.extract( File "/nis_home/user/crispr/lib/python3.8/traceback.py", line 340, in extract if limit >= 0: TypeError: '>=' not supported between instances of 'RuntimeError' and 'int'](url)

douglasyao commented 1 year ago

Hi,

Can you make sure that you're using the most recent version of FR-Perturb? Also, can you make sure that you run "conda activate FR-Perturb" before running the code? It seems like the version of python being used does not match the environment.

-Doug

On Fri, Sep 15, 2023 at 5:41 AM jr-ran @.***> wrote:

For the guide-pooled screen,article focused on the 8,448 cells with 3 or more guides. When I was follow ,there are some issue. effect size is NaN or 0.

/nis_home/FR-Perturb/bin/python /locald/FR-Perturb/run_FR_Perturb.py --input-h5ad /path/GSM6858450_KD_guide_pooled.h5ad --input-perturbation-matrix /path/GSM6858450_KD_guide_pooled_perturbations.txt --control-perturbation-name non-targeting,safe-targeting --covariates Total_RNA_count,Percent_mitochondrial_reads,Cell_cycle_phase --compute-pval --fit-zero-pval --multithreaded --guide-pooled --out GSM6858450_KD_guide_pooled http://url

[Traceback (most recent call last): File "/path/FR-Perturb/run_FR_Perturb.py", line 350, in fitted_pvals = thread_map(lambda i: fit_skew_norm(B_flattened[i], B_perms[i,:]), zero_indices) File "/nis_home/user/crispr/lib/python3.8/site-packages/tqdm/contrib/concurrent.py", line 94, in thread_map return _executor_map(ThreadPoolExecutor, fn, *iterables, tqdm_kwargs) File "/nis_home/user/crispr/lib/python3.8/site-packages/tqdm/contrib/concurrent.py", line 76, in _executor_map return list(tqdm_class(ex.map(fn, iterables, map_args), kwargs)) File "/nis_home/user/crispr/lib/python3.8/site-packages/tqdm/std.py", line 1195, in iter for obj in iterable: File "/nis_home/user/crispr/lib/python3.8/concurrent/futures/_base.py", line 619, in result_iterator yield fs.pop().result() File "/nis_home/user/crispr/lib/python3.8/concurrent/futures/_base.py", line 437, in result return self.__get_result() File "/nis_home/user/crispr/lib/python3.8/concurrent/futures/_base.py", line 389, in __get_result raise self._exception File "/nis_home/user/crispr/lib/python3.8/concurrent/futures/thread.py", line 57, in run result = self.fn(self.args, self.kwargs) File "/path/FR-Perturb/run_FR_Perturb.py", line 350, in fitted_pvals = thread_map(lambda i: fit_skew_norm(B_flattened[i], B_perms[i,:]), zero_indices) File "/path/FR-Perturb/run_FR_Perturb.py", line 81, in fit_skew_norm fit = scipy.stats.skewnorm.fit(t_nulls) File "/nis_home/user/crispr/lib/python3.8/site-packages/scipy/stats/_distn_infrastructure.py", line 2473, in fit raise RuntimeError("The data contains non-finite values.") RuntimeError: The data contains non-finite values.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/path/FR-Perturb/run_FR_Perturb.py", line 383, in log.log(traceback.format_exc(ex)) File "/nis_home/user/crispr/lib/python3.8/traceback.py", line 167, in format_exc return "".join(format_exception(sys.exc_info(), limit=limit, chain=chain)) File "/nis_home/user/crispr/lib/python3.8/traceback.py", line 120, in format_exception return list(TracebackException( File "/nis_home/user/crispr/lib/python3.8/traceback.py", line 508, in init* self.stack = StackSummary.extract( File "/nis_home/user/crispr/lib/python3.8/traceback.py", line 340, in extract if limit >= 0: TypeError: '>=' not supported between instances of 'RuntimeError' and 'int'](url)

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